From b8a3392b5908ebe3e6e07da8232cd8fd79718688 Mon Sep 17 00:00:00 2001 From: Dimitris Date: Fri, 30 Oct 2020 14:07:21 +0200 Subject: [PATCH 001/149] Commit 30102020 --- dhp-workflows/dhp-usage-stats-update/pom.xml | 78 + .../oa/graph/usagestats/export/ConnectDB.java | 125 ++ .../usagestats/export/ExecuteWorkflow.java | 197 +++ .../oa/graph/usagestats/export/IrusStats.java | 417 ++++++ .../export/LaReferenciaDownloadLogs.java | 261 ++++ .../usagestats/export/LaReferenciaStats.java | 423 ++++++ .../usagestats/export/PiwikDownloadLogs.java | 316 +++++ .../graph/usagestats/export/PiwikStatsDB.java | 1255 +++++++++++++++++ .../export/ReadCounterRobotsList.java | 54 + .../oa/graph/usagestats/export/SarcStats.java | 571 ++++++++ .../usagestats/export/UsageStatsExporter.java | 179 +++ .../export/usagestats_parameters.json | 231 +++ .../usagestats/oozie_app/config-default.xml | 38 + .../graph/usagestats/oozie_app/workflow.xml | 90 ++ 14 files changed, 4235 insertions(+) create mode 100644 dhp-workflows/dhp-usage-stats-update/pom.xml create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ExecuteWorkflow.java create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ReadCounterRobotsList.java create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/export/usagestats_parameters.json create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-usage-stats-update/pom.xml b/dhp-workflows/dhp-usage-stats-update/pom.xml new file mode 100644 index 000000000..b56257ee5 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/pom.xml @@ -0,0 +1,78 @@ + + + + + + + + + dhp-workflows + eu.dnetlib.dhp + 1.1.7-SNAPSHOT + + 4.0.0 + dhp-usage-stats-update + + + UTF-8 + UTF-8 + 0.13.1-cdh5.2.1 + 2.5.0-cdh5.2.1 + + + + + org.apache.spark + spark-core_2.11 + 2.2.0 + + + org.apache.spark + spark-sql_2.11 + 2.4.5 + + + com.googlecode.json-simple + json-simple + 1.1.1 + + + org.json + json + 20180130 + jar + + + org.apache.hive + hive-jdbc + ${cdh.hive.version} + + + org.apache.hadoop + hadoop-common + ${cdh.hadoop.version} + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + c3p0 + c3p0 + 0.9.1.2 + jar + + + diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java new file mode 100644 index 000000000..ffc7c74cd --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java @@ -0,0 +1,125 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.usagestats.export; + +import java.sql.Connection; +import java.sql.DriverManager; +import java.sql.SQLException; +import java.sql.Statement; +import java.util.Properties; + +import org.apache.log4j.Logger; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +/** + * @author D. Pierrakos, S. Zoupanos + */ +import com.mchange.v2.c3p0.ComboPooledDataSource; + +public abstract class ConnectDB { + + public static Connection DB_HIVE_CONNECTION; + public static Connection DB_IMPALA_CONNECTION; + + private static String dbHiveUrl; + private static String dbImpalaUrl; + private static String usageStatsDBSchema; + private static String statsDBSchema; + private final static Logger log = Logger.getLogger(ConnectDB.class); + + static void init() throws ClassNotFoundException { + + dbHiveUrl = ExecuteWorkflow.dbHiveUrl; + dbImpalaUrl = ExecuteWorkflow.dbImpalaUrl; + usageStatsDBSchema = ExecuteWorkflow.usageStatsDBSchema; + statsDBSchema = ExecuteWorkflow.statsDBSchema; + + Class.forName("org.apache.hive.jdbc.HiveDriver"); + } + + public static Connection getHiveConnection() throws SQLException { + if (DB_HIVE_CONNECTION != null && !DB_HIVE_CONNECTION.isClosed()) { + return DB_HIVE_CONNECTION; + } else { + DB_HIVE_CONNECTION = connectHive(); + + return DB_HIVE_CONNECTION; + } + } + + public static Connection getImpalaConnection() throws SQLException { + if (DB_IMPALA_CONNECTION != null && !DB_IMPALA_CONNECTION.isClosed()) { + return DB_IMPALA_CONNECTION; + } else { + DB_IMPALA_CONNECTION = connectImpala(); + + return DB_IMPALA_CONNECTION; + } + } + + public static String getUsageStatsDBSchema() { + return ConnectDB.usageStatsDBSchema; + } + + public static String getStatsDBSchema() { + return ConnectDB.statsDBSchema; + } + + private static Connection connectHive() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbHiveUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbHiveUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(5); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(30000); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + return cpds.getConnection(); + + } + + private static Connection connectImpala() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbImpalaUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbImpalaUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(5); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(30000); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + + return cpds.getConnection(); + + } + +} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ExecuteWorkflow.java new file mode 100644 index 000000000..50b951cbc --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ExecuteWorkflow.java @@ -0,0 +1,197 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.usagestats.export; + +import java.text.SimpleDateFormat; +import java.util.Calendar; +import java.util.Date; + +import org.apache.commons.io.IOUtils; +import org.apache.log4j.BasicConfigurator; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class ExecuteWorkflow { + + static String matomoAuthToken; + static String matomoBaseURL; + static String repoLogPath; + static String portalLogPath; + static String portalMatomoID; + static String irusUKBaseURL; + static String irusUKReportPath; + static String sarcsReportPathArray; + static String sarcsReportPathNonArray; + static String lareferenciaLogPath; + static String lareferenciaBaseURL; + static String lareferenciaAuthToken; + static String dbHiveUrl; + static String dbImpalaUrl; + static String usageStatsDBSchema; + static String statsDBSchema; + static boolean recreateDbAndTables; + + static boolean piwikEmptyDirs; + static boolean downloadPiwikLogs; + static boolean processPiwikLogs; + + static Calendar startingLogPeriod; + static Calendar endingLogPeriod; + static int numberOfPiwikIdsToDownload; + static int numberOfSiteIdsToDownload; + + static boolean laReferenciaEmptyDirs; + static boolean downloadLaReferenciaLogs; + static boolean processLaReferenciaLogs; + + static boolean irusCreateTablesEmptyDirs; + static boolean irusDownloadReports; + static boolean irusProcessStats; + static int irusNumberOfOpendoarsToDownload; + + static boolean sarcCreateTablesEmptyDirs; + static boolean sarcDownloadReports; + static boolean sarcProcessStats; + static int sarcNumberOfIssnToDownload; + + static boolean finalizeStats; + static boolean finalTablesVisibleToImpala; + + static int numberOfDownloadThreads; + + public static void main(String args[]) throws Exception { + + // Sending the logs to the console + BasicConfigurator.configure(); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + UsageStatsExporter.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/usagestats/export/usagestats_parameters.json"))); + parser.parseArgument(args); + + // Setting up the initial parameters + matomoAuthToken = parser.get("matomoAuthToken"); + matomoBaseURL = parser.get("matomoBaseURL"); + repoLogPath = parser.get("repoLogPath"); + portalLogPath = parser.get("portalLogPath"); + portalMatomoID = parser.get("portalMatomoID"); + irusUKBaseURL = parser.get("irusUKBaseURL"); + irusUKReportPath = parser.get("irusUKReportPath"); + sarcsReportPathArray = parser.get("sarcsReportPathArray"); + sarcsReportPathNonArray = parser.get("sarcsReportPathNonArray"); + lareferenciaLogPath = parser.get("lareferenciaLogPath"); + lareferenciaBaseURL = parser.get("lareferenciaBaseURL"); + lareferenciaAuthToken = parser.get("lareferenciaAuthToken"); + + dbHiveUrl = parser.get("dbHiveUrl"); + dbImpalaUrl = parser.get("dbImpalaUrl"); + usageStatsDBSchema = parser.get("usageStatsDBSchema"); + statsDBSchema = parser.get("statsDBSchema"); + + if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) + recreateDbAndTables = true; + else + recreateDbAndTables = false; + + if (parser.get("piwikEmptyDirs").toLowerCase().equals("true")) + piwikEmptyDirs = true; + else + piwikEmptyDirs = false; + + if (parser.get("downloadPiwikLogs").toLowerCase().equals("true")) + downloadPiwikLogs = true; + else + downloadPiwikLogs = false; + + if (parser.get("processPiwikLogs").toLowerCase().equals("true")) + processPiwikLogs = true; + else + processPiwikLogs = false; + + String startingLogPeriodStr = parser.get("startingLogPeriod"); + Date startingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(startingLogPeriodStr); + startingLogPeriod = startingLogPeriodStr(startingLogPeriodDate); + + String endingLogPeriodStr = parser.get("endingLogPeriod"); + Date endingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(endingLogPeriodStr); + endingLogPeriod = startingLogPeriodStr(endingLogPeriodDate); + + numberOfPiwikIdsToDownload = Integer.parseInt(parser.get("numberOfPiwikIdsToDownload")); + numberOfSiteIdsToDownload = Integer.parseInt(parser.get("numberOfSiteIdsToDownload")); + + if (parser.get("laReferenciaEmptyDirs").toLowerCase().equals("true")) + laReferenciaEmptyDirs = true; + else + laReferenciaEmptyDirs = false; + + if (parser.get("downloadLaReferenciaLogs").toLowerCase().equals("true")) + downloadLaReferenciaLogs = true; + else + downloadLaReferenciaLogs = false; + + if (parser.get("processLaReferenciaLogs").toLowerCase().equals("true")) + processLaReferenciaLogs = true; + else + processLaReferenciaLogs = false; + + if (parser.get("irusCreateTablesEmptyDirs").toLowerCase().equals("true")) + irusCreateTablesEmptyDirs = true; + else + irusCreateTablesEmptyDirs = false; + if (parser.get("irusDownloadReports").toLowerCase().equals("true")) + irusDownloadReports = true; + else + irusDownloadReports = false; + if (parser.get("irusProcessStats").toLowerCase().equals("true")) + irusProcessStats = true; + else + irusProcessStats = false; + irusNumberOfOpendoarsToDownload = Integer.parseInt(parser.get("irusNumberOfOpendoarsToDownload")); + + if (parser.get("sarcCreateTablesEmptyDirs").toLowerCase().equals("true")) + sarcCreateTablesEmptyDirs = true; + else + sarcCreateTablesEmptyDirs = false; + if (parser.get("sarcDownloadReports").toLowerCase().equals("true")) + sarcDownloadReports = true; + else + sarcDownloadReports = false; + if (parser.get("sarcProcessStats").toLowerCase().equals("true")) + sarcProcessStats = true; + else + sarcProcessStats = false; + sarcNumberOfIssnToDownload = Integer.parseInt(parser.get("sarcNumberOfIssnToDownload")); + + if (parser.get("finalizeStats").toLowerCase().equals("true")) + finalizeStats = true; + else + finalizeStats = false; + if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) + finalTablesVisibleToImpala = true; + else + finalTablesVisibleToImpala = false; + + numberOfDownloadThreads = Integer.parseInt(parser.get("numberOfDownloadThreads")); + + UsageStatsExporter usagestatsExport = new UsageStatsExporter(); + usagestatsExport.export(); + } + + private static Calendar startingLogPeriodStr(Date date) { + + Calendar calendar = Calendar.getInstance(); + calendar.setTime(date); + return calendar; + + } +} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java new file mode 100644 index 000000000..749687ec5 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java @@ -0,0 +1,417 @@ + +package eu.dnetlib.oa.graph.usagestats.export; + +import java.io.*; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class IrusStats { + + private String irusUKURL; + + private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); + + public IrusStats(String irusUKURL) throws Exception { + this.irusUKURL = irusUKURL; + // The following may not be needed - It will be created when JSON tables are created +// createTmpTables(); + } + + public void reCreateLogDirs() throws Exception { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); + dfs.delete(new Path(ExecuteWorkflow.irusUKReportPath), true); + + logger.info("Creating irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); + dfs.mkdirs(new Path(ExecuteWorkflow.irusUKReportPath)); + } + + public void createTables() throws Exception { + try { + logger.info("Creating sushilog"); + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog(source STRING, " + + "repository STRING, rid STRING, date STRING, metric_type STRING, count INT) clustered by (source, " + + "repository, rid, date, metric_type) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableSushiLog); + logger.info("Created sushilog"); + + // To see how to apply to the ignore duplicate rules and indexes +// stmt.executeUpdate(sqlCreateTableSushiLog); +// String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO sushilog " +// + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," +// + "sushilog.rid, sushilog.date " +// + "FROM sushilog " +// + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; +// stmt.executeUpdate(sqlcreateRuleSushiLog); +// String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; +// stmt.executeUpdate(createSushiIndex); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + +// // The following may not be needed - It will be created when JSON tables are created +// private void createTmpTables() throws Exception { +// try { +// +// Statement stmt = ConnectDB.getConnection().createStatement(); +// String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilogtmp(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; +// stmt.executeUpdate(sqlCreateTableSushiLog); +// +// // stmt.executeUpdate("CREATE TABLE IF NOT EXISTS public.sushilog AS TABLE sushilog;"); +// // String sqlCopyPublicSushiLog = "INSERT INTO sushilog SELECT * FROM public.sushilog;"; +// // stmt.executeUpdate(sqlCopyPublicSushiLog); +// String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO sushilogtmp " +// + " WHERE (EXISTS ( SELECT sushilogtmp.source, sushilogtmp.repository," +// + "sushilogtmp.rid, sushilogtmp.date " +// + "FROM sushilogtmp " +// + "WHERE sushilogtmp.source = new.source AND sushilogtmp.repository = new.repository AND sushilogtmp.rid = new.rid AND sushilogtmp.date = new.date AND sushilogtmp.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; +// stmt.executeUpdate(sqlcreateRuleSushiLog); +// +// stmt.close(); +// ConnectDB.getConnection().close(); +// log.info("Sushi Tmp Tables Created"); +// } catch (Exception e) { +// log.error("Failed to create tables: " + e); +// throw new Exception("Failed to create tables: " + e.toString(), e); +// } +// } + + public void processIrusStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping sushilogtmp_json table"); + String dropSushilogtmpJson = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sushilogtmp_json"; + stmt.executeUpdate(dropSushilogtmpJson); + logger.info("Dropped sushilogtmp_json table"); + + logger.info("Creating irus_sushilogtmp_json table"); + String createSushilogtmpJson = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json(\n" + + " `ItemIdentifier` ARRAY<\n" + + " struct<\n" + + " Type: STRING,\n" + + " Value: STRING\n" + + " >\n" + + " >,\n" + + " `ItemPerformance` ARRAY<\n" + + " struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.irusUKReportPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(createSushilogtmpJson); + logger.info("Created irus_sushilogtmp_json table"); + + logger.info("Dropping irus_sushilogtmp table"); + String dropSushilogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp"; + stmt.executeUpdate(dropSushilogtmp); + logger.info("Dropped irus_sushilogtmp table"); + + logger.info("Creating irus_sushilogtmp table"); + String createSushilogtmp = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp(source STRING, repository STRING, " + + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " + + + "tblproperties('transactional'='true')"; + stmt.executeUpdate(createSushilogtmp); + logger.info("Created irus_sushilogtmp table"); + + logger.info("Inserting to irus_sushilogtmp table"); + String insertSushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp " + + "SELECT 'IRUS-UK', CONCAT('opendoar____::', split(split(INPUT__FILE__NAME,'IrusIRReport_')[1],'_')[0]), " + + "`ItemIdent`.`Value`, `ItemPerf`.`Period`.`Begin`, " + + "`ItemPerf`.`Instance`.`MetricType`, `ItemPerf`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json " + + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + + "LATERAL VIEW posexplode(ItemPerformance) ItemPerformanceTable AS seqp, ItemPerf " + + "WHERE `ItemIdent`.`Type`= 'OAI'"; + stmt.executeUpdate(insertSushilogtmp); + logger.info("Inserted to irus_sushilogtmp table"); + + logger.info("Creating downloads_stats table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmt.executeUpdate(createDownloadsStats); + logger.info("Created downloads_stats table"); + + logger.info("Inserting into downloads_stats"); + String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(YEAR(date), '/', LPAD(MONTH(date), 2, '0')) as date, s.count, '0' " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE s.repository=d.oid AND s.rid=ro.oid AND metric_type='ft_total' AND s.source='IRUS-UK'"; + stmt.executeUpdate(insertDStats); + logger.info("Inserted into downloads_stats"); + + logger.info("Creating sushilog table"); + String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog " + + "(`source` string, " + + "`repository_id` string, " + + "`rid` string, " + + "`date` string, " + + "`metric_type` string, " + + "`count` int)"; + stmt.executeUpdate(createSushilog); + logger.info("Created sushilog table"); + + logger.info("Inserting to sushilog table"); + String insertToShushilog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sushilog SELECT * FROM " + + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp"; + stmt.executeUpdate(insertToShushilog); + logger.info("Inserted to sushilog table"); + + ConnectDB.getHiveConnection().close(); + } + + public void getIrusRRReport(String irusUKReportPath) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("YYYY-MM"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getIrusRRReport) Starting period for log download: " + sdf.format(start.getTime())); + + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("(getIrusRRReport) Ending period for log download: " + sdf.format(end.getTime())); + + String reportUrl = irusUKURL + "GetReport/?Report=RR1&Release=4&RequestorID=OpenAIRE&BeginDate=" + + sdf.format(start.getTime()) + "&EndDate=" + sdf.format(end.getTime()) + + "&RepositoryIdentifier=&ItemDataType=&NewJiscBand=&Granularity=Monthly&Callback="; + + logger.info("(getIrusRRReport) Getting report: " + reportUrl); + + String text = getJson(reportUrl, "", ""); + + List opendoarsToVisit = new ArrayList(); + JSONParser parser = new JSONParser(); + JSONObject jsonObject = (JSONObject) parser.parse(text); + jsonObject = (JSONObject) jsonObject.get("ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Customer"); + JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); + int i = 0; + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + JSONArray itemIdentifier = (JSONArray) jsonObjectRow.get("ItemIdentifier"); + for (Object identifier : itemIdentifier) { + JSONObject opendoar = (JSONObject) identifier; + if (opendoar.get("Type").toString().equals("OpenDOAR")) { + i++; + opendoarsToVisit.add(opendoar.get("Value").toString()); + break; + } + } + // break; + } + + logger.info("(getIrusRRReport) Found the following opendoars for download: " + opendoarsToVisit); + + if (ExecuteWorkflow.irusNumberOfOpendoarsToDownload > 0 && + ExecuteWorkflow.irusNumberOfOpendoarsToDownload <= opendoarsToVisit.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.irusNumberOfOpendoarsToDownload); + opendoarsToVisit = opendoarsToVisit.subList(0, ExecuteWorkflow.irusNumberOfOpendoarsToDownload); + } + + logger.info("(getIrusRRReport) Downloading the followins opendoars: " + opendoarsToVisit); + + for (String opendoar : opendoarsToVisit) { + logger.info("Now working on openDoar: " + opendoar); + this.getIrusIRReport(opendoar, irusUKReportPath); + } + + logger.info("(getIrusRRReport) Finished with report: " + reportUrl); + } + + private void getIrusIRReport(String opendoar, String irusUKReportPath) throws Exception { + + logger.info("(getIrusIRReport) Getting report(s) with opendoar: " + opendoar); + + ConnectDB.getHiveConnection().setAutoCommit(false); + + SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); + + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getIrusIRReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); + + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("(getIrusIRReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); + + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); + st.setString(1, "opendoar____::" + opendoar); + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + } + } + rs_date.close(); + int batch_size = 0; + + while (start.before(end)) { + // log.info("date: " + simpleDateFormat.format(start.getTime())); + String reportUrl = this.irusUKURL + "GetReport/?Report=IR1&Release=4&RequestorID=OpenAIRE&BeginDate=" + + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()) + + "&RepositoryIdentifier=opendoar%3A" + opendoar + + "&ItemIdentifier=&ItemDataType=&hasDOI=&Granularity=Monthly&Callback="; + start.add(Calendar.MONTH, 1); + + logger.info("Downloading file: " + reportUrl); + String text = getJson(reportUrl, "", ""); + if (text == null) { + continue; + } + + FileSystem fs = FileSystem.get(new Configuration()); + String filePath = irusUKReportPath + "/" + "IrusIRReport_" + + opendoar + "_" + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePath); + FSDataOutputStream fin = fs.create(new Path(filePath), true); + + JSONParser parser = new JSONParser(); + JSONObject jsonObject = (JSONObject) parser.parse(text); + jsonObject = (JSONObject) jsonObject.get("ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Customer"); + JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); + if (jsonArray == null) { + continue; + } + String oai = ""; + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + fin.write(jsonObjectRow.toJSONString().getBytes()); + fin.writeChar('\n'); + } + + fin.close(); + } + + ConnectDB.getHiveConnection().close(); + + logger.info("(getIrusIRReport) Finished downloading report(s) with opendoar: " + opendoar); + } + + private String getJson(String url) throws Exception { + try { + System.out.println("===> Connecting to: " + url); + URL website = new URL(url); + System.out.println("Connection url -----> " + url); + URLConnection connection = website.openConnection(); + + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); +// response.append("\n"); + } + } + + System.out.println("response ====> " + response.toString()); + + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + e); + System.out.println("Failed to get URL: " + e); + throw new Exception("Failed to get URL: " + e.toString(), e); + } + } + + private String getJson(String url, String username, String password) throws Exception { + // String cred=username+":"+password; + // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + response.append("\n"); + } + } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL", e); + return null; + } + } +} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java new file mode 100644 index 000000000..0e0e013cf --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java @@ -0,0 +1,261 @@ + +package eu.dnetlib.oa.graph.usagestats.export; + +import java.io.*; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class LaReferenciaDownloadLogs { + + private final String piwikUrl; + private Date startDate; + private final String tokenAuth; + + /* + * The Piwik's API method + */ + private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; + private final String format = "&format=json"; + private final String ApimethodGetAllSites = "?module=API&method=SitesManager.getSitesWithViewAccess"; + + private static final Logger logger = LoggerFactory.getLogger(LaReferenciaDownloadLogs.class); + + public LaReferenciaDownloadLogs(String piwikUrl, String tokenAuth) throws Exception { + this.piwikUrl = piwikUrl; + this.tokenAuth = tokenAuth; + this.createTables(); +// this.createTmpTables(); + } + + public void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); + + logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); + } + + private void createTables() throws Exception { + try { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating LaReferencia tables"); + String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableLareferenciaLog); + logger.info("Created LaReferencia tables"); +// String sqlcreateRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO lareferencialog " +// + " WHERE (EXISTS ( SELECT lareferencialog.matomoid, lareferencialog.source, lareferencialog.id_visit," +// + "lareferencialog.action, lareferencialog.\"timestamp\", lareferencialog.entity_id " +// + "FROM lareferencialog " +// + "WHERE lareferencialog.matomoid=new.matomoid AND lareferencialog.source = new.source AND lareferencialog.id_visit = new.id_visit AND lareferencialog.action = new.action AND lareferencialog.entity_id = new.entity_id AND lareferencialog.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; +// String sqlCreateRuleIndexLaReferenciaLog = "create index if not exists lareferencialog_rule on lareferencialog(matomoid, source, id_visit, action, entity_id, \"timestamp\");"; +// stmt.executeUpdate(sqlcreateRuleLaReferenciaLog); +// stmt.executeUpdate(sqlCreateRuleIndexLaReferenciaLog); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Lareferencia Tables Created"); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + // System.exit(0); + } + } + +// private void createTmpTables() throws Exception { +// +// try { +// Statement stmt = ConnectDB.getConnection().createStatement(); +// String sqlCreateTmpTableLaReferenciaLog = "CREATE TABLE IF NOT EXISTS lareferencialogtmp(matomoid INTEGER, source TEXT, id_visit TEXT, country TEXT, action TEXT, url TEXT, entity_id TEXT, source_item_type TEXT, timestamp TEXT, referrer_name TEXT, agent TEXT, PRIMARY KEY(source, id_visit, action, timestamp, entity_id));"; +// String sqlcreateTmpRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO lareferencialogtmp " +// + " WHERE (EXISTS ( SELECT lareferencialogtmp.matomoid, lareferencialogtmp.source, lareferencialogtmp.id_visit," +// + "lareferencialogtmp.action, lareferencialogtmp.\"timestamp\", lareferencialogtmp.entity_id " +// + "FROM lareferencialogtmp " +// + "WHERE lareferencialogtmp.matomoid=new.matomoid AND lareferencialogtmp.source = new.source AND lareferencialogtmp.id_visit = new.id_visit AND lareferencialogtmp.action = new.action AND lareferencialogtmp.entity_id = new.entity_id AND lareferencialogtmp.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; +// stmt.executeUpdate(sqlCreateTmpTableLaReferenciaLog); +// stmt.executeUpdate(sqlcreateTmpRuleLaReferenciaLog); +// +// stmt.close(); +// log.info("Lareferencia Tmp Tables Created"); +// +// } catch (Exception e) { +// log.error("Failed to create tmptables: " + e); +// throw new Exception("Failed to create tmp tables: " + e.toString(), e); +// // System.exit(0); +// } +// } + + private String getPiwikLogUrl() { + return piwikUrl + "/"; + } + + private String getJson(String url) throws Exception { + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); +// response.append("\n"); + } + } + + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + e); + throw new Exception("Failed to get URL: " + e.toString(), e); + } + } + + public void GetLaReferenciaRepos(String repoLogsPath) throws Exception { + + String baseApiUrl = getPiwikLogUrl() + ApimethodGetAllSites + format + "&token_auth=" + this.tokenAuth; + String content = ""; + + List siteIdsToVisit = new ArrayList(); + + // Getting all the siteIds in a list for logging reasons & limiting the list + // to the max number of siteIds + content = getJson(baseApiUrl); + JSONParser parser = new JSONParser(); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + siteIdsToVisit.add(Integer.parseInt(jsonObjectRow.get("idsite").toString())); + } + logger.info("Found the following siteIds for download: " + siteIdsToVisit); + + if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 && + ExecuteWorkflow.numberOfPiwikIdsToDownload <= siteIdsToVisit.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); + siteIdsToVisit = siteIdsToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); + } + + logger.info("Downloading from repos with the followins siteIds: " + siteIdsToVisit); + + for (int siteId : siteIdsToVisit) { + logger.info("Now working on piwikId: " + siteId); + this.GetLaReFerenciaLogs(repoLogsPath, siteId); + } + } + + public void GetLaReFerenciaLogs(String repoLogsPath, + int laReferencialMatomoID) throws Exception { + + logger.info("Downloading logs for LaReferencia repoid " + laReferencialMatomoID); + + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("Starting period for log download: " + sdf.format(start.getTime())); + + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("Ending period for log download: " + sdf.format(end.getTime())); + + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialog WHERE matomoid=? GROUP BY timestamp HAVING max(timestamp) is not null"); + st.setInt(1, laReferencialMatomoID); + + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + } + } + rs_date.close(); + + for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { + Date date = currDay.getTime(); + logger + .info( + "Downloading logs for LaReferencia repoid " + laReferencialMatomoID + " and for " + + sdf.format(date)); + + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + outFolder = repoLogsPath; + + FileSystem fs = FileSystem.get(new Configuration()); + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + laReferencialMatomoID + "_LaRefPiwiklog" + sdf.format((date)) + ".json"), + true); + + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + laReferencialMatomoID + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + int i = 0; + + JSONParser parser = new JSONParser(); + do { + String apiUrl = baseApiUrl; + + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } + + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) + break; + + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + fin.write(jsonObjectRaw.toJSONString().getBytes()); + fin.writeChar('\n'); + } + + logger + .info( + "Downloaded part " + i + " of logs for LaReferencia repoid " + laReferencialMatomoID + + " and for " + + sdf.format(date)); + i++; + } while (true); + fin.close(); + + } + } +} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java new file mode 100644 index 000000000..347d3de21 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java @@ -0,0 +1,423 @@ + +package eu.dnetlib.oa.graph.usagestats.export; + +import java.io.*; +import java.net.URLDecoder; +import java.sql.Connection; +import java.sql.PreparedStatement; +import java.sql.SQLException; +import java.sql.Statement; +import java.sql.Timestamp; +import java.text.SimpleDateFormat; +import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocatedFileStatus; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.RemoteIterator; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class LaReferenciaStats { + + private static final Logger logger = LoggerFactory.getLogger(LaReferenciaStats.class); + + private String logRepoPath; + + private Statement stmt = null; + + private String CounterRobotsURL; + private ArrayList robotsList; + + public LaReferenciaStats(String logRepoPath) throws Exception { + this.logRepoPath = logRepoPath; + this.createTables(); +// this.createTmpTables(); + } + + /* + * private void connectDB() throws Exception { try { ConnectDB connectDB = new ConnectDB(); } catch (Exception e) { + * log.error("Connect to db failed: " + e); throw new Exception("Failed to connect to db: " + e.toString(), e); } } + */ + private void createTables() throws Exception { + try { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating LaReferencia tables"); + String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableLareferenciaLog); + logger.info("Created LaReferencia tables"); +// String sqlcreateRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO lareferencialog " +// + " WHERE (EXISTS ( SELECT lareferencialog.matomoid, lareferencialog.source, lareferencialog.id_visit," +// + "lareferencialog.action, lareferencialog.\"timestamp\", lareferencialog.entity_id " +// + "FROM lareferencialog " +// + "WHERE lareferencialog.matomoid=new.matomoid AND lareferencialog.source = new.source AND lareferencialog.id_visit = new.id_visit AND lareferencialog.action = new.action AND lareferencialog.entity_id = new.entity_id AND lareferencialog.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; +// String sqlCreateRuleIndexLaReferenciaLog = "create index if not exists lareferencialog_rule on lareferencialog(matomoid, source, id_visit, action, entity_id, \"timestamp\");"; +// stmt.executeUpdate(sqlcreateRuleLaReferenciaLog); +// stmt.executeUpdate(sqlCreateRuleIndexLaReferenciaLog); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Lareferencia Tables Created"); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + // System.exit(0); + } + } + +// private void createTmpTables() throws Exception { +// +// try { +// Statement stmt = ConnectDB.getConnection().createStatement(); +// String sqlCreateTmpTableLaReferenciaLog = "CREATE TABLE IF NOT EXISTS lareferencialogtmp(matomoid INTEGER, source TEXT, id_visit TEXT, country TEXT, action TEXT, url TEXT, entity_id TEXT, source_item_type TEXT, timestamp TEXT, referrer_name TEXT, agent TEXT, PRIMARY KEY(source, id_visit, action, timestamp, entity_id));"; +// String sqlcreateTmpRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO lareferencialogtmp " +// + " WHERE (EXISTS ( SELECT lareferencialogtmp.matomoid, lareferencialogtmp.source, lareferencialogtmp.id_visit," +// + "lareferencialogtmp.action, lareferencialogtmp.\"timestamp\", lareferencialogtmp.entity_id " +// + "FROM lareferencialogtmp " +// + "WHERE lareferencialogtmp.matomoid=new.matomoid AND lareferencialogtmp.source = new.source AND lareferencialogtmp.id_visit = new.id_visit AND lareferencialogtmp.action = new.action AND lareferencialogtmp.entity_id = new.entity_id AND lareferencialogtmp.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; +// stmt.executeUpdate(sqlCreateTmpTableLaReferenciaLog); +// stmt.executeUpdate(sqlcreateTmpRuleLaReferenciaLog); +// +// stmt.close(); +// log.info("Lareferencia Tmp Tables Created"); +// +// } catch (Exception e) { +// log.error("Failed to create tmptables: " + e); +// throw new Exception("Failed to create tmp tables: " + e.toString(), e); +// // System.exit(0); +// } +// } + + public void processLogs() throws Exception { + try { + logger.info("Processing LaReferencia repository logs"); + processlaReferenciaLog(); + logger.info("LaReferencia repository logs process done"); + + logger.info("LaReferencia removing double clicks"); + removeDoubleClicks(); + logger.info("LaReferencia removed double clicks"); + + logger.info("LaReferencia creating viewsStats"); + viewsStats(); + logger.info("LaReferencia created viewsStats"); + logger.info("LaReferencia creating downloadsStats"); + downloadsStats(); + logger.info("LaReferencia created downloadsStats"); + logger.info("LaReferencia updating Production Tables"); + updateProdTables(); + logger.info("LaReferencia updated Production Tables"); + + } catch (Exception e) { + logger.error("Failed to process logs: " + e); + throw new Exception("Failed to process logs: " + e.toString(), e); + } + } + + public void processlaReferenciaLog() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping lareferencialogtmp_json table"); + String drop_lareferencialogtmp_json = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialogtmp_json"; + stmt.executeUpdate(drop_lareferencialogtmp_json); + logger.info("Dropped lareferencialogtmp_json table"); + + logger.info("Creating lareferencialogtmp_json"); + String create_lareferencialogtmp_json = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialogtmp_json(\n" + + " `idSite` STRING,\n" + + " `idVisit` STRING,\n" + + " `country` STRING,\n" + + " `referrerName` STRING,\n" + + " `browser` STRING,\n" + + " `repItem` STRING,\n" + + " `actionDetails` ARRAY<\n" + + " struct<\n" + + " timestamp: STRING,\n" + + " type: STRING,\n" + + " url: STRING,\n" + + " `customVariables`: struct<\n" + + " `1`: struct<\n" + + " `customVariablePageValue1`: STRING\n" + + " >,\n" + + " `2`: struct<\n" + + " `customVariablePageValue2`: STRING\n" + + " >\n" + + " >\n" + + " >\n" + + " >" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.lareferenciaLogPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_lareferencialogtmp_json); + logger.info("Created lareferencialogtmp_json"); + + logger.info("Dropping lareferencialogtmp table"); + String drop_lareferencialogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialogtmp"; + stmt.executeUpdate(drop_lareferencialogtmp); + logger.info("Dropped lareferencialogtmp table"); + + logger.info("Creating lareferencialogtmp"); + String create_lareferencialogtmp = "CREATE TABLE " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(create_lareferencialogtmp); + logger.info("Created lareferencialogtmp"); + + logger.info("Inserting into lareferencialogtmp"); + String insert_lareferencialogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp " + + "SELECT DISTINCT cast(idSite as INT) as matomoid, CONCAT('opendoar____::', " + + "actiondetail.customVariables.`2`.customVariablePageValue2) as source, idVisit as id_Visit, country, " + + "actiondetail.type as action, actiondetail.url as url, " + + "actiondetail.customVariables.`1`.`customVariablePageValue1` as entity_id, " + + "'repItem' as source_item_type, from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, " + + "referrerName as referrer_name, browser as agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp_json " + + "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; + stmt.executeUpdate(insert_lareferencialogtmp); + logger.info("Inserted into lareferencialogtmp"); + + stmt.close(); + } + + public void removeDoubleClicks() throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Cleaning download double clicks"); + // clean download double clicks + String sql = "DELETE from " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp WHERE EXISTS (" + + "SELECT DISTINCT p1.source, p1.id_visit, p1.action, p1.entity_id, p1.timestamp " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp p1, " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp p2 " + + "WHERE p1.source=p2.source AND p1.id_visit=p2.id_visit AND p1.entity_id=p2.entity_id " + + "AND p1.action=p2.action AND p1.action='download' AND p1.timestamp!=p2.timestamp " + + "AND p1.timestamp listHdfsDir(String dir) throws Exception { + FileSystem hdfs = FileSystem.get(new Configuration()); + RemoteIterator Files; + ArrayList fileNames = new ArrayList<>(); + + try { + Path exportPath = new Path(hdfs.getUri() + dir); + Files = hdfs.listFiles(exportPath, false); + while (Files.hasNext()) { + String fileName = Files.next().getPath().toString(); + // log.info("Found hdfs file " + fileName); + fileNames.add(fileName); + } + // hdfs.close(); + } catch (Exception e) { + logger.error("HDFS file path with exported data does not exist : " + new Path(hdfs.getUri() + logRepoPath)); + throw new Exception("HDFS file path with exported data does not exist : " + logRepoPath, e); + } + + return fileNames; + } + + private String readHDFSFile(String filename) throws Exception { + String result; + try { + + FileSystem fs = FileSystem.get(new Configuration()); + // log.info("reading file : " + filename); + + BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(new Path(filename)))); + + StringBuilder sb = new StringBuilder(); + String line = br.readLine(); + + while (line != null) { + if (!line.equals("[]")) { + sb.append(line); + } + // sb.append(line); + line = br.readLine(); + } + result = sb.toString().replace("][{\"idSite\"", ",{\"idSite\""); + if (result.equals("")) { + result = "[]"; + } + + // fs.close(); + } catch (Exception e) { + logger.error(e.getMessage()); + throw new Exception(e); + } + + return result; + } + +} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java new file mode 100644 index 000000000..65816518f --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java @@ -0,0 +1,316 @@ + +package eu.dnetlib.oa.graph.usagestats.export; + +import java.io.*; +import java.net.Authenticator; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class PiwikDownloadLogs { + + private final String piwikUrl; + private Date startDate; + private final String tokenAuth; + + /* + * The Piwik's API method + */ + private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; + private final String format = "&format=json"; + + private static final Logger logger = LoggerFactory.getLogger(PiwikDownloadLogs.class); + + public PiwikDownloadLogs(String piwikUrl, String tokenAuth) { + this.piwikUrl = piwikUrl; + this.tokenAuth = tokenAuth; + + } + + private String getPiwikLogUrl() { + return "https://" + piwikUrl + "/"; + } + + private String getJson(String url) throws Exception { + try { + logger.debug("Connecting to download the JSON: " + url); + URL website = new URL(url); + URLConnection connection = website.openConnection(); + + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + } + } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + url + " Exception: " + e); + throw new Exception("Failed to get URL: " + url + " Exception: " + e.toString(), e); + } + } + + class WorkerThread implements Runnable { + private Calendar currDay; + private int siteId; + private String repoLogsPath; + private String portalLogPath; + private String portalMatomoID; + + public WorkerThread(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws IOException { + this.currDay = (Calendar) currDay.clone(); + this.siteId = new Integer(siteId); + this.repoLogsPath = new String(repoLogsPath); + this.portalLogPath = new String(portalLogPath); + this.portalMatomoID = new String(portalMatomoID); + } + + public void run() { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + System.out + .println( + Thread.currentThread().getName() + " (Start) Thread for " + + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); + try { + GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + System.out + .println( + Thread.currentThread().getName() + " (End) Thread for " + + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); + } + + public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + + Date date = currDay.getTime(); + logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + if (siteId == Integer.parseInt(portalMatomoID)) { + outFolder = portalLogPath; + } else { + outFolder = repoLogsPath; + } + + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + + int i = 0; + + JSONParser parser = new JSONParser(); + StringBuffer totalContent = new StringBuffer(); + FileSystem fs = FileSystem.get(new Configuration()); + + do { + int writtenBytes = 0; + String apiUrl = baseApiUrl; + + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } + + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) + break; + + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"), + true); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); + + writtenBytes += jsonObjectRawBytes.length + 1; + } + + fin.close(); + System.out + .println( + Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes + + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"); + + i++; + } while (true); + + fs.close(); + } + } + + public void GetOpenAIRELogs(String repoLogsPath, String portalLogPath, String portalMatomoID) throws Exception { + + Statement statement = ConnectDB.getHiveConnection().createStatement(); + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + + ResultSet rs = statement + .executeQuery( + "SELECT distinct piwik_id from " + ConnectDB.getStatsDBSchema() + + ".datasource where piwik_id is not null and piwik_id <> 0 order by piwik_id"); + + // Getting all the piwikids in a list for logging reasons & limitting the list + // to the max number of piwikids + List piwikIdToVisit = new ArrayList(); + while (rs.next()) + piwikIdToVisit.add(rs.getInt(1)); + logger.info("Found the following piwikIds for download: " + piwikIdToVisit); + + if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 && + ExecuteWorkflow.numberOfPiwikIdsToDownload <= piwikIdToVisit.size()) { + logger.info("Trimming piwikIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); + piwikIdToVisit = piwikIdToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); + } + + logger.info("Downloading from repos with the followins piwikIds: " + piwikIdToVisit); + + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("Starting period for log download: " + sdf.format(start.getTime())); + + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("Ending period for log download: " + sdf.format(end.getTime())); + + //ExecutorService executor = Executors.newFixedThreadPool(ExecuteWorkflow.numberOfDownloadThreads); + for (int siteId : piwikIdToVisit) { + + logger.info("Now working on piwikId: " + siteId); + + PreparedStatement st = ConnectDB.DB_HIVE_CONNECTION + .prepareStatement( + "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + + ".piwiklog WHERE source=?"); + st.setInt(1, siteId); + + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + logger.info("Found max date: " + rs_date.getString(1) + " for repository " + siteId); + + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + } + } + rs_date.close(); + + for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { + //logger.info("Date used " + currDay.toString()); + //Runnable worker = new WorkerThread(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + //executor.execute(worker);// calling execute method of ExecutorService + GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + } + } + //executor.shutdown(); + //while (!executor.isTerminated()) { + //} + //System.out.println("Finished all threads"); + } + + public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + + Date date = currDay.getTime(); + logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + if (siteId == Integer.parseInt(portalMatomoID)) { + outFolder = portalLogPath; + } else { + outFolder = repoLogsPath; + } + + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + + int i = 0; + + JSONParser parser = new JSONParser(); + StringBuffer totalContent = new StringBuffer(); + FileSystem fs = FileSystem.get(new Configuration()); + + do { + int writtenBytes = 0; + String apiUrl = baseApiUrl; + + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } + + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) + break; + + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"), + true); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); + + writtenBytes += jsonObjectRawBytes.length + 1; + } + + fin.close(); + System.out + .println( + Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes + + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"); + + i++; + } while (true); + + fs.close(); + } +} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java new file mode 100644 index 000000000..6e015acf4 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java @@ -0,0 +1,1255 @@ + +package eu.dnetlib.oa.graph.usagestats.export; + +import java.io.*; +import java.net.URLDecoder; +import java.sql.Connection; +import java.sql.SQLException; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.*; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocatedFileStatus; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.RemoteIterator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class PiwikStatsDB { + + private String logPath; + private String logRepoPath; + private String logPortalPath; + + private Statement stmt = null; + + private static final Logger logger = LoggerFactory.getLogger(PiwikStatsDB.class); + + private String CounterRobotsURL; + private ArrayList robotsList; + + public PiwikStatsDB(String logRepoPath, String logPortalPath) throws Exception { + this.logRepoPath = logRepoPath; + this.logPortalPath = logPortalPath; + + } + + public void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.delete(new Path(ExecuteWorkflow.repoLogPath), true); + + logger.info("Deleting portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.delete(new Path(ExecuteWorkflow.portalLogPath), true); + + logger.info("Creating repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.repoLogPath)); + + logger.info("Creating portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.portalLogPath)); + } + + public void recreateDBAndTables() throws Exception { + this.createDatabase(); + this.createTables(); + // The piwiklog table is not needed since it is built + // on top of JSON files + this.createTmpTables(); + } + + public ArrayList getRobotsList() { + return robotsList; + } + + public void setRobotsList(ArrayList robotsList) { + this.robotsList = robotsList; + } + + public String getCounterRobotsURL() { + return CounterRobotsURL; + } + + public void setCounterRobotsURL(String CounterRobotsURL) { + this.CounterRobotsURL = CounterRobotsURL; + } + + private void createDatabase() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Dropping usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); + String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + " CASCADE"; + stmt.executeUpdate(dropDatabase); + } catch (Exception e) { + logger.error("Failed to drop database: " + e); + throw new Exception("Failed to drop database: " + e.toString(), e); + } + + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); + String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema(); + stmt.executeUpdate(createDatabase); + + } catch (Exception e) { + logger.error("Failed to create database: " + e); + throw new Exception("Failed to create database: " + e.toString(), e); + } + } + + private void createTables() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + // Create Piwiklog table - This table should exist + String sqlCreateTablePiwikLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklog(source INT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) " + + "into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTablePiwikLog); + + ///////////////////////////////////////// + // Rule for duplicate inserts @ piwiklog + ///////////////////////////////////////// + + String sqlCreateTablePortalLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log(source INT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTablePortalLog); + + ////////////////////////////////////////////////// + // Rule for duplicate inserts @ process_portal_log + ////////////////////////////////////////////////// + + stmt.close(); + ConnectDB.getHiveConnection().close(); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + + private void createTmpTables() throws Exception { + try { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTmpTablePiwikLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp(source INT, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTmpTablePiwikLog); + + ////////////////////////////////////////////////// + // Rule for duplicate inserts @ piwiklogtmp + ////////////////////////////////////////////////// + + ////////////////////////////////////////////////// + // Copy from public.piwiklog to piwiklog + ////////////////////////////////////////////////// + // String sqlCopyPublicPiwiklog="insert into piwiklog select * from public.piwiklog;"; + // stmt.executeUpdate(sqlCopyPublicPiwiklog); + + String sqlCreateTmpTablePortalLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp(source INT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTmpTablePortalLog); + + ////////////////////////////////////////////////// + // Rule for duplicate inserts @ process_portal_log_tmp + ////////////////////////////////////////////////// + + stmt.close(); + + } catch (Exception e) { + logger.error("Failed to create tmptables: " + e); + throw new Exception("Failed to create tmp tables: " + e.toString(), e); + // System.exit(0); + } + } + + public void processLogs() throws Exception { + try { + ReadCounterRobotsList counterRobots = new ReadCounterRobotsList(this.getCounterRobotsURL()); + this.robotsList = counterRobots.getRobotsPatterns(); + + logger.info("Processing repository logs"); + processRepositoryLog(); + logger.info("Repository logs process done"); + + logger.info("Removing double clicks"); + removeDoubleClicks(); + logger.info("Removing double clicks done"); + + logger.info("Cleaning oai"); + cleanOAI(); + logger.info("Cleaning oai done"); + + logger.info("Processing portal logs"); + processPortalLog(); + logger.info("Portal logs process done"); + + logger.info("Processing portal usagestats"); + portalStats(); + logger.info("Portal usagestats process done"); + + logger.info("ViewsStats processing starts"); + viewsStats(); + logger.info("ViewsStats processing ends"); + + logger.info("DownloadsStats processing starts"); + downloadsStats(); + logger.info("DownloadsStats processing starts"); + + + + logger.info("Updating Production Tables"); + updateProdTables(); + logger.info("Updated Production Tables"); + + } catch (Exception e) { + logger.error("Failed to process logs: " + e); + throw new Exception("Failed to process logs: " + e.toString(), e); + } + } + + public void processRepositoryLog() throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping piwiklogtmp_json table"); + String drop_piwiklogtmp_json = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp_json"; + stmt.executeUpdate(drop_piwiklogtmp_json); + logger.info("Dropped piwiklogtmp_json table"); + + logger.info("Creating piwiklogtmp_json"); + String create_piwiklogtmp_json = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp_json(\n" + + " `idSite` STRING,\n" + + " `idVisit` STRING,\n" + + " `country` STRING,\n" + + " `referrerName` STRING,\n" + + " `browser` STRING,\n" + + " `actionDetails` ARRAY<\n" + + " struct<\n" + + " type: STRING,\n" + + " url: STRING,\n" + + " `customVariables`: struct<\n" + + " `1`: struct<\n" + + " `customVariablePageValue1`: STRING\n" + + " >\n" + + " >,\n" + + " timestamp: String\n" + + " >\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.repoLogPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_piwiklogtmp_json); + logger.info("Created piwiklogtmp_json"); + + logger.info("Dropping piwiklogtmp table"); + String drop_piwiklogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp"; + stmt.executeUpdate(drop_piwiklogtmp); + logger.info("Dropped piwiklogtmp"); + + logger.info("Creating piwiklogtmp"); + String create_piwiklogtmp = "CREATE TABLE " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp (source BIGINT, id_Visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(create_piwiklogtmp); + logger.info("Created piwiklogtmp"); + + logger.info("Inserting into piwiklogtmp"); + String insert_piwiklogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, " + + "actiondetail.type as action, actiondetail.url as url, " + + "actiondetail.customVariables.`1`.`customVariablePageValue1` as entity_id, " + + "'repItem' as source_item_type, from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, " + + "referrerName as referrer_name, browser as agent\n" + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp_json\n" + + "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; + stmt.executeUpdate(insert_piwiklogtmp); + logger.info("Inserted into piwiklogtmp"); + + stmt.close(); + } + + public void removeDoubleClicks() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Cleaning download double clicks"); + // clean download double clicks + String sql = "DELETE from " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "WHERE EXISTS (\n" + + "SELECT DISTINCT p1.source, p1.id_visit, p1.action, p1.entity_id, p1.timestamp \n" + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p1, " + + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p2\n" + + "WHERE p1.source!='5' AND p1.source=p2.source AND p1.id_visit=p2.id_visit AND p1.entity_id=p2.entity_id \n" + + + "AND p1.action=p2.action AND p1.action='download' AND p1.timestamp!=p2.timestamp \n" + + "AND p1.timestamp\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.portalLogPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_process_portal_log_tmp_json); + logger.info("Created process_portal_log_tmp_json"); + + logger.info("Droping process_portal_log_tmp table"); + String drop_process_portal_log_tmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp"; + stmt.executeUpdate(drop_process_portal_log_tmp); + logger.info("Dropped process_portal_log_tmp"); + + logger.info("Creating process_portal_log_tmp"); + String create_process_portal_log_tmp = "CREATE TABLE " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp (source BIGINT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(create_process_portal_log_tmp); + logger.info("Created process_portal_log_tmp"); + + logger.info("Inserting into process_portal_log_tmp"); + String insert_process_portal_log_tmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp " + + "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, actiondetail.type as action, " + + + "actiondetail.url as url, " + + "CASE\n" + + " WHEN (actiondetail.url like '%datasourceId=%') THEN split(actiondetail.url,'datasourceId=')[1] " + + " WHEN (actiondetail.url like '%datasource=%') THEN split(actiondetail.url,'datasource=')[1] " + + " WHEN (actiondetail.url like '%datasourceFilter=%') THEN split(actiondetail.url,'datasourceFilter=')[1] " + + + " WHEN (actiondetail.url like '%articleId=%') THEN split(actiondetail.url,'articleId=')[1] " + + " WHEN (actiondetail.url like '%datasetId=%') THEN split(actiondetail.url,'datasetId=')[1] " + + " WHEN (actiondetail.url like '%projectId=%') THEN split(actiondetail.url,'projectId=')[1] " + + " WHEN (actiondetail.url like '%organizationId=%') THEN split(actiondetail.url,'organizationId=')[1] " + + " ELSE '' " + + "END AS entity_id, " + + "CASE " + + " WHEN (actiondetail.url like '%datasourceId=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%datasource=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%datasourceFilter=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%articleId=%') THEN 'result' " + + " WHEN (actiondetail.url like '%datasetId=%') THEN 'result' " + + " WHEN (actiondetail.url like '%projectId=%') THEN 'project' " + + " WHEN (actiondetail.url like '%organizationId=%') THEN 'organization' " + + " ELSE '' " + + "END AS source_item_type, " + + "from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, referrerName as referrer_name, " + + "browser as agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp_json " + + "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; + stmt.executeUpdate(insert_process_portal_log_tmp); + logger.info("Inserted into process_portal_log_tmp"); + + stmt.close(); + } + + public void portalStats() throws SQLException { + Connection con = ConnectDB.getHiveConnection(); + Statement stmt = con.createStatement(); + con.setAutoCommit(false); + +// Original queries where of the style +// +// SELECT DISTINCT source, id_visit, country, action, url, roid.oid, 'oaItem', `timestamp`, referrer_name, agent +// FROM usagestats_20200907.process_portal_log_tmp2, +// openaire_prod_stats_20200821.result_oids roid +// WHERE entity_id IS NOT null AND entity_id=roid.oid AND roid.oid IS NOT null +// +// The following query is an example of how queries should be +// +// +// INSERT INTO usagestats_20200907.piwiklogtmp +// SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent +// FROM usagestats_20200907.process_portal_log_tmp +// WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id +// IN (SELECT roid.oid FROM openaire_prod_stats_20200821.result_oids roid WHERE roid.oid IS NOT NULL); +// +// We should consider if we would like the queries to be as the following +// +// INSERT INTO usagestats_20200907.piwiklogtmp +// SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent +// FROM usagestats_20200907.process_portal_log_tmp +// WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id != '' AND process_portal_log_tmp.entity_id +// IN (SELECT roid.oid FROM openaire_prod_stats_20200821.result_oids roid WHERE roid.oid IS NOT NULL AND +// roid.oid != ''); + + logger.info("PortalStats - Step 1"); + String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent " + + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + ".result_oids roid WHERE roid.id IS NOT NULL)"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("PortalStats - Step 2"); + stmt = con.createStatement(); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'datasource', `timestamp`, referrer_name, agent " + + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + ".datasource_oids roid WHERE roid.id IS NOT NULL)"; + stmt.executeUpdate(sql); + stmt.close(); + +/* logger.info("PortalStats - Step 3"); + stmt = con.createStatement(); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'organization', `timestamp`, referrer_name, agent " + + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + ".organization_oids roid WHERE roid.id IS NOT NULL)"; +// stmt.executeUpdate(sql); + stmt.close(); +*/ + logger.info("PortalStats - Step 3"); + stmt = con.createStatement(); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'project', `timestamp`, referrer_name, agent " + + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + ".project_oids roid WHERE roid.id IS NOT NULL)"; + stmt.executeUpdate(sql); + stmt.close(); + + con.close(); + } + + private void cleanOAI() throws Exception { + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Cleaning oai - Step 1"); + stmt = ConnectDB.getHiveConnection().createStatement(); + String sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chlc.min-saude.pt/'," + + "'oai:repositorio.chlc.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.chlc.min-saude.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 2"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hospitaldebraga.pt/'," + + "'oai:repositorio.hospitaldebraga.pt:') WHERE entity_id LIKE 'oai:repositorio.hospitaldebraga.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 3"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipl.pt/'," + + "'oai:repositorio.ipl.pt:') WHERE entity_id LIKE 'oai:repositorio.ipl.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 4"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:bibliotecadigital.ipb.pt/'," + + "'oai:bibliotecadigital.ipb.pt:') WHERE entity_id LIKE 'oai:bibliotecadigital.ipb.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 5"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ismai.pt/'," + + "'oai:repositorio.ismai.pt:') WHERE entity_id LIKE 'oai:repositorio.ismai.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 6"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorioaberto.uab.pt/'," + + "'oai:repositorioaberto.uab.pt:') WHERE entity_id LIKE 'oai:repositorioaberto.uab.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 7"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.uac.pt/'," + + "'oai:repositorio.uac.pt:') WHERE entity_id LIKE 'oai:repositorio.uac.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 8"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.insa.pt/'," + + "'oai:repositorio.insa.pt:') WHERE entity_id LIKE 'oai:repositorio.insa.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 9"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipcb.pt/'," + + "'oai:repositorio.ipcb.pt:') WHERE entity_id LIKE 'oai:repositorio.ipcb.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 10"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ispa.pt/'," + + "'oai:repositorio.ispa.pt:') WHERE entity_id LIKE 'oai:repositorio.ispa.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 11"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chporto.pt/'," + + "'oai:repositorio.chporto.pt:') WHERE entity_id LIKE 'oai:repositorio.chporto.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 12"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ucp.pt/'," + + "'oai:repositorio.ucp.pt:') WHERE entity_id LIKE 'oai:repositorio.ucp.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 13"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:rihuc.huc.min-saude.pt/'," + + "'oai:rihuc.huc.min-saude.pt:') WHERE entity_id LIKE 'oai:rihuc.huc.min-saude.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 14"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipv.pt/'," + + "'oai:repositorio.ipv.pt:') WHERE entity_id LIKE 'oai:repositorio.ipv.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 15"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:www.repository.utl.pt/'," + + "'oai:www.repository.utl.pt:') WHERE entity_id LIKE 'oai:www.repository.utl.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 16"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:run.unl.pt/'," + + "'oai:run.unl.pt:') WHERE entity_id LIKE 'oai:run.unl.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 17"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:sapientia.ualg.pt/'," + + "'oai:sapientia.ualg.pt:') WHERE entity_id LIKE 'oai:sapientia.ualg.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 18"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipsantarem.pt/'," + + "'oai:repositorio.ipsantarem.pt:') WHERE entity_id LIKE 'oai:repositorio.ipsantarem.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 19"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:arca.igc.gulbenkian.pt/'," + + "'oai:arca.igc.gulbenkian.pt:') WHERE entity_id LIKE 'oai:arca.igc.gulbenkian.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 20"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:ubibliorum.ubi.pt/'," + + "'oai:ubibliorum.ubi.pt:') WHERE entity_id LIKE 'oai:ubibliorum.ubi.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 21"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:digituma.uma.pt/'," + + "'oai:digituma.uma.pt:') WHERE entity_id LIKE 'oai:digituma.uma.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 22"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ul.pt/'," + + "'oai:repositorio.ul.pt:') WHERE entity_id LIKE 'oai:repositorio.ul.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 23"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hff.min-saude.pt/'," + + "'oai:repositorio.hff.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.hff.min-saude.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 24"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorium.sdum.uminho.pt/'," + + "'oai:repositorium.sdum.uminho.pt:') WHERE entity_id LIKE 'oai:repositorium.sdum.uminho.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 25"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:recipp.ipp.pt/'," + + "'oai:recipp.ipp.pt:') WHERE entity_id LIKE 'oai:recipp.ipp.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 26"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:bdigital.ufp.pt/'," + + "'oai:bdigital.ufp.pt:') WHERE entity_id LIKE 'oai:bdigital.ufp.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 27"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.lneg.pt/'," + + "'oai:repositorio.lneg.pt:') WHERE entity_id LIKE 'oai:repositorio.lneg.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 28"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:iconline.ipleiria.pt/'," + + "'oai:iconline.ipleiria.pt:') WHERE entity_id LIKE 'oai:iconline.ipleiria.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 29"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:comum.rcaap.pt/'," + + "'oai:comum.rcaap.pt:') WHERE entity_id LIKE 'oai:comum.rcaap.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Done, closing connection"); + ConnectDB.getHiveConnection().close(); + } + + private String processPortalURL(String url) { + + if (url.indexOf("explore.openaire.eu") > 0) { + try { + url = URLDecoder.decode(url, "UTF-8"); + } catch (Exception e) { + logger.info("Error when decoding the following URL: " + url); + } + if (url.indexOf("datasourceId=") > 0 && url.substring(url.indexOf("datasourceId=") + 13).length() >= 46) { + url = "datasource|" + + url.substring(url.indexOf("datasourceId=") + 13, url.indexOf("datasourceId=") + 59); + } else if (url.indexOf("datasource=") > 0 + && url.substring(url.indexOf("datasource=") + 11).length() >= 46) { + url = "datasource|" + url.substring(url.indexOf("datasource=") + 11, url.indexOf("datasource=") + 57); + } else if (url.indexOf("datasourceFilter=") > 0 + && url.substring(url.indexOf("datasourceFilter=") + 17).length() >= 46) { + url = "datasource|" + + url.substring(url.indexOf("datasourceFilter=") + 17, url.indexOf("datasourceFilter=") + 63); + } else if (url.indexOf("articleId=") > 0 && url.substring(url.indexOf("articleId=") + 10).length() >= 46) { + url = "result|" + url.substring(url.indexOf("articleId=") + 10, url.indexOf("articleId=") + 56); + } else if (url.indexOf("datasetId=") > 0 && url.substring(url.indexOf("datasetId=") + 10).length() >= 46) { + url = "result|" + url.substring(url.indexOf("datasetId=") + 10, url.indexOf("datasetId=") + 56); + } else if (url.indexOf("projectId=") > 0 && url.substring(url.indexOf("projectId=") + 10).length() >= 46 + && !url.contains("oai:dnet:corda")) { + url = "project|" + url.substring(url.indexOf("projectId=") + 10, url.indexOf("projectId=") + 56); + } else if (url.indexOf("organizationId=") > 0 + && url.substring(url.indexOf("organizationId=") + 15).length() >= 46) { + url = "organization|" + + url.substring(url.indexOf("organizationId=") + 15, url.indexOf("organizationId=") + 61); + } else { + url = ""; + } + } else { + url = ""; + } + + return url; + } + + private void updateProdTables() throws SQLException { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Inserting data to piwiklog"); + String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklog " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; + stmt.executeUpdate(sql); + + logger.info("Inserting data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp"; + stmt.executeUpdate(sql); + + logger.info("Inserting data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp"; + stmt.executeUpdate(sql); + + logger.info("Inserting data to pageviews_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats_tmp"; + stmt.executeUpdate(sql); + +/* logger.info("Dropping table views_stats_tmp"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp"; + stmt.executeUpdate(sql); + + logger.info("Dropping table downloads_stats_tmp"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp"; + stmt.executeUpdate(sql); + + logger.info("Dropping table pageviews_stats_tmp"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats_tmp"; + stmt.executeUpdate(sql); + + logger.info("Dropping table process_portal_log_tmp"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp"; + stmt.executeUpdate(sql); +*/ + stmt.close(); + ConnectDB.getHiveConnection().close(); + + } + + private ArrayList listHdfsDir(String dir) throws Exception { + + FileSystem hdfs = FileSystem.get(new Configuration()); + RemoteIterator Files; + ArrayList fileNames = new ArrayList<>(); + + try { + Path exportPath = new Path(hdfs.getUri() + dir); + Files = hdfs.listFiles(exportPath, false); + while (Files.hasNext()) { + String fileName = Files.next().getPath().toString(); + fileNames.add(fileName); + } + + hdfs.close(); + } catch (Exception e) { + logger.error("HDFS file path with exported data does not exist : " + new Path(hdfs.getUri() + logPath)); + throw new Exception("HDFS file path with exported data does not exist : " + logPath, e); + } + + return fileNames; + } + + private String readHDFSFile(String filename) throws Exception { + String result; + try { + + FileSystem fs = FileSystem.get(new Configuration()); + // log.info("reading file : " + filename); + + BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(new Path(filename)))); + + StringBuilder sb = new StringBuilder(); + String line = br.readLine(); + + while (line != null) { + if (!line.equals("[]")) { + sb.append(line); + } + // sb.append(line); + line = br.readLine(); + } + result = sb.toString().replace("][{\"idSite\"", ",{\"idSite\""); + if (result.equals("")) { + result = "[]"; + } + + // fs.close(); + } catch (Exception e) { + logger.error(e.getMessage()); + throw new Exception(e); + } + + return result; + } + + private Connection getConnection() throws SQLException { + return ConnectDB.getHiveConnection(); + } +} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ReadCounterRobotsList.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ReadCounterRobotsList.java new file mode 100644 index 000000000..1708a1c64 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ReadCounterRobotsList.java @@ -0,0 +1,54 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.usagestats.export; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +/** + * @author D. Pierrakos, S. Zoupanos + */ +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.net.MalformedURLException; +import java.net.URL; +import java.nio.charset.Charset; +import java.util.ArrayList; + +import org.json.JSONException; +import org.json.simple.JSONArray; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; + +public class ReadCounterRobotsList { + + private ArrayList robotsPatterns = new ArrayList(); + private String COUNTER_ROBOTS_URL; + + public ReadCounterRobotsList(String url) throws IOException, JSONException, ParseException { + COUNTER_ROBOTS_URL = url; + robotsPatterns = readRobotsPartners(COUNTER_ROBOTS_URL); + } + + private ArrayList readRobotsPartners(String url) throws MalformedURLException, IOException, ParseException { + InputStream is = new URL(url).openStream(); + JSONParser parser = new JSONParser(); + BufferedReader reader = new BufferedReader(new InputStreamReader(is, Charset.forName("ISO-8859-1"))); + JSONArray jsonArray = (JSONArray) parser.parse(reader); + for (Object aJsonArray : jsonArray) { + org.json.simple.JSONObject jsonObjectRow = (org.json.simple.JSONObject) aJsonArray; + robotsPatterns.add(jsonObjectRow.get("pattern").toString().replace("\\", "\\\\")); + } + return robotsPatterns; + } + + public ArrayList getRobotsPatterns() { + return robotsPatterns; + } +} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java new file mode 100644 index 000000000..295e98280 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java @@ -0,0 +1,571 @@ + +package eu.dnetlib.oa.graph.usagestats.export; + +import java.io.*; +// import java.io.BufferedReader; +// import java.io.InputStreamReader; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class SarcStats { + + private Statement stmtHive = null; + private Statement stmtImpala = null; + + private static final Logger logger = LoggerFactory.getLogger(SarcStats.class); + + public SarcStats() throws Exception { +// createTables(); + } + + private void createTables() throws Exception { + try { + + stmtHive = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilog(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; + stmtHive.executeUpdate(sqlCreateTableSushiLog); + + // String sqlCopyPublicSushiLog="INSERT INTO sushilog SELECT * FROM public.sushilog;"; + // stmt.executeUpdate(sqlCopyPublicSushiLog); + String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " + + " ON INSERT TO sushilog " + + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," + + "sushilog.rid, sushilog.date " + + "FROM sushilog " + + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; + stmtHive.executeUpdate(sqlcreateRuleSushiLog); + String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; + stmtHive.executeUpdate(createSushiIndex); + + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + + public void reCreateLogDirs() throws IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); + dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathArray), true); + + logger.info("Deleting sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); + dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathNonArray), true); + + logger.info("Creating sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); + dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathArray)); + + logger.info("Creating sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); + dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathNonArray)); + } + + public void processSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping sarc_sushilogtmp_json_array table"); + String drop_sarc_sushilogtmp_json_array = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array"; + stmt.executeUpdate(drop_sarc_sushilogtmp_json_array); + logger.info("Dropped sarc_sushilogtmp_json_array table"); + + logger.info("Creating sarc_sushilogtmp_json_array table"); + String create_sarc_sushilogtmp_json_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array(\n" + + " `ItemIdentifier` ARRAY<\n" + + " struct<\n" + + " `Type`: STRING,\n" + + " `Value`: STRING\n" + + " >\n" + + " >,\n" + + " `ItemPerformance` struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >\n" + + ")" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + sarcsReportPathArray + "/'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_sarc_sushilogtmp_json_array); + logger.info("Created sarc_sushilogtmp_json_array table"); + + logger.info("Dropping sarc_sushilogtmp_json_non_array table"); + String drop_sarc_sushilogtmp_json_non_array = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(drop_sarc_sushilogtmp_json_non_array); + logger.info("Dropped sarc_sushilogtmp_json_non_array table"); + + logger.info("Creating sarc_sushilogtmp_json_non_array table"); + String create_sarc_sushilogtmp_json_non_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array (\n" + + " `ItemIdentifier` struct<\n" + + " `Type`: STRING,\n" + + " `Value`: STRING\n" + + " >,\n" + + " `ItemPerformance` struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >" + + ")" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + sarcsReportPathNonArray + "/'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_sarc_sushilogtmp_json_non_array); + logger.info("Created sarc_sushilogtmp_json_non_array table"); + + logger.info("Creating sarc_sushilogtmp table"); + String create_sarc_sushilogtmp = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp(source STRING, repository STRING, " + + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " + + + "tblproperties('transactional'='true')"; + stmt.executeUpdate(create_sarc_sushilogtmp); + logger.info("Created sarc_sushilogtmp table"); + + logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); + String insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + + " `ItemIdent`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array " + + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + + "WHERE `ItemIdent`.`Type`='DOI'"; + stmt.executeUpdate(insert_sarc_sushilogtmp); + logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); + + logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); + insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + + "`ItemIdentifier`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(insert_sarc_sushilogtmp); + logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); + + ConnectDB.getHiveConnection().close(); + } + + public void getAndProcessSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating sushilog table"); + String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog " + + "(`source` string, " + + "`repository` string, " + + "`rid` string, " + + "`date` string, " + + "`metric_type` string, " + + "`count` int)"; + stmt.executeUpdate(createSushilog); + logger.info("Created sushilog table"); + + logger.info("Dropping sarc_sushilogtmp table"); + String drop_sarc_sushilogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp"; + stmt.executeUpdate(drop_sarc_sushilogtmp); + logger.info("Dropped sarc_sushilogtmp table"); + ConnectDB.getHiveConnection().close(); + + List issnAndUrls = new ArrayList(); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/motricidade/sushiLite/v1_7/", "1646-107X" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/antropologicas/sushiLite/v1_7/", "0873-819X" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/interaccoes/sushiLite/v1_7/", "1646-2335" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/cct/sushiLite/v1_7/", "2182-3030" + }); + issnAndUrls.add(new String[] { + "https://actapediatrica.spp.pt/sushiLite/v1_7/", "0873-9781" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/sociologiapp/sushiLite/v1_7/", "0873-6529" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/finisterra/sushiLite/v1_7/", "0430-5027" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/sisyphus/sushiLite/v1_7/", "2182-8474" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/anestesiologia/sushiLite/v1_7/", "0871-6099" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/rpe/sushiLite/v1_7/", "0871-9187" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/psilogos/sushiLite/v1_7/", "1646-091X" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/juridica/sushiLite/v1_7/", "2183-5799" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/ecr/sushiLite/v1_7/", "1647-2098" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/nascercrescer/sushiLite/v1_7/", "0872-0754" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/cea/sushiLite/v1_7/", "1645-3794" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/proelium/sushiLite/v1_7/", "1645-8826" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/millenium/sushiLite/v1_7/", "0873-3015" + }); + + if (ExecuteWorkflow.sarcNumberOfIssnToDownload > 0 && + ExecuteWorkflow.sarcNumberOfIssnToDownload <= issnAndUrls.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.sarcNumberOfIssnToDownload); + issnAndUrls = issnAndUrls.subList(0, ExecuteWorkflow.sarcNumberOfIssnToDownload); + } + + logger.info("(getAndProcessSarc) Downloading the followins opendoars: " + issnAndUrls); + + for (String[] issnAndUrl : issnAndUrls) { + logger.info("Now working on ISSN: " + issnAndUrl[1]); + getARReport(sarcsReportPathArray, sarcsReportPathNonArray, issnAndUrl[0], issnAndUrl[1]); + } + + } + + public void finalizeSarcStats() throws Exception { + stmtHive = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + stmtImpala = ConnectDB.getImpalaConnection().createStatement(); + + logger.info("Creating downloads_stats table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmtHive.executeUpdate(createDownloadsStats); + logger.info("Created downloads_stats table"); + + logger.info("Dropping sarc_sushilogtmp_impala table"); + String drop_sarc_sushilogtmp_impala = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_impala"; + stmtHive.executeUpdate(drop_sarc_sushilogtmp_impala); + logger.info("Dropped sarc_sushilogtmp_impala table"); + + logger.info("Creating sarc_sushilogtmp_impala, a table readable by impala"); + String createSarcSushilogtmpImpala = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_impala " + + "STORED AS PARQUET AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; + stmtHive.executeUpdate(createSarcSushilogtmpImpala); + logger.info("Created sarc_sushilogtmp_impala"); + + logger.info("Making sarc_sushilogtmp visible to impala"); + String invalidateMetadata = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_impala;"; + stmtImpala.executeUpdate(invalidateMetadata); + + logger.info("Dropping downloads_stats_impala table"); + String drop_downloads_stats_impala = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats_impala"; + stmtHive.executeUpdate(drop_downloads_stats_impala); + logger.info("Dropped downloads_stats_impala table"); + + logger.info("Making downloads_stats_impala deletion visible to impala"); + try { + String invalidateMetadataDownloadsStatsImpala = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats_impala;"; + stmtImpala.executeUpdate(invalidateMetadataDownloadsStatsImpala); + } catch (SQLException sqle) { + } + + // We run the following query in Impala because it is faster + logger.info("Creating downloads_stats_impala"); + String createDownloadsStatsImpala = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats_impala AS " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(CAST(YEAR(`date`) AS STRING), '/', " + + "LPAD(CAST(MONTH(`date`) AS STRING), 2, '0')) AS `date`, s.count, '0' " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_impala s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".datasource_results dr, " + + ConnectDB.getStatsDBSchema() + ".result_pids ro " + + "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND dr.id=d.id AND dr.result=ro.id AND " + + "s.rid=ro.pid AND ro.type='Digital Object Identifier' AND metric_type='ft_total' AND s.source='SARC-OJS'"; + stmtImpala.executeUpdate(createDownloadsStatsImpala); + logger.info("Creating downloads_stats_impala"); + + // Insert into downloads_stats + logger.info("Inserting data from downloads_stats_impala into downloads_stats"); + String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats SELECT * " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_impala"; + stmtHive.executeUpdate(insertDStats); + logger.info("Inserted into downloads_stats"); + + logger.info("Creating sushilog table"); + String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog " + + "(`source` string, " + + "`repository_id` string, " + + "`rid` string, " + + "`date` string, " + + "`metric_type` string, " + + "`count` int)"; + stmtHive.executeUpdate(createSushilog); + logger.info("Created sushilog table"); + + // Insert into sushilog + logger.info("Inserting into sushilog"); + String insertSushiLog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog SELECT * " + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; + stmtHive.executeUpdate(insertSushiLog); + logger.info("Inserted into sushilog"); + + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + } + + public void getARReport(String sarcsReportPathArray, String sarcsReportPathNonArray, + String url, String issn) throws Exception { + logger.info("Processing SARC! issn: " + issn + " with url: " + url); + ConnectDB.getHiveConnection().setAutoCommit(false); + + SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getARReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); + + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("(getARReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); + + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); + st.setString(1, issn); + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + } + } + rs_date.close(); + + // Creating the needed configuration for the correct storing of data + Configuration config = new Configuration(); + config.addResource(new Path("/etc/hadoop/conf/core-site.xml")); + config.addResource(new Path("/etc/hadoop/conf/hdfs-site.xml")); + config + .set( + "fs.hdfs.impl", + org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + config + .set( + "fs.file.impl", + org.apache.hadoop.fs.LocalFileSystem.class.getName()); + FileSystem dfs = FileSystem.get(config); + + while (start.before(end)) { + String reportUrl = url + "GetReport/?Report=AR1&Format=json&BeginDate=" + + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()); + start.add(Calendar.MONTH, 1); + + logger.info("(getARReport) Getting report: " + reportUrl); + String text = getJson(reportUrl); + if (text == null) { + continue; + } + + JSONParser parser = new JSONParser(); + JSONObject jsonObject = null; + try { + jsonObject = (JSONObject) parser.parse(text); + } + // if there is a parsing error continue with the next url + catch (ParseException pe) { + continue; + } + + jsonObject = (JSONObject) jsonObject.get("sc:ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("sc:Report"); + if (jsonObject == null) { + continue; + } + jsonObject = (JSONObject) jsonObject.get("c:Report"); + jsonObject = (JSONObject) jsonObject.get("c:Customer"); + Object obj = jsonObject.get("c:ReportItems"); + JSONArray jsonArray = new JSONArray(); + if (obj instanceof JSONObject) { + jsonArray.add(obj); + } else { + jsonArray = (JSONArray) obj; + // jsonArray = (JSONArray) jsonObject.get("c:ReportItems"); + } + if (jsonArray == null) { + continue; + } + + // Creating the file in the filesystem for the ItemIdentifier as array object + String filePathArray = sarcsReportPathArray + "/SarcsARReport_" + issn + "_" + + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePathArray); + FSDataOutputStream finArray = dfs.create(new Path(filePathArray), true); + + // Creating the file in the filesystem for the ItemIdentifier as array object + String filePathNonArray = sarcsReportPathNonArray + "/SarcsARReport_" + issn + "_" + + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePathNonArray); + FSDataOutputStream finNonArray = dfs.create(new Path(filePathNonArray), true); + + for (Object aJsonArray : jsonArray) { + + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + renameKeysRecursively(":", jsonObjectRow); + + if (jsonObjectRow.get("ItemIdentifier") instanceof JSONObject) { + finNonArray.write(jsonObjectRow.toJSONString().getBytes()); + finNonArray.writeChar('\n'); + } else { + finArray.write(jsonObjectRow.toJSONString().getBytes()); + finArray.writeChar('\n'); + } + } + + finArray.close(); + finNonArray.close(); + + // Check the file size and if it is too big, delete it + File fileArray = new File(filePathArray); + if (fileArray.length() == 0) + fileArray.delete(); + File fileNonArray = new File(filePathNonArray); + if (fileNonArray.length() == 0) + fileNonArray.delete(); + + } + + dfs.close(); + + ConnectDB.getHiveConnection().close(); + } + + private void renameKeysRecursively(String delimiter, JSONArray givenJsonObj) throws Exception { + for (Object jjval : givenJsonObj) { + if (jjval instanceof JSONArray) + renameKeysRecursively(delimiter, (JSONArray) jjval); + else if (jjval instanceof JSONObject) + renameKeysRecursively(delimiter, (JSONObject) jjval); + // All other types of vals + else + ; + } + } + + private void renameKeysRecursively(String delimiter, JSONObject givenJsonObj) throws Exception { + Set jkeys = new HashSet(givenJsonObj.keySet()); + for (String jkey : jkeys) { + + String[] splitArray = jkey.split(delimiter); + String newJkey = splitArray[splitArray.length - 1]; + + Object jval = givenJsonObj.get(jkey); + givenJsonObj.remove(jkey); + givenJsonObj.put(newJkey, jval); + + if (jval instanceof JSONObject) + renameKeysRecursively(delimiter, (JSONObject) jval); + + if (jval instanceof JSONArray) { + renameKeysRecursively(delimiter, (JSONArray) jval); + } + } + } + + private String getJson(String url) throws Exception { + // String cred=username+":"+password; + // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + response.append("\n"); + } + } + return response.toString(); + } catch (Exception e) { + + // Logging error and silently continuing + logger.error("Failed to get URL: " + e); + System.out.println("Failed to get URL: " + e); +// return null; +// throw new Exception("Failed to get URL: " + e.toString(), e); + } + return ""; + } +} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java new file mode 100644 index 000000000..405b58bd5 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java @@ -0,0 +1,179 @@ + +package eu.dnetlib.oa.graph.usagestats.export; + +import java.io.IOException; +import java.sql.SQLException; +import java.sql.Statement; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Main class for downloading and processing Usage statistics + * + * @author D. Pierrakos, S. Zoupanos + */ +public class UsageStatsExporter { + + public UsageStatsExporter() { + + } + + private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); + + private void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.delete(new Path(ExecuteWorkflow.repoLogPath), true); + + logger.info("Deleting portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.delete(new Path(ExecuteWorkflow.portalLogPath), true); + + logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); + + logger.info("Creating repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.repoLogPath)); + + logger.info("Creating portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.portalLogPath)); + + logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); + } + + public void export() throws Exception { + + logger.info("Initialising DB properties"); + ConnectDB.init(); + +// runImpalaQuery(); + + PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); + + logger.info("Re-creating database and tables"); + if (ExecuteWorkflow.recreateDbAndTables) + piwikstatsdb.recreateDBAndTables(); + ; + + logger.info("Initializing the download logs module"); + PiwikDownloadLogs piwd = new PiwikDownloadLogs(ExecuteWorkflow.matomoBaseURL, ExecuteWorkflow.matomoAuthToken); + + if (ExecuteWorkflow.piwikEmptyDirs) { + logger.info("Recreating Piwik log directories"); + piwikstatsdb.reCreateLogDirs(); + } + + // Downloading piwik logs (also managing directory creation) + if (ExecuteWorkflow.downloadPiwikLogs) { + logger.info("Downloading piwik logs"); + piwd + .GetOpenAIRELogs( + ExecuteWorkflow.repoLogPath, + ExecuteWorkflow.portalLogPath, ExecuteWorkflow.portalMatomoID); + } + logger.info("Downloaded piwik logs"); + + // Create DB tables, insert/update statistics + String cRobotsUrl = "https://raw.githubusercontent.com/atmire/COUNTER-Robots/master/COUNTER_Robots_list.json"; + piwikstatsdb.setCounterRobotsURL(cRobotsUrl); + + if (ExecuteWorkflow.processPiwikLogs) { + logger.info("Processing logs"); + piwikstatsdb.processLogs(); + } + + logger.info("Creating LaReferencia tables"); + LaReferenciaDownloadLogs lrf = new LaReferenciaDownloadLogs(ExecuteWorkflow.lareferenciaBaseURL, + ExecuteWorkflow.lareferenciaAuthToken); + + if (ExecuteWorkflow.laReferenciaEmptyDirs) { + logger.info("Recreating LaReferencia log directories"); + lrf.reCreateLogDirs(); + } + + if (ExecuteWorkflow.downloadLaReferenciaLogs) { + logger.info("Downloading LaReferencia logs"); + lrf.GetLaReferenciaRepos(ExecuteWorkflow.lareferenciaLogPath); + logger.info("Downloaded LaReferencia logs"); + } + LaReferenciaStats lastats = new LaReferenciaStats(ExecuteWorkflow.lareferenciaLogPath); + + if (ExecuteWorkflow.processLaReferenciaLogs) { + logger.info("Processing LaReferencia logs"); + lastats.processLogs(); + logger.info("LaReferencia logs done"); + } + + IrusStats irusstats = new IrusStats(ExecuteWorkflow.irusUKBaseURL); + if (ExecuteWorkflow.irusCreateTablesEmptyDirs) { + logger.info("Creating Irus Stats tables"); + irusstats.createTables(); + logger.info("Created Irus Stats tables"); + + logger.info("Re-create log dirs"); + irusstats.reCreateLogDirs(); + logger.info("Re-created log dirs"); + } + + if (ExecuteWorkflow.irusDownloadReports) { + irusstats.getIrusRRReport(ExecuteWorkflow.irusUKReportPath); + } + if (ExecuteWorkflow.irusProcessStats) { + irusstats.processIrusStats(); + logger.info("Irus done"); + } + + SarcStats sarcStats = new SarcStats(); + if (ExecuteWorkflow.sarcCreateTablesEmptyDirs) { + sarcStats.reCreateLogDirs(); + } + if (ExecuteWorkflow.sarcDownloadReports) { + sarcStats.getAndProcessSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); + } + if (ExecuteWorkflow.sarcProcessStats) { + sarcStats.processSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); + sarcStats.finalizeSarcStats(); + } + logger.info("Sarc done"); + + // finalize usagestats + if (ExecuteWorkflow.finalizeStats) { + piwikstatsdb.finalizeStats(); + logger.info("Finalized stats"); + } + + // Make the tables available to Impala + if (ExecuteWorkflow.finalTablesVisibleToImpala) { + logger.info("Making tables visible to Impala"); + invalidateMetadata(); + } + + logger.info("End"); + } + + private void invalidateMetadata() throws SQLException { + Statement stmt = null; + + stmt = ConnectDB.getImpalaConnection().createStatement(); + + String sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + } +} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/export/usagestats_parameters.json b/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/export/usagestats_parameters.json new file mode 100644 index 000000000..988c23b48 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/export/usagestats_parameters.json @@ -0,0 +1,231 @@ +[ + { + "paramName": "mat", + "paramLongName": "matomoAuthToken", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "mbu", + "paramLongName": "matomoBaseURL", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + }, + { + "paramName": "rlp", + "paramLongName": "repoLogPath", + "paramDescription": "nameNode of the source cluster", + "paramRequired": true + }, + { + "paramName": "plp", + "paramLongName": "portalLogPath", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "pmi", + "paramLongName": "portalMatomoID", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "iukbuw", + "paramLongName": "irusUKBaseURL", + "paramDescription": "working directory", + "paramRequired": true + }, + { + "paramName": "iukrp", + "paramLongName": "irusUKReportPath", + "paramDescription": "maximum number of map tasks used in the distcp process", + "paramRequired": true + }, + { + "paramName": "srpa", + "paramLongName": "sarcsReportPathArray", + "paramDescription": "memory for distcp action copying actionsets from remote cluster", + "paramRequired": true + }, + { + "paramName": "srpna", + "paramLongName": "sarcsReportPathNonArray", + "paramDescription": "timeout for distcp copying actions from remote cluster", + "paramRequired": true + }, + { + "paramName": "llp", + "paramLongName": "lareferenciaLogPath", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "lbu", + "paramLongName": "lareferenciaBaseURL", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "lat", + "paramLongName": "lareferenciaAuthToken", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbhu", + "paramLongName": "dbHiveUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbiu", + "paramLongName": "dbImpalaUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "usdbs", + "paramLongName": "usageStatsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "sdbs", + "paramLongName": "statsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "rdbt", + "paramLongName": "recreateDbAndTables", + "paramDescription": "Re-create database and initial tables?", + "paramRequired": true + }, + { + "paramName": "pwed", + "paramLongName": "piwikEmptyDirs", + "paramDescription": "Empty piwik directories?", + "paramRequired": true + }, + { + "paramName": "ppwl", + "paramLongName": "processPiwikLogs", + "paramDescription": "Process the piwiklogs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "dpwl", + "paramLongName": "downloadPiwikLogs", + "paramDescription": "download piwik logs?", + "paramRequired": true + }, + { + "paramName": "slp", + "paramLongName": "startingLogPeriod", + "paramDescription": "Starting log period", + "paramRequired": true + }, + { + "paramName": "elp", + "paramLongName": "endingLogPeriod", + "paramDescription": "Ending log period", + "paramRequired": true + }, + { + "paramName": "npidd", + "paramLongName": "numberOfPiwikIdsToDownload", + "paramDescription": "Limit the number of the downloaded piwikids to the first numberOfPiwikIdsToDownload", + "paramRequired": true + }, + { + "paramName": "nsidd", + "paramLongName": "numberOfSiteIdsToDownload", + "paramDescription": "Limit the number of the downloaded siteids (La Referencia logs) to the first numberOfSiteIdsToDownload", + "paramRequired": true + }, + { + "paramName": "lerd", + "paramLongName": "laReferenciaEmptyDirs", + "paramDescription": "Empty LaReferencia directories?", + "paramRequired": true + }, + { + "paramName": "plrl", + "paramLongName": "processLaReferenciaLogs", + "paramDescription": "Process the La Referencia logs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "dlrl", + "paramLongName": "downloadLaReferenciaLogs", + "paramDescription": "download La Referencia logs?", + "paramRequired": true + }, + { + "paramName": "icted", + "paramLongName": "irusCreateTablesEmptyDirs", + "paramDescription": "Irus section: Create tables and empty JSON directories?", + "paramRequired": true + }, + { + "paramName": "idr", + "paramLongName": "irusDownloadReports", + "paramDescription": "Irus section: Download reports?", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "irusProcessStats", + "paramDescription": "Irus section: Process stats?", + "paramRequired": true + }, + { + "paramName": "inod", + "paramLongName": "irusNumberOfOpendoarsToDownload", + "paramDescription": "Limit the number of the downloaded Opendoars (Irus) to the first irusNumberOfOpendoarsToDownload", + "paramRequired": true + }, + { + "paramName": "icted", + "paramLongName": "sarcCreateTablesEmptyDirs", + "paramDescription": "Sarc section: Create tables and empty JSON directories?", + "paramRequired": true + }, + { + "paramName": "idr", + "paramLongName": "sarcDownloadReports", + "paramDescription": "Sarc section: Download reports?", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "sarcProcessStats", + "paramDescription": "Sarc section: Process stats?", + "paramRequired": true + }, + { + "paramName": "inod", + "paramLongName": "sarcNumberOfIssnToDownload", + "paramDescription": "Limit the number of the downloaded ISSN (Sarc) to the first sarcNumberOfIssnToDownload", + "paramRequired": true + }, + + { + "paramName": "fs", + "paramLongName": "finalizeStats", + "paramDescription": "Create the usage_stats table?", + "paramRequired": true + }, + { + "paramName": "ftvi", + "paramLongName": "finalTablesVisibleToImpala", + "paramDescription": "Make the usage_stats, views_stats and downloads_stats tables visible to Impala", + "paramRequired": true + }, + { + "paramName": "nodt", + "paramLongName": "numberOfDownloadThreads", + "paramDescription": "Number of download threads", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/config-default.xml b/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/config-default.xml new file mode 100644 index 000000000..b5c807378 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + jobTracker + ${jobTracker} + + + nameNode + ${nameNode} + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1 + + + impalaJdbcUrl + jdbc:hive2://iis-cdh5-test-gw.ocean.icm.edu.pl:21050/;auth=noSasl; + + + oozie.wf.workflow.notification.url + {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status + + + oozie.use.system.libpath + true + + diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/workflow.xml b/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/workflow.xml new file mode 100644 index 000000000..8d62a85a9 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/workflow.xml @@ -0,0 +1,90 @@ + + + + hiveMetastoreUris + Hive server metastore URIs + + + hiveJdbcUrl + Hive server jdbc url + + + impalaJdbcUrl + Impala server jdbc url + + + + + ${jobTracker} + ${nameNode} + + + hive.metastore.uris + ${hiveMetastoreUris} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + eu.dnetlib.oa.graph.usagestats.export.ExecuteWorkflow + --matomoAuthToken${matomoAuthToken} + --matomoBaseURL${matomoBaseURL} + --repoLogPath${repoLogPath} + --portalLogPath${portalLogPath} + --portalMatomoID${portalMatomoID} + --irusUKBaseURL${irusUKBaseURL} + --irusUKReportPath${irusUKReportPath} + --sarcsReportPathArray${sarcsReportPathArray} + --sarcsReportPathNonArray${sarcsReportPathNonArray} + --lareferenciaLogPath${lareferenciaLogPath} + --lareferenciaBaseURL${lareferenciaBaseURL} + --lareferenciaAuthToken${lareferenciaAuthToken} + --dbHiveUrl${hiveJdbcUrl} + --dbImpalaUrl${impalaJdbcUrl} + --usageStatsDBSchema${usageStatsDBSchema} + --statsDBSchema${statsDBSchema} + --recreateDbAndTables${recreateDbAndTables} + --piwikEmptyDirs${piwikEmptyDirs} + --downloadPiwikLogs${downloadPiwikLogs} + --processPiwikLogs${processPiwikLogs} + --startingLogPeriod${startingLogPeriod} + --endingLogPeriod${endingLogPeriod} + --numberOfPiwikIdsToDownload${numberOfPiwikIdsToDownload} + --numberOfSiteIdsToDownload${numberOfSiteIdsToDownload} + --laReferenciaEmptyDirs${laReferenciaEmptyDirs} + --downloadLaReferenciaLogs${downloadLaReferenciaLogs} + --processLaReferenciaLogs${processLaReferenciaLogs} + --irusCreateTablesEmptyDirs${irusCreateTablesEmptyDirs} + --irusDownloadReports${irusDownloadReports} + --irusProcessStats${irusProcessStats} + --irusNumberOfOpendoarsToDownload${irusNumberOfOpendoarsToDownload} + --sarcCreateTablesEmptyDirs${sarcCreateTablesEmptyDirs} + --sarcDownloadReports${sarcDownloadReports} + --sarcProcessStats${sarcProcessStats} + --sarcNumberOfIssnToDownload${sarcNumberOfIssnToDownload} + --finalizeStats${finalizeStats} + --finalTablesVisibleToImpala${finalTablesVisibleToImpala} + --numberOfDownloadThreads${numberOfDownloadThreads} + + + + + + + + From 32bf943979f5e111f0841bdeb7c61a2aa7cbeb1b Mon Sep 17 00:00:00 2001 From: Dimitris Date: Mon, 2 Nov 2020 09:08:25 +0200 Subject: [PATCH 002/149] Changes to download only updates --- .../oa/graph/usagestats/export/ConnectDB.java | 52 +- .../oa/graph/usagestats/export/IrusStats.java | 600 +++++------ .../export/LaReferenciaDownloadLogs.java | 324 +++--- .../usagestats/export/PiwikDownloadLogs.java | 145 +-- .../graph/usagestats/export/PiwikStatsDB.java | 85 +- .../oa/graph/usagestats/export/SarcStats.java | 929 +++++++++--------- .../usagestats/export/UsageStatsExporter.java | 2 +- 7 files changed, 1072 insertions(+), 1065 deletions(-) diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java index ffc7c74cd..29dd5648b 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java @@ -78,20 +78,20 @@ public abstract class ConnectDB { */ ComboPooledDataSource cpds = new ComboPooledDataSource(); cpds.setJdbcUrl(dbHiveUrl); - cpds.setAcquireIncrement(1); - cpds.setMaxPoolSize(100); - cpds.setMinPoolSize(1); - cpds.setInitialPoolSize(1); - cpds.setMaxIdleTime(300); - cpds.setMaxConnectionAge(36000); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); - cpds.setAcquireRetryAttempts(5); - cpds.setAcquireRetryDelay(2000); - cpds.setBreakAfterAcquireFailure(false); + cpds.setAcquireRetryAttempts(5); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); - cpds.setCheckoutTimeout(30000); - cpds.setPreferredTestQuery("SELECT 1"); - cpds.setIdleConnectionTestPeriod(60); + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); return cpds.getConnection(); } @@ -103,23 +103,23 @@ public abstract class ConnectDB { */ ComboPooledDataSource cpds = new ComboPooledDataSource(); cpds.setJdbcUrl(dbImpalaUrl); - cpds.setAcquireIncrement(1); - cpds.setMaxPoolSize(100); - cpds.setMinPoolSize(1); - cpds.setInitialPoolSize(1); - cpds.setMaxIdleTime(300); - cpds.setMaxConnectionAge(36000); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); - cpds.setAcquireRetryAttempts(5); - cpds.setAcquireRetryDelay(2000); - cpds.setBreakAfterAcquireFailure(false); + cpds.setAcquireRetryAttempts(5); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); - cpds.setCheckoutTimeout(30000); - cpds.setPreferredTestQuery("SELECT 1"); - cpds.setIdleConnectionTestPeriod(60); + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); - return cpds.getConnection(); + return cpds.getConnection(); } -} +} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java index 749687ec5..6947381c9 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java @@ -1,4 +1,3 @@ - package eu.dnetlib.oa.graph.usagestats.export; import java.io.*; @@ -28,38 +27,38 @@ import org.slf4j.LoggerFactory; */ public class IrusStats { - private String irusUKURL; + private String irusUKURL; - private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); + private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); - public IrusStats(String irusUKURL) throws Exception { - this.irusUKURL = irusUKURL; - // The following may not be needed - It will be created when JSON tables are created + public IrusStats(String irusUKURL) throws Exception { + this.irusUKURL = irusUKURL; + // The following may not be needed - It will be created when JSON tables are created // createTmpTables(); - } + } - public void reCreateLogDirs() throws Exception { - FileSystem dfs = FileSystem.get(new Configuration()); + public void reCreateLogDirs() throws Exception { + FileSystem dfs = FileSystem.get(new Configuration()); - logger.info("Deleting irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); - dfs.delete(new Path(ExecuteWorkflow.irusUKReportPath), true); + logger.info("Deleting irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); + dfs.delete(new Path(ExecuteWorkflow.irusUKReportPath), true); - logger.info("Creating irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); - dfs.mkdirs(new Path(ExecuteWorkflow.irusUKReportPath)); - } + logger.info("Creating irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); + dfs.mkdirs(new Path(ExecuteWorkflow.irusUKReportPath)); + } - public void createTables() throws Exception { - try { - logger.info("Creating sushilog"); - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog(source STRING, " + - "repository STRING, rid STRING, date STRING, metric_type STRING, count INT) clustered by (source, " + - "repository, rid, date, metric_type) into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTableSushiLog); - logger.info("Created sushilog"); + public void createTables() throws Exception { + try { + logger.info("Creating sushilog"); + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog(source STRING, " + + "repository STRING, rid STRING, date STRING, metric_type STRING, count INT) clustered by (source, " + + "repository, rid, date, metric_type) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableSushiLog); + logger.info("Created sushilog"); - // To see how to apply to the ignore duplicate rules and indexes + // To see how to apply to the ignore duplicate rules and indexes // stmt.executeUpdate(sqlCreateTableSushiLog); // String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " // + " ON INSERT TO sushilog " @@ -70,15 +69,14 @@ public class IrusStats { // stmt.executeUpdate(sqlcreateRuleSushiLog); // String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; // stmt.executeUpdate(createSushiIndex); - - stmt.close(); - ConnectDB.getHiveConnection().close(); - logger.info("Sushi Tables Created"); - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - } - } + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } // // The following may not be needed - It will be created when JSON tables are created // private void createTmpTables() throws Exception { @@ -107,311 +105,315 @@ public class IrusStats { // throw new Exception("Failed to create tables: " + e.toString(), e); // } // } + public void processIrusStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); - public void processIrusStats() throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); - logger.info("Adding JSON Serde jar"); - stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); - logger.info("Added JSON Serde jar"); + logger.info("Dropping sushilogtmp_json table"); + String dropSushilogtmpJson = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sushilogtmp_json"; + stmt.executeUpdate(dropSushilogtmpJson); + logger.info("Dropped sushilogtmp_json table"); - logger.info("Dropping sushilogtmp_json table"); - String dropSushilogtmpJson = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".sushilogtmp_json"; - stmt.executeUpdate(dropSushilogtmpJson); - logger.info("Dropped sushilogtmp_json table"); + logger.info("Creating irus_sushilogtmp_json table"); + String createSushilogtmpJson = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json(\n" + + " `ItemIdentifier` ARRAY<\n" + + " struct<\n" + + " Type: STRING,\n" + + " Value: STRING\n" + + " >\n" + + " >,\n" + + " `ItemPerformance` ARRAY<\n" + + " struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.irusUKReportPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(createSushilogtmpJson); + logger.info("Created irus_sushilogtmp_json table"); - logger.info("Creating irus_sushilogtmp_json table"); - String createSushilogtmpJson = "CREATE EXTERNAL TABLE IF NOT EXISTS " + - ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json(\n" + - " `ItemIdentifier` ARRAY<\n" + - " struct<\n" + - " Type: STRING,\n" + - " Value: STRING\n" + - " >\n" + - " >,\n" + - " `ItemPerformance` ARRAY<\n" + - " struct<\n" + - " `Period`: struct<\n" + - " `Begin`: STRING,\n" + - " `End`: STRING\n" + - " >,\n" + - " `Instance`: struct<\n" + - " `Count`: STRING,\n" + - " `MetricType`: STRING\n" + - " >\n" + - " >\n" + - " >\n" + - ")\n" + - "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + - "LOCATION '" + ExecuteWorkflow.irusUKReportPath + "'\n" + - "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(createSushilogtmpJson); - logger.info("Created irus_sushilogtmp_json table"); + logger.info("Dropping irus_sushilogtmp table"); + String dropSushilogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp"; + stmt.executeUpdate(dropSushilogtmp); + logger.info("Dropped irus_sushilogtmp table"); - logger.info("Dropping irus_sushilogtmp table"); - String dropSushilogtmp = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".irus_sushilogtmp"; - stmt.executeUpdate(dropSushilogtmp); - logger.info("Dropped irus_sushilogtmp table"); + logger.info("Creating irus_sushilogtmp table"); + String createSushilogtmp = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp(source STRING, repository STRING, " + + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " + + "tblproperties('transactional'='true')"; + stmt.executeUpdate(createSushilogtmp); + logger.info("Created irus_sushilogtmp table"); - logger.info("Creating irus_sushilogtmp table"); - String createSushilogtmp = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() - + ".irus_sushilogtmp(source STRING, repository STRING, " + - "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " - + - "tblproperties('transactional'='true')"; - stmt.executeUpdate(createSushilogtmp); - logger.info("Created irus_sushilogtmp table"); + logger.info("Inserting to irus_sushilogtmp table"); + String insertSushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp " + + "SELECT 'IRUS-UK', CONCAT('opendoar____::', split(split(INPUT__FILE__NAME,'IrusIRReport_')[1],'_')[0]), " + + "`ItemIdent`.`Value`, `ItemPerf`.`Period`.`Begin`, " + + "`ItemPerf`.`Instance`.`MetricType`, `ItemPerf`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json " + + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + + "LATERAL VIEW posexplode(ItemPerformance) ItemPerformanceTable AS seqp, ItemPerf " + + "WHERE `ItemIdent`.`Type`= 'OAI'"; + stmt.executeUpdate(insertSushilogtmp); + logger.info("Inserted to irus_sushilogtmp table"); - logger.info("Inserting to irus_sushilogtmp table"); - String insertSushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp " + - "SELECT 'IRUS-UK', CONCAT('opendoar____::', split(split(INPUT__FILE__NAME,'IrusIRReport_')[1],'_')[0]), " + - "`ItemIdent`.`Value`, `ItemPerf`.`Period`.`Begin`, " + - "`ItemPerf`.`Instance`.`MetricType`, `ItemPerf`.`Instance`.`Count` " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json " + - "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + - "LATERAL VIEW posexplode(ItemPerformance) ItemPerformanceTable AS seqp, ItemPerf " + - "WHERE `ItemIdent`.`Type`= 'OAI'"; - stmt.executeUpdate(insertSushilogtmp); - logger.info("Inserted to irus_sushilogtmp table"); + logger.info("Creating downloads_stats table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmt.executeUpdate(createDownloadsStats); + logger.info("Created downloads_stats table"); - logger.info("Creating downloads_stats table"); - String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats " + - "(`source` string, " + - "`repository_id` string, " + - "`result_id` string, " + - "`date` string, " + - "`count` bigint, " + - "`openaire` bigint)"; - stmt.executeUpdate(createDownloadsStats); - logger.info("Created downloads_stats table"); + logger.info("Inserting into downloads_stats"); + String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(YEAR(date), '/', LPAD(MONTH(date), 2, '0')) as date, s.count, '0' " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE s.repository=d.oid AND s.rid=ro.oid AND metric_type='ft_total' AND s.source='IRUS-UK'"; + stmt.executeUpdate(insertDStats); + logger.info("Inserted into downloads_stats"); - logger.info("Inserting into downloads_stats"); - String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + - "SELECT s.source, d.id AS repository_id, " + - "ro.id as result_id, CONCAT(YEAR(date), '/', LPAD(MONTH(date), 2, '0')) as date, s.count, '0' " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp s, " + - ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + - ConnectDB.getStatsDBSchema() + ".result_oids ro " + - "WHERE s.repository=d.oid AND s.rid=ro.oid AND metric_type='ft_total' AND s.source='IRUS-UK'"; - stmt.executeUpdate(insertDStats); - logger.info("Inserted into downloads_stats"); + logger.info("Creating sushilog table"); + String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog " + + "(`source` string, " + + "`repository_id` string, " + + "`rid` string, " + + "`date` string, " + + "`metric_type` string, " + + "`count` int)"; + stmt.executeUpdate(createSushilog); + logger.info("Created sushilog table"); - logger.info("Creating sushilog table"); - String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog " + - "(`source` string, " + - "`repository_id` string, " + - "`rid` string, " + - "`date` string, " + - "`metric_type` string, " + - "`count` int)"; - stmt.executeUpdate(createSushilog); - logger.info("Created sushilog table"); + logger.info("Inserting to sushilog table"); + String insertToShushilog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sushilog SELECT * FROM " + + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp"; + stmt.executeUpdate(insertToShushilog); + logger.info("Inserted to sushilog table"); - logger.info("Inserting to sushilog table"); - String insertToShushilog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sushilog SELECT * FROM " + - ConnectDB.getUsageStatsDBSchema() - + ".irus_sushilogtmp"; - stmt.executeUpdate(insertToShushilog); - logger.info("Inserted to sushilog table"); + ConnectDB.getHiveConnection().close(); + } - ConnectDB.getHiveConnection().close(); - } + public void getIrusRRReport(String irusUKReportPath) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("YYYY-MM"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getIrusRRReport) Starting period for log download: " + sdf.format(start.getTime())); - public void getIrusRRReport(String irusUKReportPath) throws Exception { - SimpleDateFormat sdf = new SimpleDateFormat("YYYY-MM"); - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("(getIrusRRReport) Starting period for log download: " + sdf.format(start.getTime())); + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("(getIrusRRReport) Ending period for log download: " + sdf.format(end.getTime())); - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("(getIrusRRReport) Ending period for log download: " + sdf.format(end.getTime())); + String reportUrl = irusUKURL + "GetReport/?Report=RR1&Release=4&RequestorID=OpenAIRE&BeginDate=" + + sdf.format(start.getTime()) + "&EndDate=" + sdf.format(end.getTime()) + + "&RepositoryIdentifier=&ItemDataType=&NewJiscBand=&Granularity=Monthly&Callback="; - String reportUrl = irusUKURL + "GetReport/?Report=RR1&Release=4&RequestorID=OpenAIRE&BeginDate=" + - sdf.format(start.getTime()) + "&EndDate=" + sdf.format(end.getTime()) + - "&RepositoryIdentifier=&ItemDataType=&NewJiscBand=&Granularity=Monthly&Callback="; + logger.info("(getIrusRRReport) Getting report: " + reportUrl); - logger.info("(getIrusRRReport) Getting report: " + reportUrl); + String text = getJson(reportUrl, "", ""); - String text = getJson(reportUrl, "", ""); + List opendoarsToVisit = new ArrayList(); + JSONParser parser = new JSONParser(); + JSONObject jsonObject = (JSONObject) parser.parse(text); + jsonObject = (JSONObject) jsonObject.get("ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Customer"); + JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); + int i = 0; + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + JSONArray itemIdentifier = (JSONArray) jsonObjectRow.get("ItemIdentifier"); + for (Object identifier : itemIdentifier) { + JSONObject opendoar = (JSONObject) identifier; + if (opendoar.get("Type").toString().equals("OpenDOAR")) { + i++; + opendoarsToVisit.add(opendoar.get("Value").toString()); + break; + } + } + // break; + } - List opendoarsToVisit = new ArrayList(); - JSONParser parser = new JSONParser(); - JSONObject jsonObject = (JSONObject) parser.parse(text); - jsonObject = (JSONObject) jsonObject.get("ReportResponse"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Customer"); - JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); - int i = 0; - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - JSONArray itemIdentifier = (JSONArray) jsonObjectRow.get("ItemIdentifier"); - for (Object identifier : itemIdentifier) { - JSONObject opendoar = (JSONObject) identifier; - if (opendoar.get("Type").toString().equals("OpenDOAR")) { - i++; - opendoarsToVisit.add(opendoar.get("Value").toString()); - break; - } - } - // break; - } + logger.info("(getIrusRRReport) Found the following opendoars for download: " + opendoarsToVisit); - logger.info("(getIrusRRReport) Found the following opendoars for download: " + opendoarsToVisit); + if (ExecuteWorkflow.irusNumberOfOpendoarsToDownload > 0 + && ExecuteWorkflow.irusNumberOfOpendoarsToDownload <= opendoarsToVisit.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.irusNumberOfOpendoarsToDownload); + opendoarsToVisit = opendoarsToVisit.subList(0, ExecuteWorkflow.irusNumberOfOpendoarsToDownload); + } - if (ExecuteWorkflow.irusNumberOfOpendoarsToDownload > 0 && - ExecuteWorkflow.irusNumberOfOpendoarsToDownload <= opendoarsToVisit.size()) { - logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.irusNumberOfOpendoarsToDownload); - opendoarsToVisit = opendoarsToVisit.subList(0, ExecuteWorkflow.irusNumberOfOpendoarsToDownload); - } + logger.info("(getIrusRRReport) Downloading the followins opendoars: " + opendoarsToVisit); - logger.info("(getIrusRRReport) Downloading the followins opendoars: " + opendoarsToVisit); + for (String opendoar : opendoarsToVisit) { + logger.info("Now working on openDoar: " + opendoar); + this.getIrusIRReport(opendoar, irusUKReportPath); + } - for (String opendoar : opendoarsToVisit) { - logger.info("Now working on openDoar: " + opendoar); - this.getIrusIRReport(opendoar, irusUKReportPath); - } + logger.info("(getIrusRRReport) Finished with report: " + reportUrl); + } - logger.info("(getIrusRRReport) Finished with report: " + reportUrl); - } + private void getIrusIRReport(String opendoar, String irusUKReportPath) throws Exception { - private void getIrusIRReport(String opendoar, String irusUKReportPath) throws Exception { + logger.info("(getIrusIRReport) Getting report(s) with opendoar: " + opendoar); - logger.info("(getIrusIRReport) Getting report(s) with opendoar: " + opendoar); + ConnectDB.getHiveConnection().setAutoCommit(false); - ConnectDB.getHiveConnection().setAutoCommit(false); + SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); - SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getIrusIRReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("(getIrusIRReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("(getIrusIRReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("(getIrusIRReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); + st.setString(1, "opendoar____::" + opendoar); + ResultSet rs_date = st.executeQuery(); + Date dateMax = null; + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); + int batch_size = 0; - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - PreparedStatement st = ConnectDB - .getHiveConnection() - .prepareStatement( - "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); - st.setString(1, "opendoar____::" + opendoar); - ResultSet rs_date = st.executeQuery(); - while (rs_date.next()) { - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - } - } - rs_date.close(); - int batch_size = 0; + if (dateMax != null && start.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + opendoar); + } else { + while (start.before(end)) { + logger.info("date: " + simpleDateFormat.format(start.getTime())); + String reportUrl = this.irusUKURL + "GetReport/?Report=IR1&Release=4&RequestorID=OpenAIRE&BeginDate=" + + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()) + + "&RepositoryIdentifier=opendoar%3A" + opendoar + + "&ItemIdentifier=&ItemDataType=&hasDOI=&Granularity=Monthly&Callback="; + start.add(Calendar.MONTH, 1); - while (start.before(end)) { - // log.info("date: " + simpleDateFormat.format(start.getTime())); - String reportUrl = this.irusUKURL + "GetReport/?Report=IR1&Release=4&RequestorID=OpenAIRE&BeginDate=" - + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()) - + "&RepositoryIdentifier=opendoar%3A" + opendoar - + "&ItemIdentifier=&ItemDataType=&hasDOI=&Granularity=Monthly&Callback="; - start.add(Calendar.MONTH, 1); + logger.info("Downloading file: " + reportUrl); + String text = getJson(reportUrl, "", ""); + if (text == null) { + continue; + } - logger.info("Downloading file: " + reportUrl); - String text = getJson(reportUrl, "", ""); - if (text == null) { - continue; - } + FileSystem fs = FileSystem.get(new Configuration()); + String filePath = irusUKReportPath + "/" + "IrusIRReport_" + + opendoar + "_" + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePath); + FSDataOutputStream fin = fs.create(new Path(filePath), true); - FileSystem fs = FileSystem.get(new Configuration()); - String filePath = irusUKReportPath + "/" + "IrusIRReport_" + - opendoar + "_" + simpleDateFormat.format(start.getTime()) + ".json"; - logger.info("Storing to file: " + filePath); - FSDataOutputStream fin = fs.create(new Path(filePath), true); + JSONParser parser = new JSONParser(); + JSONObject jsonObject = (JSONObject) parser.parse(text); + jsonObject = (JSONObject) jsonObject.get("ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Customer"); + JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); + if (jsonArray == null) { + continue; + } + String oai = ""; + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + fin.write(jsonObjectRow.toJSONString().getBytes()); + fin.writeChar('\n'); + } - JSONParser parser = new JSONParser(); - JSONObject jsonObject = (JSONObject) parser.parse(text); - jsonObject = (JSONObject) jsonObject.get("ReportResponse"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Customer"); - JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); - if (jsonArray == null) { - continue; - } - String oai = ""; - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - fin.write(jsonObjectRow.toJSONString().getBytes()); - fin.writeChar('\n'); - } + fin.close(); + } - fin.close(); - } + } + //ConnectDB.getHiveConnection().close(); - ConnectDB.getHiveConnection().close(); + logger.info("(getIrusIRReport) Finished downloading report(s) with opendoar: " + opendoar); + } - logger.info("(getIrusIRReport) Finished downloading report(s) with opendoar: " + opendoar); - } + private String getJson(String url) throws Exception { + try { + System.out.println("===> Connecting to: " + url); + URL website = new URL(url); + System.out.println("Connection url -----> " + url); + URLConnection connection = website.openConnection(); - private String getJson(String url) throws Exception { - try { - System.out.println("===> Connecting to: " + url); - URL website = new URL(url); - System.out.println("Connection url -----> " + url); - URLConnection connection = website.openConnection(); - - // connection.setRequestProperty ("Authorization", "Basic "+encoded); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); // response.append("\n"); - } - } + } + } - System.out.println("response ====> " + response.toString()); + System.out.println("response ====> " + response.toString()); - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL: " + e); - System.out.println("Failed to get URL: " + e); - throw new Exception("Failed to get URL: " + e.toString(), e); - } - } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + e); + System.out.println("Failed to get URL: " + e); + throw new Exception("Failed to get URL: " + e.toString(), e); + } + } - private String getJson(String url, String username, String password) throws Exception { - // String cred=username+":"+password; - // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); - try { - URL website = new URL(url); - URLConnection connection = website.openConnection(); - // connection.setRequestProperty ("Authorization", "Basic "+encoded); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); - response.append("\n"); - } - } - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL", e); - return null; - } - } + private String getJson(String url, String username, String password) throws Exception { + // String cred=username+":"+password; + // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + response.append("\n"); + } + } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL", e); + return null; + } + } } diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java index 0e0e013cf..7a61b1f46 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java @@ -1,4 +1,3 @@ - package eu.dnetlib.oa.graph.usagestats.export; import java.io.*; @@ -28,49 +27,49 @@ import org.slf4j.LoggerFactory; */ public class LaReferenciaDownloadLogs { - private final String piwikUrl; - private Date startDate; - private final String tokenAuth; + private final String piwikUrl; + private Date startDate; + private final String tokenAuth; - /* + /* * The Piwik's API method - */ - private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; - private final String format = "&format=json"; - private final String ApimethodGetAllSites = "?module=API&method=SitesManager.getSitesWithViewAccess"; + */ + private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; + private final String format = "&format=json"; + private final String ApimethodGetAllSites = "?module=API&method=SitesManager.getSitesWithViewAccess"; - private static final Logger logger = LoggerFactory.getLogger(LaReferenciaDownloadLogs.class); + private static final Logger logger = LoggerFactory.getLogger(LaReferenciaDownloadLogs.class); - public LaReferenciaDownloadLogs(String piwikUrl, String tokenAuth) throws Exception { - this.piwikUrl = piwikUrl; - this.tokenAuth = tokenAuth; - this.createTables(); + public LaReferenciaDownloadLogs(String piwikUrl, String tokenAuth) throws Exception { + this.piwikUrl = piwikUrl; + this.tokenAuth = tokenAuth; + this.createTables(); // this.createTmpTables(); - } + } - public void reCreateLogDirs() throws IllegalArgumentException, IOException { - FileSystem dfs = FileSystem.get(new Configuration()); + public void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); - logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); - dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); + logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); - logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); - dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); - } + logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); + } - private void createTables() throws Exception { - try { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); + private void createTables() throws Exception { + try { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); - logger.info("Creating LaReferencia tables"); - String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + - ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + - "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + - "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + - "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + - "stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTableLareferenciaLog); - logger.info("Created LaReferencia tables"); + logger.info("Creating LaReferencia tables"); + String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableLareferenciaLog); + logger.info("Created LaReferencia tables"); // String sqlcreateRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " // + " ON INSERT TO lareferencialog " // + " WHERE (EXISTS ( SELECT lareferencialog.matomoid, lareferencialog.source, lareferencialog.id_visit," @@ -81,16 +80,16 @@ public class LaReferenciaDownloadLogs { // stmt.executeUpdate(sqlcreateRuleLaReferenciaLog); // stmt.executeUpdate(sqlCreateRuleIndexLaReferenciaLog); - stmt.close(); - ConnectDB.getHiveConnection().close(); - logger.info("Lareferencia Tables Created"); + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Lareferencia Tables Created"); - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - // System.exit(0); - } - } + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + // System.exit(0); + } + } // private void createTmpTables() throws Exception { // @@ -115,147 +114,152 @@ public class LaReferenciaDownloadLogs { // // System.exit(0); // } // } + private String getPiwikLogUrl() { + return piwikUrl + "/"; + } - private String getPiwikLogUrl() { - return piwikUrl + "/"; - } + private String getJson(String url) throws Exception { + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); - private String getJson(String url) throws Exception { - try { - URL website = new URL(url); - URLConnection connection = website.openConnection(); - - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); // response.append("\n"); - } - } + } + } - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL: " + e); - throw new Exception("Failed to get URL: " + e.toString(), e); - } - } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + e); + throw new Exception("Failed to get URL: " + e.toString(), e); + } + } - public void GetLaReferenciaRepos(String repoLogsPath) throws Exception { + public void GetLaReferenciaRepos(String repoLogsPath) throws Exception { - String baseApiUrl = getPiwikLogUrl() + ApimethodGetAllSites + format + "&token_auth=" + this.tokenAuth; - String content = ""; + String baseApiUrl = getPiwikLogUrl() + ApimethodGetAllSites + format + "&token_auth=" + this.tokenAuth; + String content = ""; - List siteIdsToVisit = new ArrayList(); + List siteIdsToVisit = new ArrayList(); - // Getting all the siteIds in a list for logging reasons & limiting the list - // to the max number of siteIds - content = getJson(baseApiUrl); - JSONParser parser = new JSONParser(); - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - siteIdsToVisit.add(Integer.parseInt(jsonObjectRow.get("idsite").toString())); - } - logger.info("Found the following siteIds for download: " + siteIdsToVisit); + // Getting all the siteIds in a list for logging reasons & limiting the list + // to the max number of siteIds + content = getJson(baseApiUrl); + JSONParser parser = new JSONParser(); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + siteIdsToVisit.add(Integer.parseInt(jsonObjectRow.get("idsite").toString())); + } + logger.info("Found the following siteIds for download: " + siteIdsToVisit); - if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 && - ExecuteWorkflow.numberOfPiwikIdsToDownload <= siteIdsToVisit.size()) { - logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); - siteIdsToVisit = siteIdsToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); - } + if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 + && ExecuteWorkflow.numberOfPiwikIdsToDownload <= siteIdsToVisit.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); + siteIdsToVisit = siteIdsToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); + } - logger.info("Downloading from repos with the followins siteIds: " + siteIdsToVisit); + logger.info("Downloading from repos with the followins siteIds: " + siteIdsToVisit); - for (int siteId : siteIdsToVisit) { - logger.info("Now working on piwikId: " + siteId); - this.GetLaReFerenciaLogs(repoLogsPath, siteId); - } - } + for (int siteId : siteIdsToVisit) { + logger.info("Now working on LaReferencia MatomoId: " + siteId); + this.GetLaReFerenciaLogs(repoLogsPath, siteId); + } + } - public void GetLaReFerenciaLogs(String repoLogsPath, - int laReferencialMatomoID) throws Exception { + public void GetLaReFerenciaLogs(String repoLogsPath, + int laReferencialMatomoID) throws Exception { - logger.info("Downloading logs for LaReferencia repoid " + laReferencialMatomoID); + logger.info("Downloading logs for LaReferencia repoid " + laReferencialMatomoID); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("Starting period for log download: " + sdf.format(start.getTime())); + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("Starting period for log download: " + sdf.format(start.getTime())); - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("Ending period for log download: " + sdf.format(end.getTime())); + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("Ending period for log download: " + sdf.format(end.getTime())); - PreparedStatement st = ConnectDB - .getHiveConnection() - .prepareStatement( - "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + - ".lareferencialog WHERE matomoid=? GROUP BY timestamp HAVING max(timestamp) is not null"); - st.setInt(1, laReferencialMatomoID); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialog WHERE matomoid=?"); + st.setInt(1, laReferencialMatomoID); + Date dateMax = null; - ResultSet rs_date = st.executeQuery(); - while (rs_date.next()) { - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - } - } - rs_date.close(); + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); - for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { - Date date = currDay.getTime(); - logger - .info( - "Downloading logs for LaReferencia repoid " + laReferencialMatomoID + " and for " - + sdf.format(date)); + for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { + Date date = currDay.getTime(); + if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding Matomo logs for " + laReferencialMatomoID); + } else { + logger + .info( + "Downloading logs for LaReferencia repoid " + laReferencialMatomoID + " and for " + + sdf.format(date)); - String period = "&period=day&date=" + sdf.format(date); - String outFolder = ""; - outFolder = repoLogsPath; + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + outFolder = repoLogsPath; - FileSystem fs = FileSystem.get(new Configuration()); - FSDataOutputStream fin = fs - .create( - new Path(outFolder + "/" + laReferencialMatomoID + "_LaRefPiwiklog" + sdf.format((date)) + ".json"), - true); + FileSystem fs = FileSystem.get(new Configuration()); + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + laReferencialMatomoID + "_LaRefPiwiklog" + sdf.format((date)) + ".json"), + true); - String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + laReferencialMatomoID + period + format - + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; - String content = ""; - int i = 0; + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + laReferencialMatomoID + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + int i = 0; - JSONParser parser = new JSONParser(); - do { - String apiUrl = baseApiUrl; + JSONParser parser = new JSONParser(); + do { + String apiUrl = baseApiUrl; - if (i > 0) { - apiUrl += "&filter_offset=" + (i * 1000); - } + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } - content = getJson(apiUrl); - if (content.length() == 0 || content.equals("[]")) - break; + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRaw = (JSONObject) aJsonArray; - fin.write(jsonObjectRaw.toJSONString().getBytes()); - fin.writeChar('\n'); - } + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + fin.write(jsonObjectRaw.toJSONString().getBytes()); + fin.writeChar('\n'); + } - logger - .info( - "Downloaded part " + i + " of logs for LaReferencia repoid " + laReferencialMatomoID - + " and for " - + sdf.format(date)); - i++; - } while (true); - fin.close(); - - } - } + logger + .info( + "Downloaded part " + i + " of logs for LaReferencia repoid " + laReferencialMatomoID + + " and for " + + sdf.format(date)); + i++; + } while (true); + fin.close(); + } + } + } } diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java index 65816518f..7a64e48d2 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java @@ -204,6 +204,9 @@ public class PiwikDownloadLogs { logger.info("Downloading from repos with the followins piwikIds: " + piwikIdToVisit); + + // ExecutorService executor = Executors.newFixedThreadPool(ExecuteWorkflow.numberOfDownloadThreads); + for (int siteId : piwikIdToVisit) { // Setting the starting period Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); logger.info("Starting period for log download: " + sdf.format(start.getTime())); @@ -214,9 +217,6 @@ public class PiwikDownloadLogs { end.add(Calendar.DAY_OF_MONTH, -1); logger.info("Ending period for log download: " + sdf.format(end.getTime())); - //ExecutorService executor = Executors.newFixedThreadPool(ExecuteWorkflow.numberOfDownloadThreads); - for (int siteId : piwikIdToVisit) { - logger.info("Now working on piwikId: " + siteId); PreparedStatement st = ConnectDB.DB_HIVE_CONNECTION @@ -224,7 +224,7 @@ public class PiwikDownloadLogs { "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklog WHERE source=?"); st.setInt(1, siteId); - + Date dateMax=null; ResultSet rs_date = st.executeQuery(); while (rs_date.next()) { logger.info("Found max date: " + rs_date.getString(1) + " for repository " + siteId); @@ -232,85 +232,92 @@ public class PiwikDownloadLogs { if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") && !rs_date.getString(1).equals("")) { start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); } - } + } rs_date.close(); for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { - //logger.info("Date used " + currDay.toString()); - //Runnable worker = new WorkerThread(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); - //executor.execute(worker);// calling execute method of ExecutorService - GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + // logger.info("Date used " + currDay.toString()); + // Runnable worker = new WorkerThread(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + // executor.execute(worker);// calling execute method of ExecutorService + logger.info("Date used " + currDay.getTime().toString()); + + if(dateMax!=null && currDay.getTime().compareTo(dateMax)<=0) + logger.info("Date found in logs "+dateMax+ " and not downloanding Matomo logs for "+siteId); + else + GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + } } - //executor.shutdown(); - //while (!executor.isTerminated()) { - //} - //System.out.println("Finished all threads"); + // executor.shutdown(); + // while (!executor.isTerminated()) { + // } + // System.out.println("Finished all threads"); } - - public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, - String portalMatomoID) throws Exception { - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - Date date = currDay.getTime(); - logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - String period = "&period=day&date=" + sdf.format(date); - String outFolder = ""; - if (siteId == Integer.parseInt(portalMatomoID)) { - outFolder = portalLogPath; - } else { - outFolder = repoLogsPath; + Date date = currDay.getTime(); + logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + if (siteId == Integer.parseInt(portalMatomoID)) { + outFolder = portalLogPath; + } else { + outFolder = repoLogsPath; + } + + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + + int i = 0; + + JSONParser parser = new JSONParser(); + StringBuffer totalContent = new StringBuffer(); + FileSystem fs = FileSystem.get(new Configuration()); + + do { + int writtenBytes = 0; + String apiUrl = baseApiUrl; + + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); } - String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format - + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; - String content = ""; + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) + break; - int i = 0; + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"), + true); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); - JSONParser parser = new JSONParser(); - StringBuffer totalContent = new StringBuffer(); - FileSystem fs = FileSystem.get(new Configuration()); + writtenBytes += jsonObjectRawBytes.length + 1; + } - do { - int writtenBytes = 0; - String apiUrl = baseApiUrl; + fin.close(); + System.out + .println( + Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes + + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"); - if (i > 0) { - apiUrl += "&filter_offset=" + (i * 1000); - } + i++; + } while (true); - content = getJson(apiUrl); - if (content.length() == 0 || content.equals("[]")) - break; - - FSDataOutputStream fin = fs - .create( - new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"), - true); - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRaw = (JSONObject) aJsonArray; - byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); - fin.write(jsonObjectRawBytes); - fin.writeChar('\n'); - - writtenBytes += jsonObjectRawBytes.length + 1; - } - - fin.close(); - System.out - .println( - Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes - + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"); - - i++; - } while (true); - - fs.close(); - } + fs.close(); + } } diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java index 6e015acf4..6625c381b 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java @@ -199,14 +199,14 @@ public class PiwikStatsDB { cleanOAI(); logger.info("Cleaning oai done"); - logger.info("Processing portal logs"); + logger.info("Processing portal logs"); processPortalLog(); logger.info("Portal logs process done"); logger.info("Processing portal usagestats"); portalStats(); logger.info("Portal usagestats process done"); - + logger.info("ViewsStats processing starts"); viewsStats(); logger.info("ViewsStats processing ends"); @@ -215,8 +215,6 @@ public class PiwikStatsDB { downloadsStats(); logger.info("DownloadsStats processing starts"); - - logger.info("Updating Production Tables"); updateProdTables(); logger.info("Updated Production Tables"); @@ -313,7 +311,7 @@ public class PiwikStatsDB { "SELECT DISTINCT p1.source, p1.id_visit, p1.action, p1.entity_id, p1.timestamp \n" + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p1, " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p2\n" + - "WHERE p1.source!='5' AND p1.source=p2.source AND p1.id_visit=p2.id_visit AND p1.entity_id=p2.entity_id \n" + "WHERE p1.source=p2.source AND p1.id_visit=p2.id_visit AND p1.entity_id=p2.entity_id \n" + "AND p1.action=p2.action AND p1.action='download' AND p1.timestamp!=p2.timestamp \n" + "AND p1.timestamp\n" + - " >,\n" + - " `ItemPerformance` struct<\n" + - " `Period`: struct<\n" + - " `Begin`: STRING,\n" + - " `End`: STRING\n" + - " >,\n" + - " `Instance`: struct<\n" + - " `Count`: STRING,\n" + - " `MetricType`: STRING\n" + - " >\n" + - " >\n" + - ")" + - "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + - "LOCATION '" + sarcsReportPathArray + "/'\n" + - "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(create_sarc_sushilogtmp_json_array); - logger.info("Created sarc_sushilogtmp_json_array table"); + logger.info("Creating sarc_sushilogtmp_json_array table"); + String create_sarc_sushilogtmp_json_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array(\n" + + " `ItemIdentifier` ARRAY<\n" + + " struct<\n" + + " `Type`: STRING,\n" + + " `Value`: STRING\n" + + " >\n" + + " >,\n" + + " `ItemPerformance` struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >\n" + + ")" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + sarcsReportPathArray + "/'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_sarc_sushilogtmp_json_array); + logger.info("Created sarc_sushilogtmp_json_array table"); - logger.info("Dropping sarc_sushilogtmp_json_non_array table"); - String drop_sarc_sushilogtmp_json_non_array = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".sarc_sushilogtmp_json_non_array"; - stmt.executeUpdate(drop_sarc_sushilogtmp_json_non_array); - logger.info("Dropped sarc_sushilogtmp_json_non_array table"); + logger.info("Dropping sarc_sushilogtmp_json_non_array table"); + String drop_sarc_sushilogtmp_json_non_array = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(drop_sarc_sushilogtmp_json_non_array); + logger.info("Dropped sarc_sushilogtmp_json_non_array table"); - logger.info("Creating sarc_sushilogtmp_json_non_array table"); - String create_sarc_sushilogtmp_json_non_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " + - ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array (\n" + - " `ItemIdentifier` struct<\n" + - " `Type`: STRING,\n" + - " `Value`: STRING\n" + - " >,\n" + - " `ItemPerformance` struct<\n" + - " `Period`: struct<\n" + - " `Begin`: STRING,\n" + - " `End`: STRING\n" + - " >,\n" + - " `Instance`: struct<\n" + - " `Count`: STRING,\n" + - " `MetricType`: STRING\n" + - " >\n" + - " >" + - ")" + - "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + - "LOCATION '" + sarcsReportPathNonArray + "/'\n" + - "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(create_sarc_sushilogtmp_json_non_array); - logger.info("Created sarc_sushilogtmp_json_non_array table"); + logger.info("Creating sarc_sushilogtmp_json_non_array table"); + String create_sarc_sushilogtmp_json_non_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array (\n" + + " `ItemIdentifier` struct<\n" + + " `Type`: STRING,\n" + + " `Value`: STRING\n" + + " >,\n" + + " `ItemPerformance` struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >" + + ")" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + sarcsReportPathNonArray + "/'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_sarc_sushilogtmp_json_non_array); + logger.info("Created sarc_sushilogtmp_json_non_array table"); - logger.info("Creating sarc_sushilogtmp table"); - String create_sarc_sushilogtmp = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp(source STRING, repository STRING, " + - "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " - + - "tblproperties('transactional'='true')"; - stmt.executeUpdate(create_sarc_sushilogtmp); - logger.info("Created sarc_sushilogtmp table"); + logger.info("Creating sarc_sushilogtmp table"); + String create_sarc_sushilogtmp = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp(source STRING, repository STRING, " + + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " + + "tblproperties('transactional'='true')"; + stmt.executeUpdate(create_sarc_sushilogtmp); + logger.info("Created sarc_sushilogtmp table"); - logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); - String insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + - "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + - " `ItemIdent`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + - "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array " + - "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + - "WHERE `ItemIdent`.`Type`='DOI'"; - stmt.executeUpdate(insert_sarc_sushilogtmp); - logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); + logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); + String insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + + " `ItemIdent`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array " + + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + + "WHERE `ItemIdent`.`Type`='DOI'"; + stmt.executeUpdate(insert_sarc_sushilogtmp); + logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); - logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); - insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + - "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + - "`ItemIdentifier`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + - "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array"; - stmt.executeUpdate(insert_sarc_sushilogtmp); - logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); + logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); + insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + + "`ItemIdentifier`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(insert_sarc_sushilogtmp); + logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); - ConnectDB.getHiveConnection().close(); - } + ConnectDB.getHiveConnection().close(); + } - public void getAndProcessSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { + public void getAndProcessSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); - logger.info("Creating sushilog table"); - String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog " + - "(`source` string, " + - "`repository` string, " + - "`rid` string, " + - "`date` string, " + - "`metric_type` string, " + - "`count` int)"; - stmt.executeUpdate(createSushilog); - logger.info("Created sushilog table"); + logger.info("Creating sushilog table"); + String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog " + + "(`source` string, " + + "`repository` string, " + + "`rid` string, " + + "`date` string, " + + "`metric_type` string, " + + "`count` int)"; + stmt.executeUpdate(createSushilog); + logger.info("Created sushilog table"); - logger.info("Dropping sarc_sushilogtmp table"); - String drop_sarc_sushilogtmp = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".sarc_sushilogtmp"; - stmt.executeUpdate(drop_sarc_sushilogtmp); - logger.info("Dropped sarc_sushilogtmp table"); - ConnectDB.getHiveConnection().close(); + logger.info("Dropping sarc_sushilogtmp table"); + String drop_sarc_sushilogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp"; + stmt.executeUpdate(drop_sarc_sushilogtmp); + logger.info("Dropped sarc_sushilogtmp table"); + ConnectDB.getHiveConnection().close(); - List issnAndUrls = new ArrayList(); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/motricidade/sushiLite/v1_7/", "1646-107X" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/antropologicas/sushiLite/v1_7/", "0873-819X" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/interaccoes/sushiLite/v1_7/", "1646-2335" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/cct/sushiLite/v1_7/", "2182-3030" - }); - issnAndUrls.add(new String[] { - "https://actapediatrica.spp.pt/sushiLite/v1_7/", "0873-9781" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/sociologiapp/sushiLite/v1_7/", "0873-6529" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/finisterra/sushiLite/v1_7/", "0430-5027" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/sisyphus/sushiLite/v1_7/", "2182-8474" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/anestesiologia/sushiLite/v1_7/", "0871-6099" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/rpe/sushiLite/v1_7/", "0871-9187" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/psilogos/sushiLite/v1_7/", "1646-091X" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/juridica/sushiLite/v1_7/", "2183-5799" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/ecr/sushiLite/v1_7/", "1647-2098" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/nascercrescer/sushiLite/v1_7/", "0872-0754" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/cea/sushiLite/v1_7/", "1645-3794" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/proelium/sushiLite/v1_7/", "1645-8826" - }); - issnAndUrls.add(new String[] { - "https://revistas.rcaap.pt/millenium/sushiLite/v1_7/", "0873-3015" - }); + List issnAndUrls = new ArrayList(); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/motricidade/sushiLite/v1_7/", "1646-107X" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/antropologicas/sushiLite/v1_7/", "0873-819X" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/interaccoes/sushiLite/v1_7/", "1646-2335" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/cct/sushiLite/v1_7/", "2182-3030" + }); + issnAndUrls.add(new String[]{ + "https://actapediatrica.spp.pt/sushiLite/v1_7/", "0873-9781" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/sociologiapp/sushiLite/v1_7/", "0873-6529" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/finisterra/sushiLite/v1_7/", "0430-5027" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/sisyphus/sushiLite/v1_7/", "2182-8474" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/anestesiologia/sushiLite/v1_7/", "0871-6099" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/rpe/sushiLite/v1_7/", "0871-9187" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/psilogos/sushiLite/v1_7/", "1646-091X" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/juridica/sushiLite/v1_7/", "2183-5799" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/ecr/sushiLite/v1_7/", "1647-2098" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/nascercrescer/sushiLite/v1_7/", "0872-0754" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/cea/sushiLite/v1_7/", "1645-3794" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/proelium/sushiLite/v1_7/", "1645-8826" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/millenium/sushiLite/v1_7/", "0873-3015" + }); - if (ExecuteWorkflow.sarcNumberOfIssnToDownload > 0 && - ExecuteWorkflow.sarcNumberOfIssnToDownload <= issnAndUrls.size()) { - logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.sarcNumberOfIssnToDownload); - issnAndUrls = issnAndUrls.subList(0, ExecuteWorkflow.sarcNumberOfIssnToDownload); - } + if (ExecuteWorkflow.sarcNumberOfIssnToDownload > 0 + && ExecuteWorkflow.sarcNumberOfIssnToDownload <= issnAndUrls.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.sarcNumberOfIssnToDownload); + issnAndUrls = issnAndUrls.subList(0, ExecuteWorkflow.sarcNumberOfIssnToDownload); + } - logger.info("(getAndProcessSarc) Downloading the followins opendoars: " + issnAndUrls); + logger.info("(getAndProcessSarc) Downloading the followins opendoars: " + issnAndUrls); - for (String[] issnAndUrl : issnAndUrls) { - logger.info("Now working on ISSN: " + issnAndUrl[1]); - getARReport(sarcsReportPathArray, sarcsReportPathNonArray, issnAndUrl[0], issnAndUrl[1]); - } + for (String[] issnAndUrl : issnAndUrls) { + logger.info("Now working on ISSN: " + issnAndUrl[1]); + getARReport(sarcsReportPathArray, sarcsReportPathNonArray, issnAndUrl[0], issnAndUrl[1]); + } - } + } - public void finalizeSarcStats() throws Exception { - stmtHive = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - stmtImpala = ConnectDB.getImpalaConnection().createStatement(); + public void finalizeSarcStats() throws Exception { + stmtHive = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + stmtImpala = ConnectDB.getImpalaConnection().createStatement(); - logger.info("Creating downloads_stats table"); - String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats " + - "(`source` string, " + - "`repository_id` string, " + - "`result_id` string, " + - "`date` string, " + - "`count` bigint, " + - "`openaire` bigint)"; - stmtHive.executeUpdate(createDownloadsStats); - logger.info("Created downloads_stats table"); + logger.info("Creating downloads_stats table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmtHive.executeUpdate(createDownloadsStats); + logger.info("Created downloads_stats table"); - logger.info("Dropping sarc_sushilogtmp_impala table"); - String drop_sarc_sushilogtmp_impala = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".sarc_sushilogtmp_impala"; - stmtHive.executeUpdate(drop_sarc_sushilogtmp_impala); - logger.info("Dropped sarc_sushilogtmp_impala table"); + logger.info("Dropping sarc_sushilogtmp_impala table"); + String drop_sarc_sushilogtmp_impala = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_impala"; + stmtHive.executeUpdate(drop_sarc_sushilogtmp_impala); + logger.info("Dropped sarc_sushilogtmp_impala table"); - logger.info("Creating sarc_sushilogtmp_impala, a table readable by impala"); - String createSarcSushilogtmpImpala = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp_impala " + - "STORED AS PARQUET AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; - stmtHive.executeUpdate(createSarcSushilogtmpImpala); - logger.info("Created sarc_sushilogtmp_impala"); + logger.info("Creating sarc_sushilogtmp_impala, a table readable by impala"); + String createSarcSushilogtmpImpala = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_impala " + + "STORED AS PARQUET AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; + stmtHive.executeUpdate(createSarcSushilogtmpImpala); + logger.info("Created sarc_sushilogtmp_impala"); - logger.info("Making sarc_sushilogtmp visible to impala"); - String invalidateMetadata = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp_impala;"; - stmtImpala.executeUpdate(invalidateMetadata); + logger.info("Making sarc_sushilogtmp visible to impala"); + String invalidateMetadata = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_impala;"; + stmtImpala.executeUpdate(invalidateMetadata); - logger.info("Dropping downloads_stats_impala table"); - String drop_downloads_stats_impala = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".downloads_stats_impala"; - stmtHive.executeUpdate(drop_downloads_stats_impala); - logger.info("Dropped downloads_stats_impala table"); + logger.info("Dropping downloads_stats_impala table"); + String drop_downloads_stats_impala = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats_impala"; + stmtHive.executeUpdate(drop_downloads_stats_impala); + logger.info("Dropped downloads_stats_impala table"); - logger.info("Making downloads_stats_impala deletion visible to impala"); - try { - String invalidateMetadataDownloadsStatsImpala = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_impala;"; - stmtImpala.executeUpdate(invalidateMetadataDownloadsStatsImpala); - } catch (SQLException sqle) { - } + logger.info("Making downloads_stats_impala deletion visible to impala"); + try { + String invalidateMetadataDownloadsStatsImpala = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats_impala;"; + stmtImpala.executeUpdate(invalidateMetadataDownloadsStatsImpala); + } catch (SQLException sqle) { + } - // We run the following query in Impala because it is faster - logger.info("Creating downloads_stats_impala"); - String createDownloadsStatsImpala = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_impala AS " + - "SELECT s.source, d.id AS repository_id, " + - "ro.id as result_id, CONCAT(CAST(YEAR(`date`) AS STRING), '/', " + - "LPAD(CAST(MONTH(`date`) AS STRING), 2, '0')) AS `date`, s.count, '0' " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_impala s, " + - ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + - ConnectDB.getStatsDBSchema() + ".datasource_results dr, " + - ConnectDB.getStatsDBSchema() + ".result_pids ro " + - "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND dr.id=d.id AND dr.result=ro.id AND " + - "s.rid=ro.pid AND ro.type='Digital Object Identifier' AND metric_type='ft_total' AND s.source='SARC-OJS'"; - stmtImpala.executeUpdate(createDownloadsStatsImpala); - logger.info("Creating downloads_stats_impala"); + // We run the following query in Impala because it is faster + logger.info("Creating downloads_stats_impala"); + String createDownloadsStatsImpala = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats_impala AS " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(CAST(YEAR(`date`) AS STRING), '/', " + + "LPAD(CAST(MONTH(`date`) AS STRING), 2, '0')) AS `date`, s.count, '0' " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_impala s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".datasource_results dr, " + + ConnectDB.getStatsDBSchema() + ".result_pids ro " + + "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND dr.id=d.id AND dr.result=ro.id AND " + + "s.rid=ro.pid AND ro.type='Digital Object Identifier' AND metric_type='ft_total' AND s.source='SARC-OJS'"; + stmtImpala.executeUpdate(createDownloadsStatsImpala); + logger.info("Creating downloads_stats_impala"); - // Insert into downloads_stats - logger.info("Inserting data from downloads_stats_impala into downloads_stats"); - String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats SELECT * " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_impala"; - stmtHive.executeUpdate(insertDStats); - logger.info("Inserted into downloads_stats"); + // Insert into downloads_stats + logger.info("Inserting data from downloads_stats_impala into downloads_stats"); + String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats SELECT * " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_impala"; + stmtHive.executeUpdate(insertDStats); + logger.info("Inserted into downloads_stats"); - logger.info("Creating sushilog table"); - String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog " + - "(`source` string, " + - "`repository_id` string, " + - "`rid` string, " + - "`date` string, " + - "`metric_type` string, " + - "`count` int)"; - stmtHive.executeUpdate(createSushilog); - logger.info("Created sushilog table"); + logger.info("Creating sushilog table"); + String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog " + + "(`source` string, " + + "`repository_id` string, " + + "`rid` string, " + + "`date` string, " + + "`metric_type` string, " + + "`count` int)"; + stmtHive.executeUpdate(createSushilog); + logger.info("Created sushilog table"); - // Insert into sushilog - logger.info("Inserting into sushilog"); - String insertSushiLog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog SELECT * " + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; - stmtHive.executeUpdate(insertSushiLog); - logger.info("Inserted into sushilog"); + // Insert into sushilog + logger.info("Inserting into sushilog"); + String insertSushiLog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog SELECT * " + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; + stmtHive.executeUpdate(insertSushiLog); + logger.info("Inserted into sushilog"); - stmtHive.close(); - ConnectDB.getHiveConnection().close(); - } + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + } - public void getARReport(String sarcsReportPathArray, String sarcsReportPathNonArray, - String url, String issn) throws Exception { - logger.info("Processing SARC! issn: " + issn + " with url: " + url); - ConnectDB.getHiveConnection().setAutoCommit(false); + public void getARReport(String sarcsReportPathArray, String sarcsReportPathNonArray, + String url, String issn) throws Exception { + logger.info("Processing SARC! issn: " + issn + " with url: " + url); + ConnectDB.getHiveConnection().setAutoCommit(false); - SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("(getARReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); + SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getARReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("(getARReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("(getARReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - PreparedStatement st = ConnectDB - .getHiveConnection() - .prepareStatement( - "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); - st.setString(1, issn); - ResultSet rs_date = st.executeQuery(); - while (rs_date.next()) { - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - } - } - rs_date.close(); + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); + st.setString(1, issn); + ResultSet rs_date = st.executeQuery(); + Date dateMax = null; + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); - // Creating the needed configuration for the correct storing of data - Configuration config = new Configuration(); - config.addResource(new Path("/etc/hadoop/conf/core-site.xml")); - config.addResource(new Path("/etc/hadoop/conf/hdfs-site.xml")); - config - .set( - "fs.hdfs.impl", - org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); - config - .set( - "fs.file.impl", - org.apache.hadoop.fs.LocalFileSystem.class.getName()); - FileSystem dfs = FileSystem.get(config); + // Creating the needed configuration for the correct storing of data + Configuration config = new Configuration(); + config.addResource(new Path("/etc/hadoop/conf/core-site.xml")); + config.addResource(new Path("/etc/hadoop/conf/hdfs-site.xml")); + config + .set( + "fs.hdfs.impl", + org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + config + .set( + "fs.file.impl", + org.apache.hadoop.fs.LocalFileSystem.class.getName()); + FileSystem dfs = FileSystem.get(config); - while (start.before(end)) { - String reportUrl = url + "GetReport/?Report=AR1&Format=json&BeginDate=" - + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()); - start.add(Calendar.MONTH, 1); + if (dateMax != null && start.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + issn); + } else { + + while (start.before(end)) { + String reportUrl = url + "GetReport/?Report=AR1&Format=json&BeginDate=" + + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()); + start.add(Calendar.MONTH, 1); - logger.info("(getARReport) Getting report: " + reportUrl); - String text = getJson(reportUrl); - if (text == null) { - continue; - } + logger.info("(getARReport) Getting report: " + reportUrl); + String text = getJson(reportUrl); + if (text == null) { + continue; + } - JSONParser parser = new JSONParser(); - JSONObject jsonObject = null; - try { - jsonObject = (JSONObject) parser.parse(text); - } - // if there is a parsing error continue with the next url - catch (ParseException pe) { - continue; - } + JSONParser parser = new JSONParser(); + JSONObject jsonObject = null; + try { + jsonObject = (JSONObject) parser.parse(text); + } // if there is a parsing error continue with the next url + catch (ParseException pe) { + continue; + } - jsonObject = (JSONObject) jsonObject.get("sc:ReportResponse"); - jsonObject = (JSONObject) jsonObject.get("sc:Report"); - if (jsonObject == null) { - continue; - } - jsonObject = (JSONObject) jsonObject.get("c:Report"); - jsonObject = (JSONObject) jsonObject.get("c:Customer"); - Object obj = jsonObject.get("c:ReportItems"); - JSONArray jsonArray = new JSONArray(); - if (obj instanceof JSONObject) { - jsonArray.add(obj); - } else { - jsonArray = (JSONArray) obj; - // jsonArray = (JSONArray) jsonObject.get("c:ReportItems"); - } - if (jsonArray == null) { - continue; - } + jsonObject = (JSONObject) jsonObject.get("sc:ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("sc:Report"); + if (jsonObject == null) { + continue; + } + jsonObject = (JSONObject) jsonObject.get("c:Report"); + jsonObject = (JSONObject) jsonObject.get("c:Customer"); + Object obj = jsonObject.get("c:ReportItems"); + JSONArray jsonArray = new JSONArray(); + if (obj instanceof JSONObject) { + jsonArray.add(obj); + } else { + jsonArray = (JSONArray) obj; + // jsonArray = (JSONArray) jsonObject.get("c:ReportItems"); + } + if (jsonArray == null) { + continue; + } - // Creating the file in the filesystem for the ItemIdentifier as array object - String filePathArray = sarcsReportPathArray + "/SarcsARReport_" + issn + "_" + - simpleDateFormat.format(start.getTime()) + ".json"; - logger.info("Storing to file: " + filePathArray); - FSDataOutputStream finArray = dfs.create(new Path(filePathArray), true); + // Creating the file in the filesystem for the ItemIdentifier as array object + String filePathArray = sarcsReportPathArray + "/SarcsARReport_" + issn + "_" + + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePathArray); + FSDataOutputStream finArray = dfs.create(new Path(filePathArray), true); - // Creating the file in the filesystem for the ItemIdentifier as array object - String filePathNonArray = sarcsReportPathNonArray + "/SarcsARReport_" + issn + "_" + - simpleDateFormat.format(start.getTime()) + ".json"; - logger.info("Storing to file: " + filePathNonArray); - FSDataOutputStream finNonArray = dfs.create(new Path(filePathNonArray), true); + // Creating the file in the filesystem for the ItemIdentifier as array object + String filePathNonArray = sarcsReportPathNonArray + "/SarcsARReport_" + issn + "_" + + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePathNonArray); + FSDataOutputStream finNonArray = dfs.create(new Path(filePathNonArray), true); - for (Object aJsonArray : jsonArray) { + for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - renameKeysRecursively(":", jsonObjectRow); + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + renameKeysRecursively(":", jsonObjectRow); - if (jsonObjectRow.get("ItemIdentifier") instanceof JSONObject) { - finNonArray.write(jsonObjectRow.toJSONString().getBytes()); - finNonArray.writeChar('\n'); - } else { - finArray.write(jsonObjectRow.toJSONString().getBytes()); - finArray.writeChar('\n'); - } - } + if (jsonObjectRow.get("ItemIdentifier") instanceof JSONObject) { + finNonArray.write(jsonObjectRow.toJSONString().getBytes()); + finNonArray.writeChar('\n'); + } else { + finArray.write(jsonObjectRow.toJSONString().getBytes()); + finArray.writeChar('\n'); + } + } - finArray.close(); - finNonArray.close(); + finArray.close(); + finNonArray.close(); - // Check the file size and if it is too big, delete it - File fileArray = new File(filePathArray); + // Check the file size and if it is too big, delete it + File fileArray = new File(filePathArray); if (fileArray.length() == 0) - fileArray.delete(); - File fileNonArray = new File(filePathNonArray); + fileArray.delete(); + File fileNonArray = new File(filePathNonArray); if (fileNonArray.length() == 0) - fileNonArray.delete(); + fileNonArray.delete(); - } + } - dfs.close(); + dfs.close(); + } + //ConnectDB.getHiveConnection().close(); + } - ConnectDB.getHiveConnection().close(); - } - - private void renameKeysRecursively(String delimiter, JSONArray givenJsonObj) throws Exception { - for (Object jjval : givenJsonObj) { - if (jjval instanceof JSONArray) - renameKeysRecursively(delimiter, (JSONArray) jjval); - else if (jjval instanceof JSONObject) - renameKeysRecursively(delimiter, (JSONObject) jjval); - // All other types of vals - else + private void renameKeysRecursively(String delimiter, JSONArray givenJsonObj) throws Exception { + for (Object jjval : givenJsonObj) { + if (jjval instanceof JSONArray) { + renameKeysRecursively(delimiter, (JSONArray) jjval); + } else if (jjval instanceof JSONObject) { + renameKeysRecursively(delimiter, (JSONObject) jjval); + } // All other types of vals + else ; - } - } + } + } - private void renameKeysRecursively(String delimiter, JSONObject givenJsonObj) throws Exception { - Set jkeys = new HashSet(givenJsonObj.keySet()); - for (String jkey : jkeys) { + private void renameKeysRecursively(String delimiter, JSONObject givenJsonObj) throws Exception { + Set jkeys = new HashSet(givenJsonObj.keySet()); + for (String jkey : jkeys) { - String[] splitArray = jkey.split(delimiter); - String newJkey = splitArray[splitArray.length - 1]; + String[] splitArray = jkey.split(delimiter); + String newJkey = splitArray[splitArray.length - 1]; - Object jval = givenJsonObj.get(jkey); - givenJsonObj.remove(jkey); - givenJsonObj.put(newJkey, jval); + Object jval = givenJsonObj.get(jkey); + givenJsonObj.remove(jkey); + givenJsonObj.put(newJkey, jval); - if (jval instanceof JSONObject) - renameKeysRecursively(delimiter, (JSONObject) jval); + if (jval instanceof JSONObject) { + renameKeysRecursively(delimiter, (JSONObject) jval); + } - if (jval instanceof JSONArray) { - renameKeysRecursively(delimiter, (JSONArray) jval); - } - } - } + if (jval instanceof JSONArray) { + renameKeysRecursively(delimiter, (JSONArray) jval); + } + } + } - private String getJson(String url) throws Exception { - // String cred=username+":"+password; - // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); - try { - URL website = new URL(url); - URLConnection connection = website.openConnection(); - // connection.setRequestProperty ("Authorization", "Basic "+encoded); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); - response.append("\n"); - } - } - return response.toString(); - } catch (Exception e) { + private String getJson(String url) throws Exception { + // String cred=username+":"+password; + // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + response.append("\n"); + } + } + return response.toString(); + } catch (Exception e) { - // Logging error and silently continuing - logger.error("Failed to get URL: " + e); - System.out.println("Failed to get URL: " + e); + // Logging error and silently continuing + logger.error("Failed to get URL: " + e); + System.out.println("Failed to get URL: " + e); // return null; // throw new Exception("Failed to get URL: " + e.toString(), e); - } - return ""; - } + } + return ""; + } } diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java index 405b58bd5..ae901dfa5 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java @@ -173,7 +173,7 @@ public class UsageStatsExporter { sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; stmt.executeUpdate(sql); - stmt.close(); + stmt.close(); ConnectDB.getHiveConnection().close(); } } From 3e24c9b176736bd1e6c8bbc4314750dd6863ce0f Mon Sep 17 00:00:00 2001 From: Dimitris Date: Sat, 14 Nov 2020 18:42:07 +0200 Subject: [PATCH 003/149] Changes 14112020 --- .../dhp-usage-datasets-stats-update/pom.xml | 79 ++ .../datasetsusagestats/export/ConnectDB.java | 202 +++ .../DownloadReportsListFromDatacite.java | 97 ++ .../export/ExecuteWorkflow.java | 70 + .../export/UsageStatsExporter.java | 236 +++ .../datasets_usagestats_parameters.json | 56 + .../oozie_app/config-default.xml | 38 + .../datasetsusagestats/oozie_app/workflow.xml | 70 + .../dhp-usage-raw-data-update/pom.xml | 79 ++ .../graph/usagerawdata/export/ConnectDB.java | 125 ++ .../usagerawdata/export/ExecuteWorkflow.java | 202 +++ .../graph/usagerawdata/export/IrusStats.java | 419 ++++++ .../export/LaReferenciaDownloadLogs.java | 265 ++++ .../export/LaReferenciaStats.java | 436 ++++++ .../export/PiwikDownloadLogs.java | 327 +++++ .../usagerawdata/export/PiwikStatsDB.java | 1262 +++++++++++++++++ .../export/ReadCounterRobotsList.java | 54 + .../graph/usagerawdata/export/SarcStats.java | 575 ++++++++ .../export/UsageStatsExporter.java | 186 +++ .../export/usagerawdata_parameters.json | 231 +++ .../usagerawdata/oozie_app/config-default.xml | 38 + .../graph/usagerawdata/oozie_app/workflow.xml | 90 ++ .../oa/graph/usagestats/export/IrusStats.java | 2 +- .../usagestats/export/LaReferenciaStats.java | 13 + .../usagestats/export/PiwikDownloadLogs.java | 470 +++--- .../graph/usagestats/export/PiwikStatsDB.java | 30 +- .../oa/graph/usagestats/export/SarcStats.java | 17 +- .../usagestats/export/UsageStatsExporter.java | 2 +- 28 files changed, 5420 insertions(+), 251 deletions(-) create mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/pom.xml create mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java create mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java create mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java create mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java create mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/export/datasets_usagestats_parameters.json create mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-usage-raw-data-update/pom.xml create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ConnectDB.java create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaDownloadLogs.java create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ReadCounterRobotsList.java create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/pom.xml b/dhp-workflows/dhp-usage-datasets-stats-update/pom.xml new file mode 100644 index 000000000..14b543a57 --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/pom.xml @@ -0,0 +1,79 @@ + + + + + + + + + dhp-workflows + eu.dnetlib.dhp + 1.1.7-SNAPSHOT + + 4.0.0 + dhp-usage-datasets-stats-update + + + UTF-8 + UTF-8 + 0.13.1-cdh5.2.1 + 2.5.0-cdh5.2.1 + + + + + org.apache.spark + spark-core_2.11 + 2.2.0 + + + org.apache.spark + spark-sql_2.11 + 2.4.5 + + + com.googlecode.json-simple + json-simple + 1.1.1 + + + org.json + json + 20180130 + jar + + + org.apache.hive + hive-jdbc + ${cdh.hive.version} + + + org.apache.hadoop + hadoop-common + ${cdh.hadoop.version} + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + c3p0 + c3p0 + 0.9.1.2 + jar + + + dhp-usage-datasets-stats-update + diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java new file mode 100644 index 000000000..e6da7eff3 --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java @@ -0,0 +1,202 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.datasetsusagestats.export; + +import java.sql.Connection; +import java.sql.DriverManager; +import java.sql.SQLException; +import java.sql.Statement; +import java.util.Properties; + +import org.apache.log4j.Logger; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +/** + * @author D. Pierrakos, S. Zoupanos + */ +import com.mchange.v2.c3p0.ComboPooledDataSource; + +public abstract class ConnectDB { + + public static Connection DB_HIVE_CONNECTION; + public static Connection DB_IMPALA_CONNECTION; + + private static String dbHiveUrl; + private static String dbImpalaUrl; + private static String datasetUsageStatsDBSchema; + private static String statsDBSchema; + private final static Logger logger = Logger.getLogger(ConnectDB.class); + private Statement stmt = null; + + static void init() throws ClassNotFoundException { + + dbHiveUrl = ExecuteWorkflow.dbHiveUrl; + dbImpalaUrl = ExecuteWorkflow.dbImpalaUrl; + datasetUsageStatsDBSchema = ExecuteWorkflow.datasetUsageStatsDBSchema; + statsDBSchema = ExecuteWorkflow.statsDBSchema; + + Class.forName("org.apache.hive.jdbc.HiveDriver"); + } + + public static Connection getHiveConnection() throws SQLException { + if (DB_HIVE_CONNECTION != null && !DB_HIVE_CONNECTION.isClosed()) { + return DB_HIVE_CONNECTION; + } else { + DB_HIVE_CONNECTION = connectHive(); + + return DB_HIVE_CONNECTION; + } + } + + public static Connection getImpalaConnection() throws SQLException { + if (DB_IMPALA_CONNECTION != null && !DB_IMPALA_CONNECTION.isClosed()) { + return DB_IMPALA_CONNECTION; + } else { + DB_IMPALA_CONNECTION = connectImpala(); + + return DB_IMPALA_CONNECTION; + } + } + + public static String getDataSetUsageStatsDBSchema() { + return ConnectDB.datasetUsageStatsDBSchema; + } + + public static String getStatsDBSchema() { + return ConnectDB.statsDBSchema; + } + + private static Connection connectHive() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbHiveUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbHiveUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(5); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + + logger.info("Opened database successfully"); + + return cpds.getConnection(); + + } + + private static Connection connectImpala() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbImpalaUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbImpalaUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(5); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + + logger.info("Opened database successfully"); + return cpds.getConnection(); + + } + + private void createDatabase() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Dropping logs DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); + String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema() + " CASCADE"; + stmt.executeUpdate(dropDatabase); + } catch (Exception e) { + logger.error("Failed to drop database: " + e); + throw new Exception("Failed to drop database: " + e.toString(), e); + } + + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating usagestats DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); + String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema(); + stmt.executeUpdate(createDatabase); + + } catch (Exception e) { + logger.error("Failed to create database: " + e); + throw new Exception("Failed to create database: " + e.toString(), e); + } + } + + private void createTables() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + // Create Piwiklog table - This table should exist + String sqlCreateTablePiwikLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getDataSetUsageStatsDBSchema() + + ".piwiklog(source INT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) " + + "into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTablePiwikLog); + + ///////////////////////////////////////// + // Rule for duplicate inserts @ piwiklog + ///////////////////////////////////////// + + String sqlCreateTablePortalLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getDataSetUsageStatsDBSchema() + + ".process_portal_log(source INT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTablePortalLog); + + ////////////////////////////////////////////////// + // Rule for duplicate inserts @ process_portal_log + ////////////////////////////////////////////////// + + stmt.close(); + ConnectDB.getHiveConnection().close(); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } +} +/* +CREATE TABLE IF NOT EXISTS dataciteReports (reportid STRING, + name STRING, + source STRING, + release STRING, + createdby STRING, + report_end_date STRING, + report_start_date STRING) + CLUSTERED BY (reportid) + into 100 buckets stored as orc tblproperties('transactional'='true'); +*/ \ No newline at end of file diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java new file mode 100644 index 000000000..196238ea2 --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java @@ -0,0 +1,97 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ +package eu.dnetlib.oa.graph.datasetsusagestats.export; + +import com.google.gson.Gson; +import com.google.gson.JsonArray; +import com.google.gson.JsonElement; +import java.io.BufferedInputStream; +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import java.net.MalformedURLException; +import java.net.URL; +import com.google.gson.JsonObject; +import java.util.ArrayList; +import java.util.Iterator; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.parser.ParseException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * + * @author dpie + */ +public class DownloadReportsListFromDatacite { + + private String dataciteBaseURL; + private String dataciteReportPath; + private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); + + public DownloadReportsListFromDatacite(String dataciteBaseURL, String dataciteReportPath) throws MalformedURLException, Exception { + + this.dataciteBaseURL = dataciteBaseURL; + this.dataciteReportPath = dataciteReportPath; + } + + public void downloadReportsList() throws ParseException { + StringBuilder responseStrBuilder = new StringBuilder(); + + Gson gson = new Gson(); + + try { + BufferedInputStream in = new BufferedInputStream(new URL(dataciteBaseURL).openStream()); + logger.info("Downloading from " + dataciteBaseURL); + + BufferedReader streamReader = new BufferedReader(new InputStreamReader(in, "UTF-8")); + String inputStr; + + while ((inputStr = streamReader.readLine()) != null) { + responseStrBuilder.append(inputStr); + } + } catch (IOException e) { + logger.info(e.getMessage()); + } + JsonObject jsonObject = gson.fromJson(responseStrBuilder.toString(), JsonObject.class); + JsonArray dataArray = jsonObject.getAsJsonArray("reports"); + ArrayList reportsList = new ArrayList(); + for (JsonElement element : dataArray) { + reportsList.add(element.getAsJsonObject().get("id").getAsString()); + } + + Iterator it = reportsList.iterator(); + while (it.hasNext()) { + String reportId = it.next().toString(); + String url = dataciteBaseURL + reportId; + + try { + BufferedInputStream in = new BufferedInputStream(new URL(url).openStream()); + BufferedReader streamReader = new BufferedReader(new InputStreamReader(in, "UTF-8")); + String inputStr; + StringBuilder responseStrBuilder2 = new StringBuilder(); + while ((inputStr = streamReader.readLine()) != null) { + responseStrBuilder2.append(inputStr); + } + FileSystem fs = FileSystem.get(new Configuration()); + FSDataOutputStream fin = fs.create(new Path(dataciteReportPath + "/" + reportId + ".json"), + true); + byte[] jsonObjectRawBytes = responseStrBuilder2.toString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); + + fin.close(); + + fin.close(); + } catch (IOException e) { + System.out.println(e); + } + } + } +} diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java new file mode 100644 index 000000000..7b3db3115 --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java @@ -0,0 +1,70 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.datasetsusagestats.export; + +import org.apache.commons.io.IOUtils; +import org.apache.log4j.BasicConfigurator; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class ExecuteWorkflow { + + static String dataciteBaseURL; + static String dataciteReportPath; + static String dbHiveUrl; + static String dbImpalaUrl; + static String datasetUsageStatsDBSchema; + static String statsDBSchema; + static boolean recreateDbAndTables; + static boolean datasetsEmptyDirs; + static boolean finalTablesVisibleToImpala; + + + public static void main(String args[]) throws Exception { + + // Sending the logs to the console + BasicConfigurator.configure(); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + UsageStatsExporter.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/datasetsusagestats/export/datasets_usagestats_parameters.json"))); + parser.parseArgument(args); + + // Setting up the initial parameters + dataciteBaseURL = parser.get("dataciteBaseURL"); + dataciteReportPath = parser.get("dataciteReportPath"); + dbHiveUrl = parser.get("dbHiveUrl"); + dbImpalaUrl = parser.get("dbImpalaUrl"); + datasetUsageStatsDBSchema = parser.get("datasetUsageStatsDBSchema"); + statsDBSchema = parser.get("statsDBSchema"); + + if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) + recreateDbAndTables = true; + else + recreateDbAndTables = false; + + if (parser.get("datasetsEmptyDirs").toLowerCase().equals("true")) + datasetsEmptyDirs = true; + else + datasetsEmptyDirs = false; + + if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) + finalTablesVisibleToImpala = true; + else + finalTablesVisibleToImpala = false; + + UsageStatsExporter usagestatsExport = new UsageStatsExporter(); + usagestatsExport.export(); + } + +} diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java new file mode 100644 index 000000000..28c4f30a1 --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java @@ -0,0 +1,236 @@ +package eu.dnetlib.oa.graph.datasetsusagestats.export; + +import java.io.IOException; +import java.sql.SQLException; +import java.sql.Statement; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Main class for downloading and processing Usage statistics + * + * @author D. Pierrakos, S. Zoupanos + */ +public class UsageStatsExporter { + + private Statement stmt = null; + + public UsageStatsExporter() { + + } + + private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); + + private void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting Log directory: " + ExecuteWorkflow.dataciteReportPath); + dfs.delete(new Path(ExecuteWorkflow.dataciteReportPath), true); + + logger.info("Creating Log directory: " + ExecuteWorkflow.dataciteReportPath); + dfs.mkdirs(new Path(ExecuteWorkflow.dataciteReportPath)); + + } + + public void export() throws Exception { + + logger.info("Initialising DB properties"); + ConnectDB.init(); + ConnectDB.getHiveConnection(); + + if (ExecuteWorkflow.recreateDbAndTables) { + createDatabase(); + createTables(); + reCreateLogDirs(); + } + logger.info("Initializing the download logs module"); + DownloadReportsListFromDatacite drfd = new DownloadReportsListFromDatacite(ExecuteWorkflow.dataciteBaseURL, ExecuteWorkflow.dataciteReportPath); + + if (ExecuteWorkflow.datasetsEmptyDirs) { + logger.info("Downloading Reports List From Datacite"); + drfd.downloadReportsList(); + logger.info("Reports List has been downloaded"); + } + } + + private void createDatabase() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Dropping datasetUsageStats DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); + String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema() + " CASCADE"; + stmt.executeUpdate(dropDatabase); + } catch (Exception e) { + logger.error("Failed to drop database: " + e); + throw new Exception("Failed to drop database: " + e.toString(), e); + } + + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating datasetUsageStats DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); + String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema(); + stmt.executeUpdate(createDatabase); + + } catch (Exception e) { + logger.error("Failed to create database: " + e); + throw new Exception("Failed to create database: " + e.toString(), e); + } + } + + private void createTables() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + // Create Reports table - This table should exist + String sqlCreateTableDataciteeReports = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getDataSetUsageStatsDBSchema() + + ".datacitereports(reportid STRING, \n" + + " name STRING, \n" + + " source STRING,\n" + + " release STRING,\n" + + " createdby STRING,\n" + + " report_end_date STRING,\n" + + " report_start_date STRING)\n" + + " CLUSTERED BY (reportid)\n" + + " into 100 buckets stored as orc tblproperties('transactional'='true')"; + + stmt.executeUpdate(sqlCreateTableDataciteeReports); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + +// runImpalaQuery(); +/* + PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); + + logger.info("Re-creating database and tables"); + + logger.info("Initializing the download logs module"); + PiwikDownloadLogs piwd = new PiwikDownloadLogs(ExecuteWorkflow.matomoBaseURL, ExecuteWorkflow.matomoAuthToken); + + if (ExecuteWorkflow.piwikEmptyDirs) { + logger.info("Recreating Piwik log directories"); + piwikstatsdb.reCreateLogDirs(); + } + + // Downloading piwik logs (also managing directory creation) + if (ExecuteWorkflow.downloadPiwikLogs) { + logger.info("Downloading piwik logs"); + piwd + .GetOpenAIRELogs( + ExecuteWorkflow.repoLogPath, + ExecuteWorkflow.portalLogPath, ExecuteWorkflow.portalMatomoID); + } + logger.info("Downloaded piwik logs"); + + // Create DB tables, insert/update statistics + String cRobotsUrl = "https://raw.githubusercontent.com/atmire/COUNTER-Robots/master/COUNTER_Robots_list.json"; + piwikstatsdb.setCounterRobotsURL(cRobotsUrl); + + if (ExecuteWorkflow.processPiwikLogs) { + logger.info("Processing logs"); + piwikstatsdb.processLogs(); + } + + logger.info("Creating LaReferencia tables"); + LaReferenciaDownloadLogs lrf = new LaReferenciaDownloadLogs(ExecuteWorkflow.lareferenciaBaseURL, + ExecuteWorkflow.lareferenciaAuthToken); + + if (ExecuteWorkflow.laReferenciaEmptyDirs) { + logger.info("Recreating LaReferencia log directories"); + lrf.reCreateLogDirs(); + } + + if (ExecuteWorkflow.downloadLaReferenciaLogs) { + logger.info("Downloading LaReferencia logs"); + lrf.GetLaReferenciaRepos(ExecuteWorkflow.lareferenciaLogPath); + logger.info("Downloaded LaReferencia logs"); + } + LaReferenciaStats lastats = new LaReferenciaStats(ExecuteWorkflow.lareferenciaLogPath); + + if (ExecuteWorkflow.processLaReferenciaLogs) { + logger.info("Processing LaReferencia logs"); + lastats.processLogs(); + logger.info("LaReferencia logs done"); + } + + IrusStats irusstats = new IrusStats(ExecuteWorkflow.irusUKBaseURL); + if (ExecuteWorkflow.irusCreateTablesEmptyDirs) { + logger.info("Creating Irus Stats tables"); + irusstats.createTables(); + logger.info("Created Irus Stats tables"); + + logger.info("Re-create log dirs"); + irusstats.reCreateLogDirs(); + logger.info("Re-created log dirs"); + } + + if (ExecuteWorkflow.irusDownloadReports) { + irusstats.getIrusRRReport(ExecuteWorkflow.irusUKReportPath); + } + if (ExecuteWorkflow.irusProcessStats) { + irusstats.processIrusStats(); + logger.info("Irus done"); + } + + SarcStats sarcStats = new SarcStats(); + if (ExecuteWorkflow.sarcCreateTablesEmptyDirs) { + sarcStats.reCreateLogDirs(); + } + if (ExecuteWorkflow.sarcDownloadReports) { + sarcStats.getAndProcessSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); + } + if (ExecuteWorkflow.sarcProcessStats) { + sarcStats.processSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); + sarcStats.finalizeSarcStats(); + } + logger.info("Sarc done"); + + // finalize usagestats + if (ExecuteWorkflow.finalizeStats) { + piwikstatsdb.finalizeStats(); + logger.info("Finalized stats"); + } + + // Make the tables available to Impala + if (ExecuteWorkflow.finalTablesVisibleToImpala) { + logger.info("Making tables visible to Impala"); + invalidateMetadata(); + } + + logger.info("End"); + */ +} +/* + private void invalidateMetadata() throws SQLException { + Statement stmt = null; + + stmt = ConnectDB.getImpalaConnection().createStatement(); + + String sql = "INVALIDATE METADATA " + ConnectDB.getDataSetUsageStatsDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getDataSetUsageStatsDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getDataSetUsageStatsDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getDataSetUsageStatsDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + } + */ diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/export/datasets_usagestats_parameters.json b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/export/datasets_usagestats_parameters.json new file mode 100644 index 000000000..f8d51a882 --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/export/datasets_usagestats_parameters.json @@ -0,0 +1,56 @@ +[ + { + "paramName": "dbu", + "paramLongName": "dataciteBaseURL", + "paramDescription": "URL of Datacite Reports Endpoint", + "paramRequired": true + }, + { + "paramName": "drp", + "paramLongName": "dataciteReportPath", + "paramDescription": "Path for Datacite Reports", + "paramRequired": true + }, + { + "paramName": "dbhu", + "paramLongName": "dbHiveUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbiu", + "paramLongName": "dbImpalaUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dusdbs", + "paramLongName": "datasetUsageStatsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "sdbs", + "paramLongName": "statsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "rdbt", + "paramLongName": "recreateDbAndTables", + "paramDescription": "Re-create database and initial tables?", + "paramRequired": true + }, + { + "paramName": "pwed", + "paramLongName": "datasetsEmptyDirs", + "paramDescription": "Empty piwik directories?", + "paramRequired": true + }, + { + "paramName": "ftvi", + "paramLongName": "finalTablesVisibleToImpala", + "paramDescription": "Make the dataset_usage_stats, visible to Impala", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/config-default.xml b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/config-default.xml new file mode 100644 index 000000000..b5c807378 --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + jobTracker + ${jobTracker} + + + nameNode + ${nameNode} + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1 + + + impalaJdbcUrl + jdbc:hive2://iis-cdh5-test-gw.ocean.icm.edu.pl:21050/;auth=noSasl; + + + oozie.wf.workflow.notification.url + {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status + + + oozie.use.system.libpath + true + + diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/workflow.xml b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/workflow.xml new file mode 100644 index 000000000..3a81e497d --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/workflow.xml @@ -0,0 +1,70 @@ + + + + hiveMetastoreUris + Hive server metastore URIs + + + hiveJdbcUrl + Hive server jdbc url + + + impalaJdbcUrl + Impala server jdbc url + + + + + ${jobTracker} + ${nameNode} + + + hive.metastore.uris + ${hiveMetastoreUris} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + eu.dnetlib.oa.graph.datasetsusagestats.export.ExecuteWorkflow + --dataciteBaseURL + ${dataciteBaseURL} + --dataciteReportPath + ${dataciteReportPath} + --dbHiveUrl + ${hiveJdbcUrl} + --dbImpalaUrl + ${impalaJdbcUrl} + --datasetUsageStatsDBSchema + ${datasetUsageStatsDBSchema} + --statsDBSchema + ${statsDBSchema} + --recreateDbAndTables + ${recreateDbAndTables} + --datasetsEmptyDirs + ${datasetsEmptyDirs} + --finalTablesVisibleToImpala + ${finalTablesVisibleToImpala} + + + + + + + + diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml new file mode 100644 index 000000000..338b2a2c5 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -0,0 +1,79 @@ + + + + + + + + + dhp-workflows + eu.dnetlib.dhp + 1.1.7-SNAPSHOT + + 4.0.0 + dhp-usage-raw-data-update + + + UTF-8 + UTF-8 + 0.13.1-cdh5.2.1 + 2.5.0-cdh5.2.1 + + + + + org.apache.spark + spark-core_2.11 + 2.2.0 + + + org.apache.spark + spark-sql_2.11 + 2.4.5 + + + com.googlecode.json-simple + json-simple + 1.1.1 + + + org.json + json + 20180130 + jar + + + org.apache.hive + hive-jdbc + ${cdh.hive.version} + + + org.apache.hadoop + hadoop-common + ${cdh.hadoop.version} + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + c3p0 + c3p0 + 0.9.1.2 + jar + + + dhp-usage-raw-data-update + diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ConnectDB.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ConnectDB.java new file mode 100644 index 000000000..f76644c83 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ConnectDB.java @@ -0,0 +1,125 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.sql.Connection; +import java.sql.DriverManager; +import java.sql.SQLException; +import java.sql.Statement; +import java.util.Properties; + +import org.apache.log4j.Logger; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +/** + * @author D. Pierrakos, S. Zoupanos + */ +import com.mchange.v2.c3p0.ComboPooledDataSource; + +public abstract class ConnectDB { + + public static Connection DB_HIVE_CONNECTION; + public static Connection DB_IMPALA_CONNECTION; + + private static String dbHiveUrl; + private static String dbImpalaUrl; + private static String usageStatsDBSchema; + private static String statsDBSchema; + private final static Logger log = Logger.getLogger(ConnectDB.class); + + static void init() throws ClassNotFoundException { + + dbHiveUrl = ExecuteWorkflow.dbHiveUrl; + dbImpalaUrl = ExecuteWorkflow.dbImpalaUrl; + usageStatsDBSchema = ExecuteWorkflow.usageStatsDBSchema; + statsDBSchema = ExecuteWorkflow.statsDBSchema; + + Class.forName("org.apache.hive.jdbc.HiveDriver"); + } + + public static Connection getHiveConnection() throws SQLException { + if (DB_HIVE_CONNECTION != null && !DB_HIVE_CONNECTION.isClosed()) { + return DB_HIVE_CONNECTION; + } else { + DB_HIVE_CONNECTION = connectHive(); + + return DB_HIVE_CONNECTION; + } + } + + public static Connection getImpalaConnection() throws SQLException { + if (DB_IMPALA_CONNECTION != null && !DB_IMPALA_CONNECTION.isClosed()) { + return DB_IMPALA_CONNECTION; + } else { + DB_IMPALA_CONNECTION = connectImpala(); + + return DB_IMPALA_CONNECTION; + } + } + + public static String getUsageStatsDBSchema() { + return ConnectDB.usageStatsDBSchema; + } + + public static String getStatsDBSchema() { + return ConnectDB.statsDBSchema; + } + + private static Connection connectHive() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbHiveUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbHiveUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(5); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + return cpds.getConnection(); + + } + + private static Connection connectImpala() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbImpalaUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbImpalaUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(5); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + + return cpds.getConnection(); + + } + +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java new file mode 100644 index 000000000..774dcf0b7 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java @@ -0,0 +1,202 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.text.SimpleDateFormat; +import java.util.Calendar; +import java.util.Date; + +import org.apache.commons.io.IOUtils; +import org.apache.log4j.BasicConfigurator; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class ExecuteWorkflow { + + static String matomoAuthToken; + static String matomoBaseURL; + static String repoLogPath; + static String portalLogPath; + static String portalMatomoID; + static String irusUKBaseURL; + static String irusUKReportPath; + static String sarcsReportPathArray; + static String sarcsReportPathNonArray; + static String lareferenciaLogPath; + static String lareferenciaBaseURL; + static String lareferenciaAuthToken; + static String dbHiveUrl; + static String dbImpalaUrl; + static String usageStatsDBSchema; + static String statsDBSchema; + static boolean recreateDbAndTables; + + static boolean piwikEmptyDirs; + static boolean downloadPiwikLogs; + static boolean processPiwikLogs; + + static Calendar startingLogPeriod; + static Calendar endingLogPeriod; + static int numberOfPiwikIdsToDownload; + static int numberOfSiteIdsToDownload; + + static boolean laReferenciaEmptyDirs; + static boolean downloadLaReferenciaLogs; + static boolean processLaReferenciaLogs; + + static boolean irusCreateTablesEmptyDirs; + static boolean irusDownloadReports; + static boolean irusProcessStats; + static int irusNumberOfOpendoarsToDownload; + + static boolean sarcCreateTablesEmptyDirs; + static boolean sarcDownloadReports; + static boolean sarcProcessStats; + static int sarcNumberOfIssnToDownload; + + static boolean finalizeStats; + static boolean finalTablesVisibleToImpala; + + static int numberOfDownloadThreads; + + public static void main(String args[]) throws Exception { + + // Sending the logs to the console + BasicConfigurator.configure(); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + UsageStatsExporter.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json"))); + parser.parseArgument(args); + + // Setting up the initial parameters + matomoAuthToken = parser.get("matomoAuthToken"); + matomoBaseURL = parser.get("matomoBaseURL"); + repoLogPath = parser.get("repoLogPath"); + portalLogPath = parser.get("portalLogPath"); + portalMatomoID = parser.get("portalMatomoID"); + irusUKBaseURL = parser.get("irusUKBaseURL"); + irusUKReportPath = parser.get("irusUKReportPath"); + sarcsReportPathArray = parser.get("sarcsReportPathArray"); + sarcsReportPathNonArray = parser.get("sarcsReportPathNonArray"); + lareferenciaLogPath = parser.get("lareferenciaLogPath"); + lareferenciaBaseURL = parser.get("lareferenciaBaseURL"); + lareferenciaAuthToken = parser.get("lareferenciaAuthToken"); + + dbHiveUrl = parser.get("dbHiveUrl"); + dbImpalaUrl = parser.get("dbImpalaUrl"); + usageStatsDBSchema = parser.get("usageStatsDBSchema"); + statsDBSchema = parser.get("statsDBSchema"); + + if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) + recreateDbAndTables = true; + else + recreateDbAndTables = false; + + if (parser.get("piwikEmptyDirs").toLowerCase().equals("true")) + piwikEmptyDirs = true; + else + piwikEmptyDirs = false; + + if (parser.get("downloadPiwikLogs").toLowerCase().equals("true")) + downloadPiwikLogs = true; + else + downloadPiwikLogs = false; +/* + if (parser.get("processPiwikLogs").toLowerCase().equals("true")) + processPiwikLogs = true; + else + processPiwikLogs = false; +*/ + String startingLogPeriodStr = parser.get("startingLogPeriod"); + Date startingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(startingLogPeriodStr); + startingLogPeriod = startingLogPeriodStr(startingLogPeriodDate); + + String endingLogPeriodStr = parser.get("endingLogPeriod"); + Date endingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(endingLogPeriodStr); + endingLogPeriod = startingLogPeriodStr(endingLogPeriodDate); + + numberOfPiwikIdsToDownload = Integer.parseInt(parser.get("numberOfPiwikIdsToDownload")); + numberOfSiteIdsToDownload = Integer.parseInt(parser.get("numberOfSiteIdsToDownload")); + + if (parser.get("laReferenciaEmptyDirs").toLowerCase().equals("true")) + laReferenciaEmptyDirs = true; + else + laReferenciaEmptyDirs = false; + + if (parser.get("downloadLaReferenciaLogs").toLowerCase().equals("true")) + downloadLaReferenciaLogs = true; + else + downloadLaReferenciaLogs = false; +/* + if (parser.get("processLaReferenciaLogs").toLowerCase().equals("true")) + processLaReferenciaLogs = true; + else + processLaReferenciaLogs = false; +*/ + if (parser.get("irusCreateTablesEmptyDirs").toLowerCase().equals("true")) + irusCreateTablesEmptyDirs = true; + else + irusCreateTablesEmptyDirs = false; + + if (parser.get("irusDownloadReports").toLowerCase().equals("true")) + irusDownloadReports = true; + else + irusDownloadReports = false; +/* + if (parser.get("irusProcessStats").toLowerCase().equals("true")) + irusProcessStats = true; + else + irusProcessStats = false; + irusNumberOfOpendoarsToDownload = Integer.parseInt(parser.get("irusNumberOfOpendoarsToDownload")); +*/ + if (parser.get("sarcCreateTablesEmptyDirs").toLowerCase().equals("true")) + sarcCreateTablesEmptyDirs = true; + else + sarcCreateTablesEmptyDirs = false; + + if (parser.get("sarcDownloadReports").toLowerCase().equals("true")) + sarcDownloadReports = true; + else + sarcDownloadReports = false; +/* + if (parser.get("sarcProcessStats").toLowerCase().equals("true")) + sarcProcessStats = true; + else + sarcProcessStats = false; + sarcNumberOfIssnToDownload = Integer.parseInt(parser.get("sarcNumberOfIssnToDownload")); +*/ +/* + if (parser.get("finalizeStats").toLowerCase().equals("true")) + finalizeStats = true; + else + finalizeStats = false; + if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) + finalTablesVisibleToImpala = true; + else +*/ finalTablesVisibleToImpala = false; + + numberOfDownloadThreads = Integer.parseInt(parser.get("numberOfDownloadThreads")); + + UsageStatsExporter usagestatsExport = new UsageStatsExporter(); + usagestatsExport.export(); + } + + private static Calendar startingLogPeriodStr(Date date) { + + Calendar calendar = Calendar.getInstance(); + calendar.setTime(date); + return calendar; + + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java new file mode 100644 index 000000000..090f76ff5 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java @@ -0,0 +1,419 @@ +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class IrusStats { + + private String irusUKURL; + + private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); + + public IrusStats(String irusUKURL) throws Exception { + this.irusUKURL = irusUKURL; + // The following may not be needed - It will be created when JSON tables are created +// createTmpTables(); + } + + public void reCreateLogDirs() throws Exception { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); + dfs.delete(new Path(ExecuteWorkflow.irusUKReportPath), true); + + logger.info("Creating irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); + dfs.mkdirs(new Path(ExecuteWorkflow.irusUKReportPath)); + } + + public void createTables() throws Exception { + try { + logger.info("Creating sushilog"); + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog(source STRING, " + + "repository STRING, rid STRING, date STRING, metric_type STRING, count INT) clustered by (source, " + + "repository, rid, date, metric_type) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableSushiLog); + logger.info("Created sushilog"); + + // To see how to apply to the ignore duplicate rules and indexes +// stmt.executeUpdate(sqlCreateTableSushiLog); +// String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO sushilog " +// + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," +// + "sushilog.rid, sushilog.date " +// + "FROM sushilog " +// + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; +// stmt.executeUpdate(sqlcreateRuleSushiLog); +// String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; +// stmt.executeUpdate(createSushiIndex); + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + +// // The following may not be needed - It will be created when JSON tables are created +// private void createTmpTables() throws Exception { +// try { +// +// Statement stmt = ConnectDB.getConnection().createStatement(); +// String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilogtmp(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; +// stmt.executeUpdate(sqlCreateTableSushiLog); +// +// // stmt.executeUpdate("CREATE TABLE IF NOT EXISTS public.sushilog AS TABLE sushilog;"); +// // String sqlCopyPublicSushiLog = "INSERT INTO sushilog SELECT * FROM public.sushilog;"; +// // stmt.executeUpdate(sqlCopyPublicSushiLog); +// String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO sushilogtmp " +// + " WHERE (EXISTS ( SELECT sushilogtmp.source, sushilogtmp.repository," +// + "sushilogtmp.rid, sushilogtmp.date " +// + "FROM sushilogtmp " +// + "WHERE sushilogtmp.source = new.source AND sushilogtmp.repository = new.repository AND sushilogtmp.rid = new.rid AND sushilogtmp.date = new.date AND sushilogtmp.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; +// stmt.executeUpdate(sqlcreateRuleSushiLog); +// +// stmt.close(); +// ConnectDB.getConnection().close(); +// log.info("Sushi Tmp Tables Created"); +// } catch (Exception e) { +// log.error("Failed to create tables: " + e); +// throw new Exception("Failed to create tables: " + e.toString(), e); +// } +// } + public void processIrusStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping sushilogtmp_json table"); + String dropSushilogtmpJson = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sushilogtmp_json"; + stmt.executeUpdate(dropSushilogtmpJson); + logger.info("Dropped sushilogtmp_json table"); + + logger.info("Creating irus_sushilogtmp_json table"); + String createSushilogtmpJson = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json(\n" + + " `ItemIdentifier` ARRAY<\n" + + " struct<\n" + + " Type: STRING,\n" + + " Value: STRING\n" + + " >\n" + + " >,\n" + + " `ItemPerformance` ARRAY<\n" + + " struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.irusUKReportPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(createSushilogtmpJson); + logger.info("Created irus_sushilogtmp_json table"); + + logger.info("Dropping irus_sushilogtmp table"); + String dropSushilogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp"; + stmt.executeUpdate(dropSushilogtmp); + logger.info("Dropped irus_sushilogtmp table"); + + logger.info("Creating irus_sushilogtmp table"); + String createSushilogtmp = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp(source STRING, repository STRING, " + + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " + + "tblproperties('transactional'='true')"; + stmt.executeUpdate(createSushilogtmp); + logger.info("Created irus_sushilogtmp table"); + + logger.info("Inserting to irus_sushilogtmp table"); + String insertSushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp " + + "SELECT 'IRUS-UK', CONCAT('opendoar____::', split(split(INPUT__FILE__NAME,'IrusIRReport_')[1],'_')[0]), " + + "`ItemIdent`.`Value`, `ItemPerf`.`Period`.`Begin`, " + + "`ItemPerf`.`Instance`.`MetricType`, `ItemPerf`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json " + + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + + "LATERAL VIEW posexplode(ItemPerformance) ItemPerformanceTable AS seqp, ItemPerf " + + "WHERE `ItemIdent`.`Type`= 'OAI'"; + stmt.executeUpdate(insertSushilogtmp); + logger.info("Inserted to irus_sushilogtmp table"); + + logger.info("Creating downloads_stats table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmt.executeUpdate(createDownloadsStats); + logger.info("Created downloads_stats table"); + + logger.info("Inserting into downloads_stats"); + String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(YEAR(date), '/', LPAD(MONTH(date), 2, '0')) as date, s.count, '0' " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE s.repository=d.oid AND s.rid=ro.oid AND metric_type='ft_total' AND s.source='IRUS-UK'"; + stmt.executeUpdate(insertDStats); + logger.info("Inserted into downloads_stats"); + + logger.info("Creating sushilog table"); + String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog " + + "(`source` string, " + + "`repository_id` string, " + + "`rid` string, " + + "`date` string, " + + "`metric_type` string, " + + "`count` int)"; + stmt.executeUpdate(createSushilog); + logger.info("Created sushilog table"); + + logger.info("Inserting to sushilog table"); + String insertToShushilog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sushilog SELECT * FROM " + + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp"; + stmt.executeUpdate(insertToShushilog); + logger.info("Inserted to sushilog table"); + + ConnectDB.getHiveConnection().close(); + } + + public void getIrusRRReport(String irusUKReportPath) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("YYYY-MM"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getIrusRRReport) Starting period for log download: " + sdf.format(start.getTime())); + + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("(getIrusRRReport) Ending period for log download: " + sdf.format(end.getTime())); + + String reportUrl = irusUKURL + "GetReport/?Report=RR1&Release=4&RequestorID=OpenAIRE&BeginDate=" + + sdf.format(start.getTime()) + "&EndDate=" + sdf.format(end.getTime()) + + "&RepositoryIdentifier=&ItemDataType=&NewJiscBand=&Granularity=Monthly&Callback="; + + logger.info("(getIrusRRReport) Getting report: " + reportUrl); + + String text = getJson(reportUrl, "", ""); + + List opendoarsToVisit = new ArrayList(); + JSONParser parser = new JSONParser(); + JSONObject jsonObject = (JSONObject) parser.parse(text); + jsonObject = (JSONObject) jsonObject.get("ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Customer"); + JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); + int i = 0; + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + JSONArray itemIdentifier = (JSONArray) jsonObjectRow.get("ItemIdentifier"); + for (Object identifier : itemIdentifier) { + JSONObject opendoar = (JSONObject) identifier; + if (opendoar.get("Type").toString().equals("OpenDOAR")) { + i++; + opendoarsToVisit.add(opendoar.get("Value").toString()); + break; + } + } + // break; + } + + logger.info("(getIrusRRReport) Found the following opendoars for download: " + opendoarsToVisit); + + if (ExecuteWorkflow.irusNumberOfOpendoarsToDownload > 0 + && ExecuteWorkflow.irusNumberOfOpendoarsToDownload <= opendoarsToVisit.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.irusNumberOfOpendoarsToDownload); + opendoarsToVisit = opendoarsToVisit.subList(0, ExecuteWorkflow.irusNumberOfOpendoarsToDownload); + } + + logger.info("(getIrusRRReport) Downloading the followins opendoars: " + opendoarsToVisit); + + for (String opendoar : opendoarsToVisit) { + logger.info("Now working on openDoar: " + opendoar); + this.getIrusIRReport(opendoar, irusUKReportPath); + } + + logger.info("(getIrusRRReport) Finished with report: " + reportUrl); + } + + private void getIrusIRReport(String opendoar, String irusUKReportPath) throws Exception { + + logger.info("(getIrusIRReport) Getting report(s) with opendoar: " + opendoar); + + ConnectDB.getHiveConnection().setAutoCommit(false); + + SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); + + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getIrusIRReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); + + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("(getIrusIRReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); + + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); + st.setString(1, "opendoar____::" + opendoar); + ResultSet rs_date = st.executeQuery(); + Date dateMax = null; + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); + int batch_size = 0; + + if (dateMax != null && start.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + opendoar); + } else { + while (start.before(end)) { + logger.info("date: " + simpleDateFormat.format(start.getTime())); + String reportUrl = this.irusUKURL + "GetReport/?Report=IR1&Release=4&RequestorID=OpenAIRE&BeginDate=" + + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()) + + "&RepositoryIdentifier=opendoar%3A" + opendoar + + "&ItemIdentifier=&ItemDataType=&hasDOI=&Granularity=Monthly&Callback="; + start.add(Calendar.MONTH, 1); + + logger.info("Downloading file: " + reportUrl); + String text = getJson(reportUrl, "", ""); + if (text == null) { + continue; + } + + FileSystem fs = FileSystem.get(new Configuration()); + String filePath = irusUKReportPath + "/" + "IrusIRReport_" + + opendoar + "_" + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePath); + FSDataOutputStream fin = fs.create(new Path(filePath), true); + + JSONParser parser = new JSONParser(); + JSONObject jsonObject = (JSONObject) parser.parse(text); + jsonObject = (JSONObject) jsonObject.get("ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Customer"); + JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); + if (jsonArray == null) { + continue; + } + String oai = ""; + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + fin.write(jsonObjectRow.toJSONString().getBytes()); + fin.writeChar('\n'); + } + + fin.close(); + } + + } + //ConnectDB.getHiveConnection().close(); + + logger.info("(getIrusIRReport) Finished downloading report(s) with opendoar: " + opendoar); + } + + private String getJson(String url) throws Exception { + try { + System.out.println("===> Connecting to: " + url); + URL website = new URL(url); + System.out.println("Connection url -----> " + url); + URLConnection connection = website.openConnection(); + + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); +// response.append("\n"); + } + } + + System.out.println("response ====> " + response.toString()); + + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + e); + System.out.println("Failed to get URL: " + e); + throw new Exception("Failed to get URL: " + e.toString(), e); + } + } + + private String getJson(String url, String username, String password) throws Exception { + // String cred=username+":"+password; + // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + response.append("\n"); + } + } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL", e); + return null; + } + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaDownloadLogs.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaDownloadLogs.java new file mode 100644 index 000000000..88550579b --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaDownloadLogs.java @@ -0,0 +1,265 @@ +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class LaReferenciaDownloadLogs { + + private final String piwikUrl; + private Date startDate; + private final String tokenAuth; + + /* + * The Piwik's API method + */ + private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; + private final String format = "&format=json"; + private final String ApimethodGetAllSites = "?module=API&method=SitesManager.getSitesWithViewAccess"; + + private static final Logger logger = LoggerFactory.getLogger(LaReferenciaDownloadLogs.class); + + public LaReferenciaDownloadLogs(String piwikUrl, String tokenAuth) throws Exception { + this.piwikUrl = piwikUrl; + this.tokenAuth = tokenAuth; + this.createTables(); +// this.createTmpTables(); + } + + public void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); + + logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); + } + + private void createTables() throws Exception { + try { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating LaReferencia tables"); + String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableLareferenciaLog); + logger.info("Created LaReferencia tables"); +// String sqlcreateRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO lareferencialog " +// + " WHERE (EXISTS ( SELECT lareferencialog.matomoid, lareferencialog.source, lareferencialog.id_visit," +// + "lareferencialog.action, lareferencialog.\"timestamp\", lareferencialog.entity_id " +// + "FROM lareferencialog " +// + "WHERE lareferencialog.matomoid=new.matomoid AND lareferencialog.source = new.source AND lareferencialog.id_visit = new.id_visit AND lareferencialog.action = new.action AND lareferencialog.entity_id = new.entity_id AND lareferencialog.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; +// String sqlCreateRuleIndexLaReferenciaLog = "create index if not exists lareferencialog_rule on lareferencialog(matomoid, source, id_visit, action, entity_id, \"timestamp\");"; +// stmt.executeUpdate(sqlcreateRuleLaReferenciaLog); +// stmt.executeUpdate(sqlCreateRuleIndexLaReferenciaLog); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Lareferencia Tables Created"); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + // System.exit(0); + } + } + +// private void createTmpTables() throws Exception { +// +// try { +// Statement stmt = ConnectDB.getConnection().createStatement(); +// String sqlCreateTmpTableLaReferenciaLog = "CREATE TABLE IF NOT EXISTS lareferencialogtmp(matomoid INTEGER, source TEXT, id_visit TEXT, country TEXT, action TEXT, url TEXT, entity_id TEXT, source_item_type TEXT, timestamp TEXT, referrer_name TEXT, agent TEXT, PRIMARY KEY(source, id_visit, action, timestamp, entity_id));"; +// String sqlcreateTmpRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO lareferencialogtmp " +// + " WHERE (EXISTS ( SELECT lareferencialogtmp.matomoid, lareferencialogtmp.source, lareferencialogtmp.id_visit," +// + "lareferencialogtmp.action, lareferencialogtmp.\"timestamp\", lareferencialogtmp.entity_id " +// + "FROM lareferencialogtmp " +// + "WHERE lareferencialogtmp.matomoid=new.matomoid AND lareferencialogtmp.source = new.source AND lareferencialogtmp.id_visit = new.id_visit AND lareferencialogtmp.action = new.action AND lareferencialogtmp.entity_id = new.entity_id AND lareferencialogtmp.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; +// stmt.executeUpdate(sqlCreateTmpTableLaReferenciaLog); +// stmt.executeUpdate(sqlcreateTmpRuleLaReferenciaLog); +// +// stmt.close(); +// log.info("Lareferencia Tmp Tables Created"); +// +// } catch (Exception e) { +// log.error("Failed to create tmptables: " + e); +// throw new Exception("Failed to create tmp tables: " + e.toString(), e); +// // System.exit(0); +// } +// } + private String getPiwikLogUrl() { + return piwikUrl + "/"; + } + + private String getJson(String url) throws Exception { + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); +// response.append("\n"); + } + } + + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + e); + throw new Exception("Failed to get URL: " + e.toString(), e); + } + } + + public void GetLaReferenciaRepos(String repoLogsPath) throws Exception { + + String baseApiUrl = getPiwikLogUrl() + ApimethodGetAllSites + format + "&token_auth=" + this.tokenAuth; + String content = ""; + + List siteIdsToVisit = new ArrayList(); + + // Getting all the siteIds in a list for logging reasons & limiting the list + // to the max number of siteIds + content = getJson(baseApiUrl); + JSONParser parser = new JSONParser(); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + siteIdsToVisit.add(Integer.parseInt(jsonObjectRow.get("idsite").toString())); + } + logger.info("Found the following siteIds for download: " + siteIdsToVisit); + + if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 + && ExecuteWorkflow.numberOfPiwikIdsToDownload <= siteIdsToVisit.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); + siteIdsToVisit = siteIdsToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); + } + + logger.info("Downloading from repos with the followins siteIds: " + siteIdsToVisit); + + for (int siteId : siteIdsToVisit) { + logger.info("Now working on LaReferencia MatomoId: " + siteId); + this.GetLaReFerenciaLogs(repoLogsPath, siteId); + } + } + + public void GetLaReFerenciaLogs(String repoLogsPath, + int laReferencialMatomoID) throws Exception { + + logger.info("Downloading logs for LaReferencia repoid " + laReferencialMatomoID); + + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("Starting period for log download: " + sdf.format(start.getTime())); + + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("Ending period for log download: " + sdf.format(end.getTime())); + + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialog WHERE matomoid=?"); + st.setInt(1, laReferencialMatomoID); + Date dateMax = null; + + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); + + for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { + Date date = currDay.getTime(); + if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding Matomo logs for " + laReferencialMatomoID); + } else { + logger + .info( + "Downloading logs for LaReferencia repoid " + laReferencialMatomoID + " and for " + + sdf.format(date)); + + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + outFolder = repoLogsPath; + + FileSystem fs = FileSystem.get(new Configuration()); + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + laReferencialMatomoID + "_LaRefPiwiklog" + sdf.format((date)) + ".json"), + true); + + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + laReferencialMatomoID + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + int i = 0; + + JSONParser parser = new JSONParser(); + do { + String apiUrl = baseApiUrl; + + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } + + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } + + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + fin.write(jsonObjectRaw.toJSONString().getBytes()); + fin.writeChar('\n'); + } + + logger + .info( + "Downloaded part " + i + " of logs for LaReferencia repoid " + laReferencialMatomoID + + " and for " + + sdf.format(date)); + i++; + } while (true); + fin.close(); + } + } + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java new file mode 100644 index 000000000..ef7636099 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java @@ -0,0 +1,436 @@ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +import java.net.URLDecoder; +import java.sql.Connection; +import java.sql.PreparedStatement; +import java.sql.SQLException; +import java.sql.Statement; +import java.sql.Timestamp; +import java.text.SimpleDateFormat; +import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocatedFileStatus; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.RemoteIterator; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class LaReferenciaStats { + + private static final Logger logger = LoggerFactory.getLogger(LaReferenciaStats.class); + + private String logRepoPath; + + private Statement stmt = null; + + private String CounterRobotsURL; + private ArrayList robotsList; + + public LaReferenciaStats(String logRepoPath) throws Exception { + this.logRepoPath = logRepoPath; + this.createTables(); +// this.createTmpTables(); + } + + /* + * private void connectDB() throws Exception { try { ConnectDB connectDB = new ConnectDB(); } catch (Exception e) { + * log.error("Connect to db failed: " + e); throw new Exception("Failed to connect to db: " + e.toString(), e); } } + */ + private void createTables() throws Exception { + try { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating LaReferencia tables"); + String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableLareferenciaLog); + logger.info("Created LaReferencia tables"); +// String sqlcreateRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO lareferencialog " +// + " WHERE (EXISTS ( SELECT lareferencialog.matomoid, lareferencialog.source, lareferencialog.id_visit," +// + "lareferencialog.action, lareferencialog.\"timestamp\", lareferencialog.entity_id " +// + "FROM lareferencialog " +// + "WHERE lareferencialog.matomoid=new.matomoid AND lareferencialog.source = new.source AND lareferencialog.id_visit = new.id_visit AND lareferencialog.action = new.action AND lareferencialog.entity_id = new.entity_id AND lareferencialog.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; +// String sqlCreateRuleIndexLaReferenciaLog = "create index if not exists lareferencialog_rule on lareferencialog(matomoid, source, id_visit, action, entity_id, \"timestamp\");"; +// stmt.executeUpdate(sqlcreateRuleLaReferenciaLog); +// stmt.executeUpdate(sqlCreateRuleIndexLaReferenciaLog); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Lareferencia Tables Created"); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + // System.exit(0); + } + } + +// private void createTmpTables() throws Exception { +// +// try { +// Statement stmt = ConnectDB.getConnection().createStatement(); +// String sqlCreateTmpTableLaReferenciaLog = "CREATE TABLE IF NOT EXISTS lareferencialogtmp(matomoid INTEGER, source TEXT, id_visit TEXT, country TEXT, action TEXT, url TEXT, entity_id TEXT, source_item_type TEXT, timestamp TEXT, referrer_name TEXT, agent TEXT, PRIMARY KEY(source, id_visit, action, timestamp, entity_id));"; +// String sqlcreateTmpRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " +// + " ON INSERT TO lareferencialogtmp " +// + " WHERE (EXISTS ( SELECT lareferencialogtmp.matomoid, lareferencialogtmp.source, lareferencialogtmp.id_visit," +// + "lareferencialogtmp.action, lareferencialogtmp.\"timestamp\", lareferencialogtmp.entity_id " +// + "FROM lareferencialogtmp " +// + "WHERE lareferencialogtmp.matomoid=new.matomoid AND lareferencialogtmp.source = new.source AND lareferencialogtmp.id_visit = new.id_visit AND lareferencialogtmp.action = new.action AND lareferencialogtmp.entity_id = new.entity_id AND lareferencialogtmp.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; +// stmt.executeUpdate(sqlCreateTmpTableLaReferenciaLog); +// stmt.executeUpdate(sqlcreateTmpRuleLaReferenciaLog); +// +// stmt.close(); +// log.info("Lareferencia Tmp Tables Created"); +// +// } catch (Exception e) { +// log.error("Failed to create tmptables: " + e); +// throw new Exception("Failed to create tmp tables: " + e.toString(), e); +// // System.exit(0); +// } +// } + + public void processLogs() throws Exception { + try { + logger.info("Processing LaReferencia repository logs"); + processlaReferenciaLog(); + logger.info("LaReferencia repository logs process done"); + + logger.info("LaReferencia removing double clicks"); + removeDoubleClicks(); + logger.info("LaReferencia removed double clicks"); + + logger.info("LaReferencia creating viewsStats"); + viewsStats(); + logger.info("LaReferencia created viewsStats"); + logger.info("LaReferencia creating downloadsStats"); + downloadsStats(); + logger.info("LaReferencia created downloadsStats"); + logger.info("LaReferencia updating Production Tables"); + updateProdTables(); + logger.info("LaReferencia updated Production Tables"); + + } catch (Exception e) { + logger.error("Failed to process logs: " + e); + throw new Exception("Failed to process logs: " + e.toString(), e); + } + } + + public void processlaReferenciaLog() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping lareferencialogtmp_json table"); + String drop_lareferencialogtmp_json = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialogtmp_json"; + stmt.executeUpdate(drop_lareferencialogtmp_json); + logger.info("Dropped lareferencialogtmp_json table"); + + logger.info("Creating lareferencialogtmp_json"); + String create_lareferencialogtmp_json = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialogtmp_json(\n" + + " `idSite` STRING,\n" + + " `idVisit` STRING,\n" + + " `country` STRING,\n" + + " `referrerName` STRING,\n" + + " `browser` STRING,\n" + + " `repItem` STRING,\n" + + " `actionDetails` ARRAY<\n" + + " struct<\n" + + " timestamp: STRING,\n" + + " type: STRING,\n" + + " url: STRING,\n" + + " `customVariables`: struct<\n" + + " `1`: struct<\n" + + " `customVariablePageValue1`: STRING\n" + + " >,\n" + + " `2`: struct<\n" + + " `customVariablePageValue2`: STRING\n" + + " >\n" + + " >\n" + + " >\n" + + " >" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.lareferenciaLogPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_lareferencialogtmp_json); + logger.info("Created lareferencialogtmp_json"); + + logger.info("Dropping lareferencialogtmp table"); + String drop_lareferencialogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialogtmp"; + stmt.executeUpdate(drop_lareferencialogtmp); + logger.info("Dropped lareferencialogtmp table"); + + logger.info("Creating lareferencialogtmp"); + String create_lareferencialogtmp = "CREATE TABLE " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(create_lareferencialogtmp); + logger.info("Created lareferencialogtmp"); + + logger.info("Inserting into lareferencialogtmp"); + String insert_lareferencialogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp " + + "SELECT DISTINCT cast(idSite as INT) as matomoid, CONCAT('opendoar____::', " + + "actiondetail.customVariables.`2`.customVariablePageValue2) as source, idVisit as id_Visit, country, " + + "actiondetail.type as action, actiondetail.url as url, " + + "actiondetail.customVariables.`1`.`customVariablePageValue1` as entity_id, " + + "'repItem' as source_item_type, from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, " + + "referrerName as referrer_name, browser as agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp_json " + + "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; + stmt.executeUpdate(insert_lareferencialogtmp); + logger.info("Inserted into lareferencialogtmp"); + + stmt.close(); + } + + public void removeDoubleClicks() throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Cleaning download double clicks"); + // clean download double clicks + String sql = "DELETE from " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp WHERE EXISTS (" + + "SELECT DISTINCT p1.source, p1.id_visit, p1.action, p1.entity_id, p1.timestamp " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp p1, " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp p2 " + + "WHERE p1.source=p2.source AND p1.id_visit=p2.id_visit AND p1.entity_id=p2.entity_id " + + "AND p1.action=p2.action AND p1.action='download' AND p1.timestamp!=p2.timestamp " + + "AND p1.timestamp listHdfsDir(String dir) throws Exception { + FileSystem hdfs = FileSystem.get(new Configuration()); + RemoteIterator Files; + ArrayList fileNames = new ArrayList<>(); + + try { + Path exportPath = new Path(hdfs.getUri() + dir); + Files = hdfs.listFiles(exportPath, false); + while (Files.hasNext()) { + String fileName = Files.next().getPath().toString(); + // log.info("Found hdfs file " + fileName); + fileNames.add(fileName); + } + // hdfs.close(); + } catch (Exception e) { + logger.error("HDFS file path with exported data does not exist : " + new Path(hdfs.getUri() + logRepoPath)); + throw new Exception("HDFS file path with exported data does not exist : " + logRepoPath, e); + } + + return fileNames; + } + + private String readHDFSFile(String filename) throws Exception { + String result; + try { + + FileSystem fs = FileSystem.get(new Configuration()); + // log.info("reading file : " + filename); + + BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(new Path(filename)))); + + StringBuilder sb = new StringBuilder(); + String line = br.readLine(); + + while (line != null) { + if (!line.equals("[]")) { + sb.append(line); + } + // sb.append(line); + line = br.readLine(); + } + result = sb.toString().replace("][{\"idSite\"", ",{\"idSite\""); + if (result.equals("")) { + result = "[]"; + } + + // fs.close(); + } catch (Exception e) { + logger.error(e.getMessage()); + throw new Exception(e); + } + + return result; + } + +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java new file mode 100644 index 000000000..681105de4 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java @@ -0,0 +1,327 @@ +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +import java.net.Authenticator; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class PiwikDownloadLogs { + + private final String piwikUrl; + private Date startDate; + private final String tokenAuth; + + /* + * The Piwik's API method + */ + private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; + private final String format = "&format=json"; + + private static final Logger logger = LoggerFactory.getLogger(PiwikDownloadLogs.class); + + public PiwikDownloadLogs(String piwikUrl, String tokenAuth) { + this.piwikUrl = piwikUrl; + this.tokenAuth = tokenAuth; + + } + + private String getPiwikLogUrl() { + return "https://" + piwikUrl + "/"; + } + + private String getJson(String url) throws Exception { + try { + logger.debug("Connecting to download the JSON: " + url); + URL website = new URL(url); + URLConnection connection = website.openConnection(); + + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + } + } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + url + " Exception: " + e); + throw new Exception("Failed to get URL: " + url + " Exception: " + e.toString(), e); + } + } + + class WorkerThread implements Runnable { + + private Calendar currDay; + private int siteId; + private String repoLogsPath; + private String portalLogPath; + private String portalMatomoID; + + public WorkerThread(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws IOException { + this.currDay = (Calendar) currDay.clone(); + this.siteId = new Integer(siteId); + this.repoLogsPath = new String(repoLogsPath); + this.portalLogPath = new String(portalLogPath); + this.portalMatomoID = new String(portalMatomoID); + } + + public void run() { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + System.out + .println( + Thread.currentThread().getName() + " (Start) Thread for " + + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); + try { + GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + System.out + .println( + Thread.currentThread().getName() + " (End) Thread for " + + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); + } + + public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + + Date date = currDay.getTime(); + logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + if (siteId == Integer.parseInt(portalMatomoID)) { + outFolder = portalLogPath; + } else { + outFolder = repoLogsPath; + } + + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + + int i = 0; + + JSONParser parser = new JSONParser(); + StringBuffer totalContent = new StringBuffer(); + FileSystem fs = FileSystem.get(new Configuration()); + + do { + int writtenBytes = 0; + String apiUrl = baseApiUrl; + + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } + + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } + + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"), + true); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); + + writtenBytes += jsonObjectRawBytes.length + 1; + } + + fin.close(); + System.out + .println( + Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes + + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"); + + i++; + } while (true); + + fs.close(); + } + } + + public void GetOpenAIRELogs(String repoLogsPath, String portalLogPath, String portalMatomoID) throws Exception { + + Statement statement = ConnectDB.getHiveConnection().createStatement(); + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + + ResultSet rs = statement + .executeQuery( + "SELECT distinct piwik_id from " + ConnectDB.getStatsDBSchema() + + ".datasource where piwik_id is not null and piwik_id <> 0 order by piwik_id"); + + // Getting all the piwikids in a list for logging reasons & limitting the list + // to the max number of piwikids + List piwikIdToVisit = new ArrayList(); + //while (rs.next()) + //piwikIdToVisit.add(rs.getInt(1)); + piwikIdToVisit.add(13); + + logger.info("Found the following piwikIds for download: " + piwikIdToVisit); + + if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 + && ExecuteWorkflow.numberOfPiwikIdsToDownload <= piwikIdToVisit.size()) { + logger.info("Trimming piwikIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); + piwikIdToVisit = piwikIdToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); + } + + logger.info("Downloading from repos with the followins piwikIds: " + piwikIdToVisit); + + // ExecutorService executor = Executors.newFixedThreadPool(ExecuteWorkflow.numberOfDownloadThreads); + for (int siteId : piwikIdToVisit) { + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("Starting period for log download: " + sdf.format(start.getTime())); + + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("Ending period for log download: " + sdf.format(end.getTime())); + + logger.info("Now working on piwikId: " + siteId); + + PreparedStatement st = ConnectDB.DB_HIVE_CONNECTION + .prepareStatement( + "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + + ".piwiklog WHERE source=?"); + st.setInt(1, siteId); + Date dateMax = null; + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + logger.info("Found max date: " + rs_date.getString(1) + " for repository " + siteId); + + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); + + for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { + // logger.info("Date used " + currDay.toString()); + // Runnable worker = new WorkerThread(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + // executor.execute(worker);// calling execute method of ExecutorService + logger.info("Date used " + currDay.getTime().toString()); + + if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding Matomo logs for " + siteId); + } else { + GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + } + + } + } + // executor.shutdown(); + // while (!executor.isTerminated()) { + // } + // System.out.println("Finished all threads"); + } + + public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + + Date date = currDay.getTime(); + logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + if (siteId == Integer.parseInt(portalMatomoID)) { + outFolder = portalLogPath; + } else { + outFolder = repoLogsPath; + } + + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + + int i = 0; + + JSONParser parser = new JSONParser(); + StringBuffer totalContent = new StringBuffer(); + FileSystem fs = FileSystem.get(new Configuration()); + + do { + int writtenBytes = 0; + String apiUrl = baseApiUrl; + + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } + + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } + + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"), + true); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); + + writtenBytes += jsonObjectRawBytes.length + 1; + } + + fin.close(); + System.out + .println( + Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes + + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"); + + i++; + } while (true); + + fs.close(); + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java new file mode 100644 index 000000000..e0225d49a --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java @@ -0,0 +1,1262 @@ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +import java.net.URLDecoder; +import java.sql.Connection; +import java.sql.SQLException; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.*; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocatedFileStatus; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.RemoteIterator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class PiwikStatsDB { + + private String logPath; + private String logRepoPath; + private String logPortalPath; + + private Statement stmt = null; + + private static final Logger logger = LoggerFactory.getLogger(PiwikStatsDB.class); + + private String CounterRobotsURL; + private ArrayList robotsList; + + public PiwikStatsDB(String logRepoPath, String logPortalPath) throws Exception { + this.logRepoPath = logRepoPath; + this.logPortalPath = logPortalPath; + + } + + public void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.delete(new Path(ExecuteWorkflow.repoLogPath), true); + + logger.info("Deleting portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.delete(new Path(ExecuteWorkflow.portalLogPath), true); + + logger.info("Creating repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.repoLogPath)); + + logger.info("Creating portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.portalLogPath)); + } + + public void recreateDBAndTables() throws Exception { + this.createDatabase(); + this.createTables(); + // The piwiklog table is not needed since it is built + // on top of JSON files + this.createTmpTables(); + } + + public ArrayList getRobotsList() { + return robotsList; + } + + public void setRobotsList(ArrayList robotsList) { + this.robotsList = robotsList; + } + + public String getCounterRobotsURL() { + return CounterRobotsURL; + } + + public void setCounterRobotsURL(String CounterRobotsURL) { + this.CounterRobotsURL = CounterRobotsURL; + } + + private void createDatabase() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Dropping usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); + String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + " CASCADE"; + stmt.executeUpdate(dropDatabase); + } catch (Exception e) { + logger.error("Failed to drop database: " + e); + throw new Exception("Failed to drop database: " + e.toString(), e); + } + + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); + String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema(); + stmt.executeUpdate(createDatabase); + + } catch (Exception e) { + logger.error("Failed to create database: " + e); + throw new Exception("Failed to create database: " + e.toString(), e); + } + } + + private void createTables() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + // Create Piwiklog table - This table should exist + String sqlCreateTablePiwikLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklog(source INT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) " + + "into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTablePiwikLog); + + ///////////////////////////////////////// + // Rule for duplicate inserts @ piwiklog + ///////////////////////////////////////// + + String sqlCreateTablePortalLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log(source INT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTablePortalLog); + + ////////////////////////////////////////////////// + // Rule for duplicate inserts @ process_portal_log + ////////////////////////////////////////////////// + + stmt.close(); + ConnectDB.getHiveConnection().close(); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + + private void createTmpTables() throws Exception { + try { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTmpTablePiwikLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp(source INT, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTmpTablePiwikLog); + + ////////////////////////////////////////////////// + // Rule for duplicate inserts @ piwiklogtmp + ////////////////////////////////////////////////// + + ////////////////////////////////////////////////// + // Copy from public.piwiklog to piwiklog + ////////////////////////////////////////////////// + // String sqlCopyPublicPiwiklog="insert into piwiklog select * from public.piwiklog;"; + // stmt.executeUpdate(sqlCopyPublicPiwiklog); + + String sqlCreateTmpTablePortalLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp(source INT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTmpTablePortalLog); + + ////////////////////////////////////////////////// + // Rule for duplicate inserts @ process_portal_log_tmp + ////////////////////////////////////////////////// + + stmt.close(); + + } catch (Exception e) { + logger.error("Failed to create tmptables: " + e); + throw new Exception("Failed to create tmp tables: " + e.toString(), e); + // System.exit(0); + } + } + + public void processLogs() throws Exception { + try { + ReadCounterRobotsList counterRobots = new ReadCounterRobotsList(this.getCounterRobotsURL()); + this.robotsList = counterRobots.getRobotsPatterns(); + + logger.info("Processing repository logs"); + processRepositoryLog(); + logger.info("Repository logs process done"); + + logger.info("Removing double clicks"); + removeDoubleClicks(); + logger.info("Removing double clicks done"); + + logger.info("Cleaning oai"); + cleanOAI(); + logger.info("Cleaning oai done"); + + logger.info("Processing portal logs"); + processPortalLog(); + logger.info("Portal logs process done"); + + logger.info("Processing portal usagestats"); + portalStats(); + logger.info("Portal usagestats process done"); + + logger.info("ViewsStats processing starts"); + viewsStats(); + logger.info("ViewsStats processing ends"); + + logger.info("DownloadsStats processing starts"); + downloadsStats(); + logger.info("DownloadsStats processing starts"); + + logger.info("Updating Production Tables"); + updateProdTables(); + logger.info("Updated Production Tables"); + + } catch (Exception e) { + logger.error("Failed to process logs: " + e); + throw new Exception("Failed to process logs: " + e.toString(), e); + } + } + + public void processRepositoryLog() throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping piwiklogtmp_json table"); + String drop_piwiklogtmp_json = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp_json"; + stmt.executeUpdate(drop_piwiklogtmp_json); + logger.info("Dropped piwiklogtmp_json table"); + + logger.info("Creating piwiklogtmp_json"); + String create_piwiklogtmp_json = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp_json(\n" + + " `idSite` STRING,\n" + + " `idVisit` STRING,\n" + + " `country` STRING,\n" + + " `referrerName` STRING,\n" + + " `browser` STRING,\n" + + " `actionDetails` ARRAY<\n" + + " struct<\n" + + " type: STRING,\n" + + " url: STRING,\n" + + " `customVariables`: struct<\n" + + " `1`: struct<\n" + + " `customVariablePageValue1`: STRING\n" + + " >\n" + + " >,\n" + + " timestamp: String\n" + + " >\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.repoLogPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_piwiklogtmp_json); + logger.info("Created piwiklogtmp_json"); + + logger.info("Dropping piwiklogtmp table"); + String drop_piwiklogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp"; + stmt.executeUpdate(drop_piwiklogtmp); + logger.info("Dropped piwiklogtmp"); + + logger.info("Creating piwiklogtmp"); + String create_piwiklogtmp = "CREATE TABLE " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp (source BIGINT, id_Visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(create_piwiklogtmp); + logger.info("Created piwiklogtmp"); + + logger.info("Inserting into piwiklogtmp"); + String insert_piwiklogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, " + + "actiondetail.type as action, actiondetail.url as url, " + + "actiondetail.customVariables.`1`.`customVariablePageValue1` as entity_id, " + + "'repItem' as source_item_type, from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, " + + "referrerName as referrer_name, browser as agent\n" + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp_json\n" + + "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; + stmt.executeUpdate(insert_piwiklogtmp); + logger.info("Inserted into piwiklogtmp"); + + stmt.close(); + } + + public void removeDoubleClicks() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Cleaning download double clicks"); + // clean download double clicks + String sql = "DELETE from " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "WHERE EXISTS (\n" + + "SELECT DISTINCT p1.source, p1.id_visit, p1.action, p1.entity_id, p1.timestamp \n" + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p1, " + + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p2\n" + + "WHERE p1.source=p2.source AND p1.id_visit=p2.id_visit AND p1.entity_id=p2.entity_id \n" + + + "AND p1.action=p2.action AND p1.action='download' AND p1.timestamp!=p2.timestamp \n" + + "AND p1.timestamp\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.portalLogPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_process_portal_log_tmp_json); + logger.info("Created process_portal_log_tmp_json"); + + logger.info("Droping process_portal_log_tmp table"); + String drop_process_portal_log_tmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp"; + stmt.executeUpdate(drop_process_portal_log_tmp); + logger.info("Dropped process_portal_log_tmp"); + + logger.info("Creating process_portal_log_tmp"); + String create_process_portal_log_tmp = "CREATE TABLE " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp (source BIGINT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(create_process_portal_log_tmp); + logger.info("Created process_portal_log_tmp"); + + logger.info("Inserting into process_portal_log_tmp"); + String insert_process_portal_log_tmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp " + + "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, actiondetail.type as action, " + + + "actiondetail.url as url, " + + "CASE\n" + + " WHEN (actiondetail.url like '%datasourceId=%') THEN split(actiondetail.url,'datasourceId=')[1] " + + " WHEN (actiondetail.url like '%datasource=%') THEN split(actiondetail.url,'datasource=')[1] " + + " WHEN (actiondetail.url like '%datasourceFilter=%') THEN split(actiondetail.url,'datasourceFilter=')[1] " + + + " WHEN (actiondetail.url like '%articleId=%') THEN split(actiondetail.url,'articleId=')[1] " + + " WHEN (actiondetail.url like '%datasetId=%') THEN split(actiondetail.url,'datasetId=')[1] " + + " WHEN (actiondetail.url like '%projectId=%') THEN split(actiondetail.url,'projectId=')[1] " + + " WHEN (actiondetail.url like '%organizationId=%') THEN split(actiondetail.url,'organizationId=')[1] " + + " ELSE '' " + + "END AS entity_id, " + + "CASE " + + " WHEN (actiondetail.url like '%datasourceId=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%datasource=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%datasourceFilter=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%articleId=%') THEN 'result' " + + " WHEN (actiondetail.url like '%datasetId=%') THEN 'result' " + + " WHEN (actiondetail.url like '%projectId=%') THEN 'project' " + + " WHEN (actiondetail.url like '%organizationId=%') THEN 'organization' " + + " ELSE '' " + + "END AS source_item_type, " + + "from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, referrerName as referrer_name, " + + "browser as agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp_json " + + "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; + stmt.executeUpdate(insert_process_portal_log_tmp); + logger.info("Inserted into process_portal_log_tmp"); + + stmt.close(); + } + + public void portalStats() throws SQLException { + Connection con = ConnectDB.getHiveConnection(); + Statement stmt = con.createStatement(); + con.setAutoCommit(false); + +// Original queries where of the style +// +// SELECT DISTINCT source, id_visit, country, action, url, roid.oid, 'oaItem', `timestamp`, referrer_name, agent +// FROM usagestats_20200907.process_portal_log_tmp2, +// openaire_prod_stats_20200821.result_oids roid +// WHERE entity_id IS NOT null AND entity_id=roid.oid AND roid.oid IS NOT null +// +// The following query is an example of how queries should be +// +// +// INSERT INTO usagestats_20200907.piwiklogtmp +// SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent +// FROM usagestats_20200907.process_portal_log_tmp +// WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id +// IN (SELECT roid.oid FROM openaire_prod_stats_20200821.result_oids roid WHERE roid.oid IS NOT NULL); +// +// We should consider if we would like the queries to be as the following +// +// INSERT INTO usagestats_20200907.piwiklogtmp +// SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent +// FROM usagestats_20200907.process_portal_log_tmp +// WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id != '' AND process_portal_log_tmp.entity_id +// IN (SELECT roid.oid FROM openaire_prod_stats_20200821.result_oids roid WHERE roid.oid IS NOT NULL AND +// roid.oid != ''); + + logger.info("PortalStats - Step 1"); + String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent " + + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + ".result_oids roid WHERE roid.id IS NOT NULL)"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("PortalStats - Step 2"); + stmt = con.createStatement(); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'datasource', `timestamp`, referrer_name, agent " + + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + ".datasource_oids roid WHERE roid.id IS NOT NULL)"; + stmt.executeUpdate(sql); + stmt.close(); + + /* + * logger.info("PortalStats - Step 3"); stmt = con.createStatement(); sql = "INSERT INTO " + + * ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + * "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'organization', `timestamp`, referrer_name, agent " + * + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + * "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + * "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + * ".organization_oids roid WHERE roid.id IS NOT NULL)"; // stmt.executeUpdate(sql); stmt.close(); + */ + logger.info("PortalStats - Step 3"); + stmt = con.createStatement(); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'project', `timestamp`, referrer_name, agent " + + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + + ".project_oids roid WHERE roid.id IS NOT NULL)"; + stmt.executeUpdate(sql); + stmt.close(); + + con.close(); + } + + private void cleanOAI() throws Exception { + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Cleaning oai - Step 1"); + stmt = ConnectDB.getHiveConnection().createStatement(); + String sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chlc.min-saude.pt/'," + + "'oai:repositorio.chlc.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.chlc.min-saude.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 2"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hospitaldebraga.pt/'," + + "'oai:repositorio.hospitaldebraga.pt:') WHERE entity_id LIKE 'oai:repositorio.hospitaldebraga.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 3"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipl.pt/'," + + "'oai:repositorio.ipl.pt:') WHERE entity_id LIKE 'oai:repositorio.ipl.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 4"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:bibliotecadigital.ipb.pt/'," + + "'oai:bibliotecadigital.ipb.pt:') WHERE entity_id LIKE 'oai:bibliotecadigital.ipb.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 5"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ismai.pt/'," + + "'oai:repositorio.ismai.pt:') WHERE entity_id LIKE 'oai:repositorio.ismai.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 6"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorioaberto.uab.pt/'," + + "'oai:repositorioaberto.uab.pt:') WHERE entity_id LIKE 'oai:repositorioaberto.uab.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 7"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.uac.pt/'," + + "'oai:repositorio.uac.pt:') WHERE entity_id LIKE 'oai:repositorio.uac.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 8"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.insa.pt/'," + + "'oai:repositorio.insa.pt:') WHERE entity_id LIKE 'oai:repositorio.insa.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 9"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipcb.pt/'," + + "'oai:repositorio.ipcb.pt:') WHERE entity_id LIKE 'oai:repositorio.ipcb.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 10"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ispa.pt/'," + + "'oai:repositorio.ispa.pt:') WHERE entity_id LIKE 'oai:repositorio.ispa.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 11"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chporto.pt/'," + + "'oai:repositorio.chporto.pt:') WHERE entity_id LIKE 'oai:repositorio.chporto.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 12"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ucp.pt/'," + + "'oai:repositorio.ucp.pt:') WHERE entity_id LIKE 'oai:repositorio.ucp.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 13"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:rihuc.huc.min-saude.pt/'," + + "'oai:rihuc.huc.min-saude.pt:') WHERE entity_id LIKE 'oai:rihuc.huc.min-saude.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 14"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipv.pt/'," + + "'oai:repositorio.ipv.pt:') WHERE entity_id LIKE 'oai:repositorio.ipv.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 15"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:www.repository.utl.pt/'," + + "'oai:www.repository.utl.pt:') WHERE entity_id LIKE 'oai:www.repository.utl.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 16"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:run.unl.pt/'," + + "'oai:run.unl.pt:') WHERE entity_id LIKE 'oai:run.unl.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 17"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:sapientia.ualg.pt/'," + + "'oai:sapientia.ualg.pt:') WHERE entity_id LIKE 'oai:sapientia.ualg.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 18"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipsantarem.pt/'," + + "'oai:repositorio.ipsantarem.pt:') WHERE entity_id LIKE 'oai:repositorio.ipsantarem.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 19"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:arca.igc.gulbenkian.pt/'," + + "'oai:arca.igc.gulbenkian.pt:') WHERE entity_id LIKE 'oai:arca.igc.gulbenkian.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 20"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:ubibliorum.ubi.pt/'," + + "'oai:ubibliorum.ubi.pt:') WHERE entity_id LIKE 'oai:ubibliorum.ubi.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 21"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:digituma.uma.pt/'," + + "'oai:digituma.uma.pt:') WHERE entity_id LIKE 'oai:digituma.uma.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 22"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ul.pt/'," + + "'oai:repositorio.ul.pt:') WHERE entity_id LIKE 'oai:repositorio.ul.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 23"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hff.min-saude.pt/'," + + "'oai:repositorio.hff.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.hff.min-saude.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 24"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorium.sdum.uminho.pt/'," + + "'oai:repositorium.sdum.uminho.pt:') WHERE entity_id LIKE 'oai:repositorium.sdum.uminho.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 25"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:recipp.ipp.pt/'," + + "'oai:recipp.ipp.pt:') WHERE entity_id LIKE 'oai:recipp.ipp.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 26"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:bdigital.ufp.pt/'," + + "'oai:bdigital.ufp.pt:') WHERE entity_id LIKE 'oai:bdigital.ufp.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 27"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.lneg.pt/'," + + "'oai:repositorio.lneg.pt:') WHERE entity_id LIKE 'oai:repositorio.lneg.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 28"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:iconline.ipleiria.pt/'," + + "'oai:iconline.ipleiria.pt:') WHERE entity_id LIKE 'oai:iconline.ipleiria.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Step 29"); + stmt = ConnectDB.getHiveConnection().createStatement(); + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:comum.rcaap.pt/'," + + "'oai:comum.rcaap.pt:') WHERE entity_id LIKE 'oai:comum.rcaap.pt/%'"; + stmt.executeUpdate(sql); + stmt.close(); + + logger.info("Cleaning oai - Done, closing connection"); + ConnectDB.getHiveConnection().close(); + } + + private String processPortalURL(String url) { + + if (url.indexOf("explore.openaire.eu") > 0) { + try { + url = URLDecoder.decode(url, "UTF-8"); + } catch (Exception e) { + logger.info("Error when decoding the following URL: " + url); + } + if (url.indexOf("datasourceId=") > 0 && url.substring(url.indexOf("datasourceId=") + 13).length() >= 46) { + url = "datasource|" + + url.substring(url.indexOf("datasourceId=") + 13, url.indexOf("datasourceId=") + 59); + } else if (url.indexOf("datasource=") > 0 + && url.substring(url.indexOf("datasource=") + 11).length() >= 46) { + url = "datasource|" + url.substring(url.indexOf("datasource=") + 11, url.indexOf("datasource=") + 57); + } else if (url.indexOf("datasourceFilter=") > 0 + && url.substring(url.indexOf("datasourceFilter=") + 17).length() >= 46) { + url = "datasource|" + + url.substring(url.indexOf("datasourceFilter=") + 17, url.indexOf("datasourceFilter=") + 63); + } else if (url.indexOf("articleId=") > 0 && url.substring(url.indexOf("articleId=") + 10).length() >= 46) { + url = "result|" + url.substring(url.indexOf("articleId=") + 10, url.indexOf("articleId=") + 56); + } else if (url.indexOf("datasetId=") > 0 && url.substring(url.indexOf("datasetId=") + 10).length() >= 46) { + url = "result|" + url.substring(url.indexOf("datasetId=") + 10, url.indexOf("datasetId=") + 56); + } else if (url.indexOf("projectId=") > 0 && url.substring(url.indexOf("projectId=") + 10).length() >= 46 + && !url.contains("oai:dnet:corda")) { + url = "project|" + url.substring(url.indexOf("projectId=") + 10, url.indexOf("projectId=") + 56); + } else if (url.indexOf("organizationId=") > 0 + && url.substring(url.indexOf("organizationId=") + 15).length() >= 46) { + url = "organization|" + + url.substring(url.indexOf("organizationId=") + 15, url.indexOf("organizationId=") + 61); + } else { + url = ""; + } + } else { + url = ""; + } + + return url; + } + + private void updateProdTables() throws SQLException { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Inserting data to piwiklog"); + String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklog " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; + stmt.executeUpdate(sql); + + logger.info("Inserting data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp"; + stmt.executeUpdate(sql); + + logger.info("Inserting data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp"; + stmt.executeUpdate(sql); + + logger.info("Inserting data to pageviews_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats_tmp"; + stmt.executeUpdate(sql); + + logger.info("Creating usage_stats table"); + String createUsageStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats " + + "AS SELECT coalesce(ds.source, vs.source) as source, " + + "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + + "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + + "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + + "coalesce(ds.openaire, 0) as openaire_downloads, " + + "coalesce(vs.openaire, 0) as openaire_views " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats AS ds FULL OUTER JOIN " + + ConnectDB.getUsageStatsDBSchema() + ".views_stats AS vs ON ds.source=vs.source " + + "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; + stmt.executeUpdate(createUsageStats); + logger.info("Created usage_stats table"); + + + /* + * logger.info("Dropping table views_stats_tmp"); sql = "DROP TABLE IF EXISTS " + + * ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp"; stmt.executeUpdate(sql); + * logger.info("Dropping table downloads_stats_tmp"); sql = "DROP TABLE IF EXISTS " + + * ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp"; stmt.executeUpdate(sql); + * logger.info("Dropping table pageviews_stats_tmp"); sql = "DROP TABLE IF EXISTS " + + * ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats_tmp"; stmt.executeUpdate(sql); + * logger.info("Dropping table process_portal_log_tmp"); sql = "DROP TABLE IF EXISTS " + + * ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp"; stmt.executeUpdate(sql); + */ + stmt.close(); + ConnectDB.getHiveConnection().close(); + + } + + private ArrayList listHdfsDir(String dir) throws Exception { + + FileSystem hdfs = FileSystem.get(new Configuration()); + RemoteIterator Files; + ArrayList fileNames = new ArrayList<>(); + + try { + Path exportPath = new Path(hdfs.getUri() + dir); + Files = hdfs.listFiles(exportPath, false); + while (Files.hasNext()) { + String fileName = Files.next().getPath().toString(); + fileNames.add(fileName); + } + + hdfs.close(); + } catch (Exception e) { + logger.error("HDFS file path with exported data does not exist : " + new Path(hdfs.getUri() + logPath)); + throw new Exception("HDFS file path with exported data does not exist : " + logPath, e); + } + + return fileNames; + } + + private String readHDFSFile(String filename) throws Exception { + String result; + try { + + FileSystem fs = FileSystem.get(new Configuration()); + // log.info("reading file : " + filename); + + BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(new Path(filename)))); + + StringBuilder sb = new StringBuilder(); + String line = br.readLine(); + + while (line != null) { + if (!line.equals("[]")) { + sb.append(line); + } + // sb.append(line); + line = br.readLine(); + } + result = sb.toString().replace("][{\"idSite\"", ",{\"idSite\""); + if (result.equals("")) { + result = "[]"; + } + + // fs.close(); + } catch (Exception e) { + logger.error(e.getMessage()); + throw new Exception(e); + } + + return result; + } + + private Connection getConnection() throws SQLException { + return ConnectDB.getHiveConnection(); + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ReadCounterRobotsList.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ReadCounterRobotsList.java new file mode 100644 index 000000000..6f020daa0 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ReadCounterRobotsList.java @@ -0,0 +1,54 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +/** + * @author D. Pierrakos, S. Zoupanos + */ +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.net.MalformedURLException; +import java.net.URL; +import java.nio.charset.Charset; +import java.util.ArrayList; + +import org.json.JSONException; +import org.json.simple.JSONArray; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; + +public class ReadCounterRobotsList { + + private ArrayList robotsPatterns = new ArrayList(); + private String COUNTER_ROBOTS_URL; + + public ReadCounterRobotsList(String url) throws IOException, JSONException, ParseException { + COUNTER_ROBOTS_URL = url; + robotsPatterns = readRobotsPartners(COUNTER_ROBOTS_URL); + } + + private ArrayList readRobotsPartners(String url) throws MalformedURLException, IOException, ParseException { + InputStream is = new URL(url).openStream(); + JSONParser parser = new JSONParser(); + BufferedReader reader = new BufferedReader(new InputStreamReader(is, Charset.forName("ISO-8859-1"))); + JSONArray jsonArray = (JSONArray) parser.parse(reader); + for (Object aJsonArray : jsonArray) { + org.json.simple.JSONObject jsonObjectRow = (org.json.simple.JSONObject) aJsonArray; + robotsPatterns.add(jsonObjectRow.get("pattern").toString().replace("\\", "\\\\")); + } + return robotsPatterns; + } + + public ArrayList getRobotsPatterns() { + return robotsPatterns; + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java new file mode 100644 index 000000000..54ed286cb --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java @@ -0,0 +1,575 @@ +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.*; +// import java.io.BufferedReader; +// import java.io.InputStreamReader; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class SarcStats { + + private Statement stmtHive = null; + private Statement stmtImpala = null; + + private static final Logger logger = LoggerFactory.getLogger(SarcStats.class); + + public SarcStats() throws Exception { +// createTables(); + } + + private void createTables() throws Exception { + try { + + stmtHive = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilog(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; + stmtHive.executeUpdate(sqlCreateTableSushiLog); + + // String sqlCopyPublicSushiLog="INSERT INTO sushilog SELECT * FROM public.sushilog;"; + // stmt.executeUpdate(sqlCopyPublicSushiLog); + String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " + + " ON INSERT TO sushilog " + + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," + + "sushilog.rid, sushilog.date " + + "FROM sushilog " + + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; + stmtHive.executeUpdate(sqlcreateRuleSushiLog); + String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; + stmtHive.executeUpdate(createSushiIndex); + + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + + public void reCreateLogDirs() throws IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); + dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathArray), true); + + logger.info("Deleting sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); + dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathNonArray), true); + + logger.info("Creating sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); + dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathArray)); + + logger.info("Creating sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); + dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathNonArray)); + } + + public void processSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); + + logger.info("Dropping sarc_sushilogtmp_json_array table"); + String drop_sarc_sushilogtmp_json_array = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array"; + stmt.executeUpdate(drop_sarc_sushilogtmp_json_array); + logger.info("Dropped sarc_sushilogtmp_json_array table"); + + logger.info("Creating sarc_sushilogtmp_json_array table"); + String create_sarc_sushilogtmp_json_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array(\n" + + " `ItemIdentifier` ARRAY<\n" + + " struct<\n" + + " `Type`: STRING,\n" + + " `Value`: STRING\n" + + " >\n" + + " >,\n" + + " `ItemPerformance` struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >\n" + + ")" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + sarcsReportPathArray + "/'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_sarc_sushilogtmp_json_array); + logger.info("Created sarc_sushilogtmp_json_array table"); + + logger.info("Dropping sarc_sushilogtmp_json_non_array table"); + String drop_sarc_sushilogtmp_json_non_array = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(drop_sarc_sushilogtmp_json_non_array); + logger.info("Dropped sarc_sushilogtmp_json_non_array table"); + + logger.info("Creating sarc_sushilogtmp_json_non_array table"); + String create_sarc_sushilogtmp_json_non_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array (\n" + + " `ItemIdentifier` struct<\n" + + " `Type`: STRING,\n" + + " `Value`: STRING\n" + + " >,\n" + + " `ItemPerformance` struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >" + + ")" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + sarcsReportPathNonArray + "/'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_sarc_sushilogtmp_json_non_array); + logger.info("Created sarc_sushilogtmp_json_non_array table"); + + logger.info("Creating sarc_sushilogtmp table"); + String create_sarc_sushilogtmp = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp(source STRING, repository STRING, " + + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " + + "tblproperties('transactional'='true')"; + stmt.executeUpdate(create_sarc_sushilogtmp); + logger.info("Created sarc_sushilogtmp table"); + + logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); + String insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + + " `ItemIdent`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array " + + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + + "WHERE `ItemIdent`.`Type`='DOI'"; + stmt.executeUpdate(insert_sarc_sushilogtmp); + logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); + + logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); + insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + + "`ItemIdentifier`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(insert_sarc_sushilogtmp); + logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); + + ConnectDB.getHiveConnection().close(); + } + + public void getAndProcessSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating sushilog table"); + String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog " + + "(`source` string, " + + "`repository` string, " + + "`rid` string, " + + "`date` string, " + + "`metric_type` string, " + + "`count` int)"; + stmt.executeUpdate(createSushilog); + logger.info("Created sushilog table"); + + logger.info("Dropping sarc_sushilogtmp table"); + String drop_sarc_sushilogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp"; + stmt.executeUpdate(drop_sarc_sushilogtmp); + logger.info("Dropped sarc_sushilogtmp table"); + ConnectDB.getHiveConnection().close(); + + List issnAndUrls = new ArrayList(); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/motricidade/sushiLite/v1_7/", "1646-107X" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/antropologicas/sushiLite/v1_7/", "0873-819X" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/interaccoes/sushiLite/v1_7/", "1646-2335" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/cct/sushiLite/v1_7/", "2182-3030" + }); + issnAndUrls.add(new String[]{ + "https://actapediatrica.spp.pt/sushiLite/v1_7/", "0873-9781" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/sociologiapp/sushiLite/v1_7/", "0873-6529" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/finisterra/sushiLite/v1_7/", "0430-5027" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/sisyphus/sushiLite/v1_7/", "2182-8474" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/anestesiologia/sushiLite/v1_7/", "0871-6099" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/rpe/sushiLite/v1_7/", "0871-9187" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/psilogos/sushiLite/v1_7/", "1646-091X" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/juridica/sushiLite/v1_7/", "2183-5799" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/ecr/sushiLite/v1_7/", "1647-2098" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/nascercrescer/sushiLite/v1_7/", "0872-0754" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/cea/sushiLite/v1_7/", "1645-3794" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/proelium/sushiLite/v1_7/", "1645-8826" + }); + issnAndUrls.add(new String[]{ + "https://revistas.rcaap.pt/millenium/sushiLite/v1_7/", "0873-3015" + }); + + if (ExecuteWorkflow.sarcNumberOfIssnToDownload > 0 + && ExecuteWorkflow.sarcNumberOfIssnToDownload <= issnAndUrls.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.sarcNumberOfIssnToDownload); + issnAndUrls = issnAndUrls.subList(0, ExecuteWorkflow.sarcNumberOfIssnToDownload); + } + + logger.info("(getAndProcessSarc) Downloading the followins opendoars: " + issnAndUrls); + + for (String[] issnAndUrl : issnAndUrls) { + logger.info("Now working on ISSN: " + issnAndUrl[1]); + getARReport(sarcsReportPathArray, sarcsReportPathNonArray, issnAndUrl[0], issnAndUrl[1]); + } + + } + + public void finalizeSarcStats() throws Exception { + stmtHive = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + stmtImpala = ConnectDB.getImpalaConnection().createStatement(); + + logger.info("Creating downloads_stats table_tmp"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats_tmp " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmtHive.executeUpdate(createDownloadsStats); + logger.info("Created downloads_stats_tmp table"); + + logger.info("Dropping sarc_sushilogtmp_impala table"); + String drop_sarc_sushilogtmp_impala = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_impala"; + stmtHive.executeUpdate(drop_sarc_sushilogtmp_impala); + logger.info("Dropped sarc_sushilogtmp_impala table"); + + logger.info("Creating sarc_sushilogtmp_impala, a table readable by impala"); + String createSarcSushilogtmpImpala = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_impala " + + "STORED AS PARQUET AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; + stmtHive.executeUpdate(createSarcSushilogtmpImpala); + logger.info("Created sarc_sushilogtmp_impala"); + + logger.info("Making sarc_sushilogtmp visible to impala"); + String invalidateMetadata = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_impala;"; + stmtImpala.executeUpdate(invalidateMetadata); + + logger.info("Dropping downloads_stats_impala table"); + String drop_downloads_stats_impala = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats_impala"; + stmtHive.executeUpdate(drop_downloads_stats_impala); + logger.info("Dropped downloads_stats_impala table"); + + logger.info("Making downloads_stats_impala deletion visible to impala"); + try { + String invalidateMetadataDownloadsStatsImpala = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats_impala;"; + stmtImpala.executeUpdate(invalidateMetadataDownloadsStatsImpala); + } catch (SQLException sqle) { + } + + // We run the following query in Impala because it is faster + logger.info("Creating downloads_stats_impala"); + String createDownloadsStatsImpala = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats_impala AS " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(CAST(YEAR(`date`) AS STRING), '/', " + + "LPAD(CAST(MONTH(`date`) AS STRING), 2, '0')) AS `date`, s.count, '0' " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_impala s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".result_pids ro " + + "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND d.id like CONCAT('%', 'sarcservicod', '%') " + + "AND s.rid=ro.pid AND ro.type='Digital Object Identifier' AND s.metric_type='ft_total' AND s.source='SARC-OJS'"; + stmtImpala.executeUpdate(createDownloadsStatsImpala); + logger.info("Creating downloads_stats_impala"); + + // Insert into downloads_stats + logger.info("Inserting data from downloads_stats_impala into downloads_stats_tmp"); + String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats_tmp SELECT * " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_impala"; + stmtHive.executeUpdate(insertDStats); + logger.info("Inserted into downloads_stats_tmp"); + + logger.info("Creating sushilog table"); + String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog " + + "(`source` string, " + + "`repository_id` string, " + + "`rid` string, " + + "`date` string, " + + "`metric_type` string, " + + "`count` int)"; + stmtHive.executeUpdate(createSushilog); + logger.info("Created sushilog table"); + + // Insert into sushilog + logger.info("Inserting into sushilog"); + String insertSushiLog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog SELECT * " + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; + stmtHive.executeUpdate(insertSushiLog); + logger.info("Inserted into sushilog"); + + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + } + + public void getARReport(String sarcsReportPathArray, String sarcsReportPathNonArray, + String url, String issn) throws Exception { + logger.info("Processing SARC! issn: " + issn + " with url: " + url); + ConnectDB.getHiveConnection().setAutoCommit(false); + + SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getARReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); + + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("(getARReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); + + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); + st.setString(1, issn); + ResultSet rs_date = st.executeQuery(); + Date dateMax = null; + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); + + // Creating the needed configuration for the correct storing of data + Configuration config = new Configuration(); + config.addResource(new Path("/etc/hadoop/conf/core-site.xml")); + config.addResource(new Path("/etc/hadoop/conf/hdfs-site.xml")); + config + .set( + "fs.hdfs.impl", + org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + config + .set( + "fs.file.impl", + org.apache.hadoop.fs.LocalFileSystem.class.getName()); + FileSystem dfs = FileSystem.get(config); + + if (dateMax != null && start.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + issn); + } else { + + while (start.before(end)) { + String reportUrl = url + "GetReport/?Report=AR1&Format=json&BeginDate=" + + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()); + start.add(Calendar.MONTH, 1); + + logger.info("(getARReport) Getting report: " + reportUrl); + String text = getJson(reportUrl); + if (text == null) { + continue; + } + + JSONParser parser = new JSONParser(); + JSONObject jsonObject = null; + try { + jsonObject = (JSONObject) parser.parse(text); + } // if there is a parsing error continue with the next url + catch (ParseException pe) { + continue; + } + + jsonObject = (JSONObject) jsonObject.get("sc:ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("sc:Report"); + if (jsonObject == null) { + continue; + } + jsonObject = (JSONObject) jsonObject.get("c:Report"); + jsonObject = (JSONObject) jsonObject.get("c:Customer"); + Object obj = jsonObject.get("c:ReportItems"); + JSONArray jsonArray = new JSONArray(); + if (obj instanceof JSONObject) { + jsonArray.add(obj); + } else { + jsonArray = (JSONArray) obj; + // jsonArray = (JSONArray) jsonObject.get("c:ReportItems"); + } + if (jsonArray == null) { + continue; + } + + // Creating the file in the filesystem for the ItemIdentifier as array object + String filePathArray = sarcsReportPathArray + "/SarcsARReport_" + issn + "_" + + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePathArray); + FSDataOutputStream finArray = dfs.create(new Path(filePathArray), true); + + // Creating the file in the filesystem for the ItemIdentifier as array object + String filePathNonArray = sarcsReportPathNonArray + "/SarcsARReport_" + issn + "_" + + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePathNonArray); + FSDataOutputStream finNonArray = dfs.create(new Path(filePathNonArray), true); + + for (Object aJsonArray : jsonArray) { + + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + renameKeysRecursively(":", jsonObjectRow); + + if (jsonObjectRow.get("ItemIdentifier") instanceof JSONObject) { + finNonArray.write(jsonObjectRow.toJSONString().getBytes()); + finNonArray.writeChar('\n'); + } else { + finArray.write(jsonObjectRow.toJSONString().getBytes()); + finArray.writeChar('\n'); + } + } + + finArray.close(); + finNonArray.close(); + + // Check the file size and if it is too big, delete it + File fileArray = new File(filePathArray); + if (fileArray.length() == 0) + fileArray.delete(); + File fileNonArray = new File(filePathNonArray); + if (fileNonArray.length() == 0) + fileNonArray.delete(); + + } + + dfs.close(); + } + //ConnectDB.getHiveConnection().close(); + } + + private void renameKeysRecursively(String delimiter, JSONArray givenJsonObj) throws Exception { + for (Object jjval : givenJsonObj) { + if (jjval instanceof JSONArray) { + renameKeysRecursively(delimiter, (JSONArray) jjval); + } else if (jjval instanceof JSONObject) { + renameKeysRecursively(delimiter, (JSONObject) jjval); + } // All other types of vals + else + ; + } + } + + private void renameKeysRecursively(String delimiter, JSONObject givenJsonObj) throws Exception { + Set jkeys = new HashSet(givenJsonObj.keySet()); + for (String jkey : jkeys) { + + String[] splitArray = jkey.split(delimiter); + String newJkey = splitArray[splitArray.length - 1]; + + Object jval = givenJsonObj.get(jkey); + givenJsonObj.remove(jkey); + givenJsonObj.put(newJkey, jval); + + if (jval instanceof JSONObject) { + renameKeysRecursively(delimiter, (JSONObject) jval); + } + + if (jval instanceof JSONArray) { + renameKeysRecursively(delimiter, (JSONArray) jval); + } + } + } + + private String getJson(String url) throws Exception { + // String cred=username+":"+password; + // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + response.append("\n"); + } + } + return response.toString(); + } catch (Exception e) { + + // Logging error and silently continuing + logger.error("Failed to get URL: " + e); + System.out.println("Failed to get URL: " + e); +// return null; +// throw new Exception("Failed to get URL: " + e.toString(), e); + } + return ""; + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java new file mode 100644 index 000000000..c4ee7d63c --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java @@ -0,0 +1,186 @@ + +package eu.dnetlib.oa.graph.usagerawdata.export; + +import java.io.IOException; +import java.sql.SQLException; +import java.sql.Statement; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Main class for downloading and processing Usage statistics + * + * @author D. Pierrakos, S. Zoupanos + */ +public class UsageStatsExporter { + + public UsageStatsExporter() { + + } + + private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); + + private void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); + + logger.info("Deleting repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.delete(new Path(ExecuteWorkflow.repoLogPath), true); + + logger.info("Deleting portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.delete(new Path(ExecuteWorkflow.portalLogPath), true); + + logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); + + logger.info("Creating repoLog directory: " + ExecuteWorkflow.repoLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.repoLogPath)); + + logger.info("Creating portalLog directory: " + ExecuteWorkflow.portalLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.portalLogPath)); + + logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); + } + + public void export() throws Exception { + + logger.info("Initialising DB properties"); + ConnectDB.init(); + +// runImpalaQuery(); + + PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); + + logger.info("Re-creating database and tables"); + if (ExecuteWorkflow.recreateDbAndTables) + piwikstatsdb.recreateDBAndTables(); + ; + + logger.info("Initializing the download logs module"); + PiwikDownloadLogs piwd = new PiwikDownloadLogs(ExecuteWorkflow.matomoBaseURL, ExecuteWorkflow.matomoAuthToken); + + if (ExecuteWorkflow.piwikEmptyDirs) { + logger.info("Recreating Piwik log directories"); + piwikstatsdb.reCreateLogDirs(); + } + + // Downloading piwik logs (also managing directory creation) + if (ExecuteWorkflow.downloadPiwikLogs) { + logger.info("Downloading piwik logs"); + piwd + .GetOpenAIRELogs( + ExecuteWorkflow.repoLogPath, + ExecuteWorkflow.portalLogPath, ExecuteWorkflow.portalMatomoID); + } + logger.info("Downloaded piwik logs"); +/* + // Create DB tables, insert/update statistics + String cRobotsUrl = "https://raw.githubusercontent.com/atmire/COUNTER-Robots/master/COUNTER_Robots_list.json"; + piwikstatsdb.setCounterRobotsURL(cRobotsUrl); + + if (ExecuteWorkflow.processPiwikLogs) { + logger.info("Processing logs"); + piwikstatsdb.processLogs(); + } +*/ + logger.info("Creating LaReferencia tables"); + LaReferenciaDownloadLogs lrf = new LaReferenciaDownloadLogs(ExecuteWorkflow.lareferenciaBaseURL, + ExecuteWorkflow.lareferenciaAuthToken); + + if (ExecuteWorkflow.laReferenciaEmptyDirs) { + logger.info("Recreating LaReferencia log directories"); + lrf.reCreateLogDirs(); + } + + if (ExecuteWorkflow.downloadLaReferenciaLogs) { + logger.info("Downloading LaReferencia logs"); + lrf.GetLaReferenciaRepos(ExecuteWorkflow.lareferenciaLogPath); + logger.info("Downloaded LaReferencia logs"); + } +/* + LaReferenciaStats lastats = new LaReferenciaStats(ExecuteWorkflow.lareferenciaLogPath); + + if (ExecuteWorkflow.processLaReferenciaLogs) { + logger.info("Processing LaReferencia logs"); + lastats.processLogs(); + logger.info("LaReferencia logs done"); + } +*/ + IrusStats irusstats = new IrusStats(ExecuteWorkflow.irusUKBaseURL); + if (ExecuteWorkflow.irusCreateTablesEmptyDirs) { + logger.info("Creating Irus Stats tables"); + irusstats.createTables(); + logger.info("Created Irus Stats tables"); + + logger.info("Re-create log dirs"); + irusstats.reCreateLogDirs(); + logger.info("Re-created log dirs"); + } + + if (ExecuteWorkflow.irusDownloadReports) { + irusstats.getIrusRRReport(ExecuteWorkflow.irusUKReportPath); + } +/* + if (ExecuteWorkflow.irusProcessStats) { + irusstats.processIrusStats(); + logger.info("Irus done"); + } +*/ + SarcStats sarcStats = new SarcStats(); + if (ExecuteWorkflow.sarcCreateTablesEmptyDirs) { + sarcStats.reCreateLogDirs(); + } + if (ExecuteWorkflow.sarcDownloadReports) { + sarcStats.getAndProcessSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); + } +/* + if (ExecuteWorkflow.sarcProcessStats) { + sarcStats.processSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); + sarcStats.finalizeSarcStats(); + } + logger.info("Sarc done"); +*/ + +/* + // finalize usagestats + if (ExecuteWorkflow.finalizeStats) { + piwikstatsdb.finalizeStats(); + logger.info("Finalized stats"); + } +*/ + +/* + // Make the tables available to Impala + if (ExecuteWorkflow.finalTablesVisibleToImpala) { + logger.info("Making tables visible to Impala"); + invalidateMetadata(); + } +*/ + logger.info("End"); + } + + private void invalidateMetadata() throws SQLException { + Statement stmt = null; + + stmt = ConnectDB.getImpalaConnection().createStatement(); + + String sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + } +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json new file mode 100644 index 000000000..988c23b48 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json @@ -0,0 +1,231 @@ +[ + { + "paramName": "mat", + "paramLongName": "matomoAuthToken", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "mbu", + "paramLongName": "matomoBaseURL", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + }, + { + "paramName": "rlp", + "paramLongName": "repoLogPath", + "paramDescription": "nameNode of the source cluster", + "paramRequired": true + }, + { + "paramName": "plp", + "paramLongName": "portalLogPath", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "pmi", + "paramLongName": "portalMatomoID", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "iukbuw", + "paramLongName": "irusUKBaseURL", + "paramDescription": "working directory", + "paramRequired": true + }, + { + "paramName": "iukrp", + "paramLongName": "irusUKReportPath", + "paramDescription": "maximum number of map tasks used in the distcp process", + "paramRequired": true + }, + { + "paramName": "srpa", + "paramLongName": "sarcsReportPathArray", + "paramDescription": "memory for distcp action copying actionsets from remote cluster", + "paramRequired": true + }, + { + "paramName": "srpna", + "paramLongName": "sarcsReportPathNonArray", + "paramDescription": "timeout for distcp copying actions from remote cluster", + "paramRequired": true + }, + { + "paramName": "llp", + "paramLongName": "lareferenciaLogPath", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "lbu", + "paramLongName": "lareferenciaBaseURL", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "lat", + "paramLongName": "lareferenciaAuthToken", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbhu", + "paramLongName": "dbHiveUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbiu", + "paramLongName": "dbImpalaUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "usdbs", + "paramLongName": "usageStatsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "sdbs", + "paramLongName": "statsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "rdbt", + "paramLongName": "recreateDbAndTables", + "paramDescription": "Re-create database and initial tables?", + "paramRequired": true + }, + { + "paramName": "pwed", + "paramLongName": "piwikEmptyDirs", + "paramDescription": "Empty piwik directories?", + "paramRequired": true + }, + { + "paramName": "ppwl", + "paramLongName": "processPiwikLogs", + "paramDescription": "Process the piwiklogs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "dpwl", + "paramLongName": "downloadPiwikLogs", + "paramDescription": "download piwik logs?", + "paramRequired": true + }, + { + "paramName": "slp", + "paramLongName": "startingLogPeriod", + "paramDescription": "Starting log period", + "paramRequired": true + }, + { + "paramName": "elp", + "paramLongName": "endingLogPeriod", + "paramDescription": "Ending log period", + "paramRequired": true + }, + { + "paramName": "npidd", + "paramLongName": "numberOfPiwikIdsToDownload", + "paramDescription": "Limit the number of the downloaded piwikids to the first numberOfPiwikIdsToDownload", + "paramRequired": true + }, + { + "paramName": "nsidd", + "paramLongName": "numberOfSiteIdsToDownload", + "paramDescription": "Limit the number of the downloaded siteids (La Referencia logs) to the first numberOfSiteIdsToDownload", + "paramRequired": true + }, + { + "paramName": "lerd", + "paramLongName": "laReferenciaEmptyDirs", + "paramDescription": "Empty LaReferencia directories?", + "paramRequired": true + }, + { + "paramName": "plrl", + "paramLongName": "processLaReferenciaLogs", + "paramDescription": "Process the La Referencia logs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "dlrl", + "paramLongName": "downloadLaReferenciaLogs", + "paramDescription": "download La Referencia logs?", + "paramRequired": true + }, + { + "paramName": "icted", + "paramLongName": "irusCreateTablesEmptyDirs", + "paramDescription": "Irus section: Create tables and empty JSON directories?", + "paramRequired": true + }, + { + "paramName": "idr", + "paramLongName": "irusDownloadReports", + "paramDescription": "Irus section: Download reports?", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "irusProcessStats", + "paramDescription": "Irus section: Process stats?", + "paramRequired": true + }, + { + "paramName": "inod", + "paramLongName": "irusNumberOfOpendoarsToDownload", + "paramDescription": "Limit the number of the downloaded Opendoars (Irus) to the first irusNumberOfOpendoarsToDownload", + "paramRequired": true + }, + { + "paramName": "icted", + "paramLongName": "sarcCreateTablesEmptyDirs", + "paramDescription": "Sarc section: Create tables and empty JSON directories?", + "paramRequired": true + }, + { + "paramName": "idr", + "paramLongName": "sarcDownloadReports", + "paramDescription": "Sarc section: Download reports?", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "sarcProcessStats", + "paramDescription": "Sarc section: Process stats?", + "paramRequired": true + }, + { + "paramName": "inod", + "paramLongName": "sarcNumberOfIssnToDownload", + "paramDescription": "Limit the number of the downloaded ISSN (Sarc) to the first sarcNumberOfIssnToDownload", + "paramRequired": true + }, + + { + "paramName": "fs", + "paramLongName": "finalizeStats", + "paramDescription": "Create the usage_stats table?", + "paramRequired": true + }, + { + "paramName": "ftvi", + "paramLongName": "finalTablesVisibleToImpala", + "paramDescription": "Make the usage_stats, views_stats and downloads_stats tables visible to Impala", + "paramRequired": true + }, + { + "paramName": "nodt", + "paramLongName": "numberOfDownloadThreads", + "paramDescription": "Number of download threads", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/config-default.xml b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/config-default.xml new file mode 100644 index 000000000..b5c807378 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + jobTracker + ${jobTracker} + + + nameNode + ${nameNode} + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1 + + + impalaJdbcUrl + jdbc:hive2://iis-cdh5-test-gw.ocean.icm.edu.pl:21050/;auth=noSasl; + + + oozie.wf.workflow.notification.url + {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status + + + oozie.use.system.libpath + true + + diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml new file mode 100644 index 000000000..a6600516d --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml @@ -0,0 +1,90 @@ + + + + hiveMetastoreUris + Hive server metastore URIs + + + hiveJdbcUrl + Hive server jdbc url + + + impalaJdbcUrl + Impala server jdbc url + + + + + ${jobTracker} + ${nameNode} + + + hive.metastore.uris + ${hiveMetastoreUris} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + eu.dnetlib.oa.graph.usagerawdata.export.ExecuteWorkflow + --matomoAuthToken${matomoAuthToken} + --matomoBaseURL${matomoBaseURL} + --repoLogPath${repoLogPath} + --portalLogPath${portalLogPath} + --portalMatomoID${portalMatomoID} + --irusUKBaseURL${irusUKBaseURL} + --irusUKReportPath${irusUKReportPath} + --sarcsReportPathArray${sarcsReportPathArray} + --sarcsReportPathNonArray${sarcsReportPathNonArray} + --lareferenciaLogPath${lareferenciaLogPath} + --lareferenciaBaseURL${lareferenciaBaseURL} + --lareferenciaAuthToken${lareferenciaAuthToken} + --dbHiveUrl${hiveJdbcUrl} + --dbImpalaUrl${impalaJdbcUrl} + --usageStatsDBSchema${usageStatsDBSchema} + --statsDBSchema${statsDBSchema} + --recreateDbAndTables${recreateDbAndTables} + --piwikEmptyDirs${piwikEmptyDirs} + --downloadPiwikLogs${downloadPiwikLogs} + --processPiwikLogs${processPiwikLogs} + --startingLogPeriod${startingLogPeriod} + --endingLogPeriod${endingLogPeriod} + --numberOfPiwikIdsToDownload${numberOfPiwikIdsToDownload} + --numberOfSiteIdsToDownload${numberOfSiteIdsToDownload} + --laReferenciaEmptyDirs${laReferenciaEmptyDirs} + --downloadLaReferenciaLogs${downloadLaReferenciaLogs} + --processLaReferenciaLogs${processLaReferenciaLogs} + --irusCreateTablesEmptyDirs${irusCreateTablesEmptyDirs} + --irusDownloadReports${irusDownloadReports} + --irusProcessStats${irusProcessStats} + --irusNumberOfOpendoarsToDownload${irusNumberOfOpendoarsToDownload} + --sarcCreateTablesEmptyDirs${sarcCreateTablesEmptyDirs} + --sarcDownloadReports${sarcDownloadReports} + --sarcProcessStats${sarcProcessStats} + --sarcNumberOfIssnToDownload${sarcNumberOfIssnToDownload} + --finalizeStats${finalizeStats} + --finalTablesVisibleToImpala${finalTablesVisibleToImpala} + --numberOfDownloadThreads${numberOfDownloadThreads} + + + + + + + + diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java index 6947381c9..011c90532 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java @@ -174,7 +174,7 @@ public class IrusStats { + "WHERE `ItemIdent`.`Type`= 'OAI'"; stmt.executeUpdate(insertSushilogtmp); logger.info("Inserted to irus_sushilogtmp table"); - + logger.info("Creating downloads_stats table"); String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java index 347d3de21..747b5ce0e 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java @@ -357,6 +357,19 @@ public class LaReferenciaStats { "select * from " + ConnectDB.getUsageStatsDBSchema() + ".la_downloads_stats_tmp"; stmt.executeUpdate(sql); + logger.info("Inserting data to usage_stats from lareferencia"); + sql = "INSERT INTO "+ConnectDB.getUsageStatsDBSchema() + ".usage_stats " + + "SELECT coalesce(ds.source, vs.source) as source, " + + "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + + "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + + "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + + "coalesce(ds.openaire, 0) as openaire_downloads, " + + "coalesce(vs.openaire, 0) as openaire_views " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_downloads_stats_tmp AS ds FULL OUTER JOIN " + + ConnectDB.getUsageStatsDBSchema() + ".la_views_stats_tmp AS vs ON ds.source=vs.source " + + "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; + stmt.executeUpdate(sql); + logger.info("Inserted data to usage_stats from lareferencia"); // sql = "insert into public.downloads_stats select * from la_downloads_stats_tmp;"; // stmt.executeUpdate(sql); diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java index 7a64e48d2..8f7fffa9f 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java @@ -1,4 +1,3 @@ - package eu.dnetlib.oa.graph.usagestats.export; import java.io.*; @@ -31,293 +30,296 @@ import org.slf4j.LoggerFactory; */ public class PiwikDownloadLogs { - private final String piwikUrl; - private Date startDate; - private final String tokenAuth; + private final String piwikUrl; + private Date startDate; + private final String tokenAuth; - /* + /* * The Piwik's API method - */ - private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; - private final String format = "&format=json"; + */ + private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; + private final String format = "&format=json"; - private static final Logger logger = LoggerFactory.getLogger(PiwikDownloadLogs.class); + private static final Logger logger = LoggerFactory.getLogger(PiwikDownloadLogs.class); - public PiwikDownloadLogs(String piwikUrl, String tokenAuth) { - this.piwikUrl = piwikUrl; - this.tokenAuth = tokenAuth; + public PiwikDownloadLogs(String piwikUrl, String tokenAuth) { + this.piwikUrl = piwikUrl; + this.tokenAuth = tokenAuth; - } + } - private String getPiwikLogUrl() { - return "https://" + piwikUrl + "/"; - } + private String getPiwikLogUrl() { + return "https://" + piwikUrl + "/"; + } - private String getJson(String url) throws Exception { - try { - logger.debug("Connecting to download the JSON: " + url); - URL website = new URL(url); - URLConnection connection = website.openConnection(); + private String getJson(String url) throws Exception { + try { + logger.debug("Connecting to download the JSON: " + url); + URL website = new URL(url); + URLConnection connection = website.openConnection(); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); - } - } - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL: " + url + " Exception: " + e); - throw new Exception("Failed to get URL: " + url + " Exception: " + e.toString(), e); - } - } + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + } + } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + url + " Exception: " + e); + throw new Exception("Failed to get URL: " + url + " Exception: " + e.toString(), e); + } + } - class WorkerThread implements Runnable { - private Calendar currDay; - private int siteId; - private String repoLogsPath; - private String portalLogPath; - private String portalMatomoID; + class WorkerThread implements Runnable { - public WorkerThread(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, - String portalMatomoID) throws IOException { - this.currDay = (Calendar) currDay.clone(); - this.siteId = new Integer(siteId); - this.repoLogsPath = new String(repoLogsPath); - this.portalLogPath = new String(portalLogPath); - this.portalMatomoID = new String(portalMatomoID); - } + private Calendar currDay; + private int siteId; + private String repoLogsPath; + private String portalLogPath; + private String portalMatomoID; - public void run() { - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - System.out - .println( - Thread.currentThread().getName() + " (Start) Thread for " - + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + - ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + - ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); - try { - GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + public WorkerThread(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws IOException { + this.currDay = (Calendar) currDay.clone(); + this.siteId = new Integer(siteId); + this.repoLogsPath = new String(repoLogsPath); + this.portalLogPath = new String(portalLogPath); + this.portalMatomoID = new String(portalMatomoID); + } - } catch (Exception e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - System.out - .println( - Thread.currentThread().getName() + " (End) Thread for " - + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + - ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + - ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); - } + public void run() { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + System.out + .println( + Thread.currentThread().getName() + " (Start) Thread for " + + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); + try { + GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); - public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, - String portalMatomoID) throws Exception { - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + System.out + .println( + Thread.currentThread().getName() + " (End) Thread for " + + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); + } - Date date = currDay.getTime(); - logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - String period = "&period=day&date=" + sdf.format(date); - String outFolder = ""; - if (siteId == Integer.parseInt(portalMatomoID)) { - outFolder = portalLogPath; - } else { - outFolder = repoLogsPath; - } + Date date = currDay.getTime(); + logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); - String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format - + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; - String content = ""; + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + if (siteId == Integer.parseInt(portalMatomoID)) { + outFolder = portalLogPath; + } else { + outFolder = repoLogsPath; + } - int i = 0; + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; - JSONParser parser = new JSONParser(); - StringBuffer totalContent = new StringBuffer(); - FileSystem fs = FileSystem.get(new Configuration()); + int i = 0; - do { - int writtenBytes = 0; - String apiUrl = baseApiUrl; + JSONParser parser = new JSONParser(); + StringBuffer totalContent = new StringBuffer(); + FileSystem fs = FileSystem.get(new Configuration()); - if (i > 0) { - apiUrl += "&filter_offset=" + (i * 1000); - } + do { + int writtenBytes = 0; + String apiUrl = baseApiUrl; - content = getJson(apiUrl); - if (content.length() == 0 || content.equals("[]")) - break; + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } - FSDataOutputStream fin = fs - .create( - new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"), - true); - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRaw = (JSONObject) aJsonArray; - byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); - fin.write(jsonObjectRawBytes); - fin.writeChar('\n'); + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } - writtenBytes += jsonObjectRawBytes.length + 1; - } + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"), + true); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); - fin.close(); - System.out - .println( - Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes - + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"); + writtenBytes += jsonObjectRawBytes.length + 1; + } - i++; - } while (true); + fin.close(); + System.out + .println( + Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes + + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"); - fs.close(); - } - } + i++; + } while (true); - public void GetOpenAIRELogs(String repoLogsPath, String portalLogPath, String portalMatomoID) throws Exception { + fs.close(); + } + } - Statement statement = ConnectDB.getHiveConnection().createStatement(); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + public void GetOpenAIRELogs(String repoLogsPath, String portalLogPath, String portalMatomoID) throws Exception { - ResultSet rs = statement - .executeQuery( - "SELECT distinct piwik_id from " + ConnectDB.getStatsDBSchema() - + ".datasource where piwik_id is not null and piwik_id <> 0 order by piwik_id"); + Statement statement = ConnectDB.getHiveConnection().createStatement(); + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - // Getting all the piwikids in a list for logging reasons & limitting the list - // to the max number of piwikids - List piwikIdToVisit = new ArrayList(); + ResultSet rs = statement + .executeQuery( + "SELECT distinct piwik_id from " + ConnectDB.getStatsDBSchema() + + ".datasource where piwik_id is not null and piwik_id <> 0 order by piwik_id"); + + // Getting all the piwikids in a list for logging reasons & limitting the list + // to the max number of piwikids + List piwikIdToVisit = new ArrayList(); while (rs.next()) piwikIdToVisit.add(rs.getInt(1)); - logger.info("Found the following piwikIds for download: " + piwikIdToVisit); + logger.info("Found the following piwikIds for download: " + piwikIdToVisit); - if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 && - ExecuteWorkflow.numberOfPiwikIdsToDownload <= piwikIdToVisit.size()) { - logger.info("Trimming piwikIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); - piwikIdToVisit = piwikIdToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); - } + if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 + && ExecuteWorkflow.numberOfPiwikIdsToDownload <= piwikIdToVisit.size()) { + logger.info("Trimming piwikIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); + piwikIdToVisit = piwikIdToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); + } - logger.info("Downloading from repos with the followins piwikIds: " + piwikIdToVisit); + logger.info("Downloading from repos with the followins piwikIds: " + piwikIdToVisit); + // ExecutorService executor = Executors.newFixedThreadPool(ExecuteWorkflow.numberOfDownloadThreads); + for (int siteId : piwikIdToVisit) { + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("Starting period for log download: " + sdf.format(start.getTime())); - // ExecutorService executor = Executors.newFixedThreadPool(ExecuteWorkflow.numberOfDownloadThreads); - for (int siteId : piwikIdToVisit) { - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("Starting period for log download: " + sdf.format(start.getTime())); + // Setting the ending period (last day of the month) + Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + end.add(Calendar.MONTH, +1); + end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("Ending period for log download: " + sdf.format(end.getTime())); - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("Ending period for log download: " + sdf.format(end.getTime())); + logger.info("Now working on piwikId: " + siteId); - logger.info("Now working on piwikId: " + siteId); + PreparedStatement st = ConnectDB.DB_HIVE_CONNECTION + .prepareStatement( + "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + + ".piwiklog WHERE source=?"); + st.setInt(1, siteId); + Date dateMax = null; + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + logger.info("Found max date: " + rs_date.getString(1) + " for repository " + siteId); - PreparedStatement st = ConnectDB.DB_HIVE_CONNECTION - .prepareStatement( - "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() - + ".piwiklog WHERE source=?"); - st.setInt(1, siteId); - Date dateMax=null; - ResultSet rs_date = st.executeQuery(); - while (rs_date.next()) { - logger.info("Found max date: " + rs_date.getString(1) + " for repository " + siteId); + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - dateMax = sdf.parse(rs_date.getString(1)); - } - } - rs_date.close(); + for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { + // logger.info("Date used " + currDay.toString()); + // Runnable worker = new WorkerThread(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + // executor.execute(worker);// calling execute method of ExecutorService + logger.info("Date used " + currDay.getTime().toString()); - for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { - // logger.info("Date used " + currDay.toString()); - // Runnable worker = new WorkerThread(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); - // executor.execute(worker);// calling execute method of ExecutorService - logger.info("Date used " + currDay.getTime().toString()); + if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding Matomo logs for " + siteId); + } else { + GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + } - if(dateMax!=null && currDay.getTime().compareTo(dateMax)<=0) - logger.info("Date found in logs "+dateMax+ " and not downloanding Matomo logs for "+siteId); - else - GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + } + } + // executor.shutdown(); + // while (!executor.isTerminated()) { + // } + // System.out.println("Finished all threads"); + } - } - } - // executor.shutdown(); - // while (!executor.isTerminated()) { - // } - // System.out.println("Finished all threads"); - } + public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, - String portalMatomoID) throws Exception { - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + Date date = currDay.getTime(); + logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); - Date date = currDay.getTime(); - logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + if (siteId == Integer.parseInt(portalMatomoID)) { + outFolder = portalLogPath; + } else { + outFolder = repoLogsPath; + } - String period = "&period=day&date=" + sdf.format(date); - String outFolder = ""; - if (siteId == Integer.parseInt(portalMatomoID)) { - outFolder = portalLogPath; - } else { - outFolder = repoLogsPath; - } + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; - String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format - + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; - String content = ""; + int i = 0; - int i = 0; + JSONParser parser = new JSONParser(); + StringBuffer totalContent = new StringBuffer(); + FileSystem fs = FileSystem.get(new Configuration()); - JSONParser parser = new JSONParser(); - StringBuffer totalContent = new StringBuffer(); - FileSystem fs = FileSystem.get(new Configuration()); + do { + int writtenBytes = 0; + String apiUrl = baseApiUrl; - do { - int writtenBytes = 0; - String apiUrl = baseApiUrl; + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } - if (i > 0) { - apiUrl += "&filter_offset=" + (i * 1000); - } + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } - content = getJson(apiUrl); - if (content.length() == 0 || content.equals("[]")) - break; + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"), + true); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); - FSDataOutputStream fin = fs - .create( - new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"), - true); - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRaw = (JSONObject) aJsonArray; - byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); - fin.write(jsonObjectRawBytes); - fin.writeChar('\n'); + writtenBytes += jsonObjectRawBytes.length + 1; + } - writtenBytes += jsonObjectRawBytes.length + 1; - } + fin.close(); + System.out + .println( + Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes + + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"); - fin.close(); - System.out - .println( - Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes - + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"); + i++; + } while (true); - i++; - } while (true); - - fs.close(); - } + fs.close(); + } } diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java index 6625c381b..6d5bdfac0 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java @@ -551,17 +551,20 @@ public class PiwikStatsDB { stmt.executeUpdate(createViewsStats); logger.info("Created views_stats table"); - String createUsageStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats " + - "AS SELECT coalesce(ds.source, vs.source) as source, " + + logger.info("Inserting data to usage_stats"); + sql = "INSERT INTO "+ConnectDB.getUsageStatsDBSchema() + ".usage_stats " + + "SELECT coalesce(ds.source, vs.source) as source, " + "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + "coalesce(ds.openaire, 0) as openaire_downloads, " + "coalesce(vs.openaire, 0) as openaire_views " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats AS ds FULL OUTER JOIN " + - ConnectDB.getUsageStatsDBSchema() + ".views_stats AS vs ON ds.source=vs.source " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp AS ds FULL OUTER JOIN " + + ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp AS vs ON ds.source=vs.source " + "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; - stmt.executeUpdate(createUsageStats); + stmt.executeUpdate(sql); + logger.info("Inserted data to usage_stats"); + stmt.close(); ConnectDB.getHiveConnection().close(); @@ -1167,7 +1170,22 @@ public class PiwikStatsDB { "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats_tmp"; stmt.executeUpdate(sql); - /* + logger.info("Creating usage_stats table"); + String createUsageStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats " + + "AS SELECT coalesce(ds.source, vs.source) as source, " + + "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + + "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + + "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + + "coalesce(ds.openaire, 0) as openaire_downloads, " + + "coalesce(vs.openaire, 0) as openaire_views " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats AS ds FULL OUTER JOIN " + + ConnectDB.getUsageStatsDBSchema() + ".views_stats AS vs ON ds.source=vs.source " + + "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; + stmt.executeUpdate(createUsageStats); + logger.info("Created usage_stats table"); + + + /* * logger.info("Dropping table views_stats_tmp"); sql = "DROP TABLE IF EXISTS " + * ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp"; stmt.executeUpdate(sql); * logger.info("Dropping table downloads_stats_tmp"); sql = "DROP TABLE IF EXISTS " + diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java index 71dfc6f61..06e350c9e 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java @@ -286,9 +286,9 @@ public class SarcStats { ConnectDB.getHiveConnection().setAutoCommit(false); stmtImpala = ConnectDB.getImpalaConnection().createStatement(); - logger.info("Creating downloads_stats table"); + logger.info("Creating downloads_stats table_tmp"); String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats " + + ".downloads_stats_tmp " + "(`source` string, " + "`repository_id` string, " + "`result_id` string, " @@ -296,7 +296,7 @@ public class SarcStats { + "`count` bigint, " + "`openaire` bigint)"; stmtHive.executeUpdate(createDownloadsStats); - logger.info("Created downloads_stats table"); + logger.info("Created downloads_stats_tmp table"); logger.info("Dropping sarc_sushilogtmp_impala table"); String drop_sarc_sushilogtmp_impala = "DROP TABLE IF EXISTS " @@ -341,20 +341,19 @@ public class SarcStats { + "LPAD(CAST(MONTH(`date`) AS STRING), 2, '0')) AS `date`, s.count, '0' " + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_impala s, " + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " - + ConnectDB.getStatsDBSchema() + ".datasource_results dr, " + ConnectDB.getStatsDBSchema() + ".result_pids ro " - + "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND dr.id=d.id AND dr.result=ro.id AND " - + "s.rid=ro.pid AND ro.type='Digital Object Identifier' AND metric_type='ft_total' AND s.source='SARC-OJS'"; + + "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND d.id like CONCAT('%', 'sarcservicod', '%') " + + "AND s.rid=ro.pid AND ro.type='Digital Object Identifier' AND s.metric_type='ft_total' AND s.source='SARC-OJS'"; stmtImpala.executeUpdate(createDownloadsStatsImpala); logger.info("Creating downloads_stats_impala"); // Insert into downloads_stats - logger.info("Inserting data from downloads_stats_impala into downloads_stats"); + logger.info("Inserting data from downloads_stats_impala into downloads_stats_tmp"); String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats SELECT * " + + ".downloads_stats_tmp SELECT * " + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_impala"; stmtHive.executeUpdate(insertDStats); - logger.info("Inserted into downloads_stats"); + logger.info("Inserted into downloads_stats_tmp"); logger.info("Creating sushilog table"); String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java index ae901dfa5..405b58bd5 100644 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java +++ b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java @@ -173,7 +173,7 @@ public class UsageStatsExporter { sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; stmt.executeUpdate(sql); - stmt.close(); + stmt.close(); ConnectDB.getHiveConnection().close(); } } From bbcf6b7c8b0e29ae52371f4c5694dc10f5d53c7a Mon Sep 17 00:00:00 2001 From: Dimitris Date: Tue, 17 Nov 2020 08:36:51 +0200 Subject: [PATCH 004/149] Commit 17112020 --- .../usagerawdata/export/ExecuteWorkflow.java | 22 +- .../graph/usagerawdata/export/IrusStats.java | 4 +- .../export/LaReferenciaStats.java | 12 +- .../export/PiwikDownloadLogs.java | 1 + .../usagerawdata/export/PiwikStatsDB.java | 425 +----------------- .../graph/usagerawdata/export/SarcStats.java | 4 +- .../export/UsageStatsExporter.java | 32 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 79 ++++ .../usagestatsbuild/export/ConnectDB.java | 130 ++++++ .../export/ExecuteWorkflow.java | 172 +++++++ .../usagestatsbuild/export/IrusStats.java | 71 +++ .../export/LaReferenciaStats.java | 149 ++++++ .../usagestatsbuild/export/PiwikStatsDB.java | 345 ++++++++++++++ .../usagestatsbuild/export/SarcStats.java | 106 +++++ .../export/UsageStatsExporter.java | 106 +++++ .../export/usagestatsbuild_parameters.json | 237 ++++++++++ .../oozie_app/config-default.xml | 38 ++ .../usagestatsbuild/oozie_app/workflow.xml | 91 ++++ 18 files changed, 1589 insertions(+), 435 deletions(-) create mode 100644 dhp-workflows/dhp-usage-stats-build/pom.xml create mode 100644 dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ConnectDB.java create mode 100644 dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ExecuteWorkflow.java create mode 100644 dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/IrusStats.java create mode 100644 dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/LaReferenciaStats.java create mode 100644 dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/PiwikStatsDB.java create mode 100644 dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/SarcStats.java create mode 100644 dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/UsageStatsExporter.java create mode 100644 dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json create mode 100644 dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java index 774dcf0b7..81e34b3e7 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java @@ -112,13 +112,13 @@ public class ExecuteWorkflow { downloadPiwikLogs = true; else downloadPiwikLogs = false; -/* + if (parser.get("processPiwikLogs").toLowerCase().equals("true")) processPiwikLogs = true; else processPiwikLogs = false; -*/ - String startingLogPeriodStr = parser.get("startingLogPeriod"); + + String startingLogPeriodStr = parser.get("startingLogPeriod"); Date startingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(startingLogPeriodStr); startingLogPeriod = startingLogPeriodStr(startingLogPeriodDate); @@ -138,12 +138,12 @@ public class ExecuteWorkflow { downloadLaReferenciaLogs = true; else downloadLaReferenciaLogs = false; -/* + if (parser.get("processLaReferenciaLogs").toLowerCase().equals("true")) processLaReferenciaLogs = true; else processLaReferenciaLogs = false; -*/ + if (parser.get("irusCreateTablesEmptyDirs").toLowerCase().equals("true")) irusCreateTablesEmptyDirs = true; else @@ -153,13 +153,13 @@ public class ExecuteWorkflow { irusDownloadReports = true; else irusDownloadReports = false; -/* + if (parser.get("irusProcessStats").toLowerCase().equals("true")) irusProcessStats = true; else irusProcessStats = false; irusNumberOfOpendoarsToDownload = Integer.parseInt(parser.get("irusNumberOfOpendoarsToDownload")); -*/ + if (parser.get("sarcCreateTablesEmptyDirs").toLowerCase().equals("true")) sarcCreateTablesEmptyDirs = true; else @@ -169,13 +169,13 @@ public class ExecuteWorkflow { sarcDownloadReports = true; else sarcDownloadReports = false; -/* + if (parser.get("sarcProcessStats").toLowerCase().equals("true")) sarcProcessStats = true; else sarcProcessStats = false; sarcNumberOfIssnToDownload = Integer.parseInt(parser.get("sarcNumberOfIssnToDownload")); -*/ + /* if (parser.get("finalizeStats").toLowerCase().equals("true")) finalizeStats = true; @@ -184,8 +184,8 @@ public class ExecuteWorkflow { if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) finalTablesVisibleToImpala = true; else -*/ finalTablesVisibleToImpala = false; - + finalTablesVisibleToImpala = false; +*/ numberOfDownloadThreads = Integer.parseInt(parser.get("numberOfDownloadThreads")); UsageStatsExporter usagestatsExport = new UsageStatsExporter(); diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java index 090f76ff5..bb8d8565e 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java @@ -174,7 +174,7 @@ public class IrusStats { + "WHERE `ItemIdent`.`Type`= 'OAI'"; stmt.executeUpdate(insertSushilogtmp); logger.info("Inserted to irus_sushilogtmp table"); - +/* logger.info("Creating downloads_stats table"); String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " @@ -209,7 +209,7 @@ public class IrusStats { + "`count` int)"; stmt.executeUpdate(createSushilog); logger.info("Created sushilog table"); - +*/ logger.info("Inserting to sushilog table"); String insertToShushilog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sushilog SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java index ef7636099..c20781767 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java @@ -116,13 +116,16 @@ public class LaReferenciaStats { removeDoubleClicks(); logger.info("LaReferencia removed double clicks"); +/******** logger.info("LaReferencia creating viewsStats"); viewsStats(); logger.info("LaReferencia created viewsStats"); logger.info("LaReferencia creating downloadsStats"); downloadsStats(); logger.info("LaReferencia created downloadsStats"); - logger.info("LaReferencia updating Production Tables"); + +************/ + logger.info("LaReferencia updating Production Tables"); updateProdTables(); logger.info("LaReferencia updated Production Tables"); @@ -343,7 +346,7 @@ public class LaReferenciaStats { String sql = "insert into " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog " + "select * from " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp"; stmt.executeUpdate(sql); - +/***** logger.info("Updating views_stats"); sql = "insert into " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + "select * from " + ConnectDB.getUsageStatsDBSchema() + ".la_views_stats_tmp"; @@ -372,6 +375,11 @@ public class LaReferenciaStats { logger.info("Inserted data to usage_stats from lareferencia"); // sql = "insert into public.downloads_stats select * from la_downloads_stats_tmp;"; // stmt.executeUpdate(sql); +****/ + logger.info("Dropping lareferencialogtmp"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp"; + logger.info("Dropped lareferencialogtmp"); + stmt.executeUpdate(sql); stmt.close(); ConnectDB.getHiveConnection().close(); diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java index 681105de4..5cc9ec563 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java @@ -196,6 +196,7 @@ public class PiwikDownloadLogs { //while (rs.next()) //piwikIdToVisit.add(rs.getInt(1)); piwikIdToVisit.add(13); + piwikIdToVisit.add(109); logger.info("Found the following piwikIds for download: " + piwikIdToVisit); diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java index e0225d49a..4903d9599 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java @@ -60,7 +60,7 @@ public class PiwikStatsDB { this.createTables(); // The piwiklog table is not needed since it is built // on top of JSON files - this.createTmpTables(); + ////////////this.createTmpTables(); } public ArrayList getRobotsList() { @@ -141,7 +141,7 @@ public class PiwikStatsDB { } } - private void createTmpTables() throws Exception { +/***** public void createTmpTables() throws Exception { try { Statement stmt = ConnectDB.getHiveConnection().createStatement(); String sqlCreateTmpTablePiwikLog = "CREATE TABLE IF NOT EXISTS " @@ -181,7 +181,7 @@ public class PiwikStatsDB { // System.exit(0); } } - +******/ public void processLogs() throws Exception { try { ReadCounterRobotsList counterRobots = new ReadCounterRobotsList(this.getCounterRobotsURL()); @@ -203,9 +203,10 @@ public class PiwikStatsDB { processPortalLog(); logger.info("Portal logs process done"); - logger.info("Processing portal usagestats"); + logger.info("Processing portal usagestats"); portalStats(); logger.info("Portal usagestats process done"); +/***** logger.info("ViewsStats processing starts"); viewsStats(); @@ -214,11 +215,12 @@ public class PiwikStatsDB { logger.info("DownloadsStats processing starts"); downloadsStats(); logger.info("DownloadsStats processing starts"); - +*****/ logger.info("Updating Production Tables"); updateProdTables(); logger.info("Updated Production Tables"); + } catch (Exception e) { logger.error("Failed to process logs: " + e); throw new Exception("Failed to process logs: " + e.toString(), e); @@ -338,369 +340,6 @@ public class PiwikStatsDB { stmt.close(); } - public void viewsStats() throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Dropping result_views_monthly_tmp table"); - String drop_result_views_monthly_tmp = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".result_views_monthly_tmp"; - stmt.executeUpdate(drop_result_views_monthly_tmp); - logger.info("Dropped result_views_monthly_tmp table"); - - logger.info("Creating result_views_monthly_tmp table"); - String create_result_views_monthly_tmp = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() - + ".result_views_monthly_tmp " + - "AS SELECT entity_id AS id, " + - "COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) " + - "AS openaire_referrer, " + - "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + - "FROM " + ConnectDB.getUsageStatsDBSchema() - + ".piwiklogtmp where action='action' and (source_item_type='oaItem' or " + - "source_item_type='repItem') " + - "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), " + - "source ORDER BY source, entity_id"; - stmt.executeUpdate(create_result_views_monthly_tmp); - logger.info("Created result_views_monthly_tmp table"); - - logger.info("Dropping views_stats_tmp table"); - String drop_views_stats_tmp = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".views_stats_tmp"; - stmt.executeUpdate(drop_views_stats_tmp); - logger.info("Dropped views_stats_tmp table"); - - logger.info("Creating views_stats_tmp table"); - String create_views_stats_tmp = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".views_stats_tmp " + - "AS SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + - "max(views) AS count, max(openaire_referrer) AS openaire " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".result_views_monthly_tmp p, " + - ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + - "WHERE p.source=d.piwik_id AND p.id=ro.oid " + - "GROUP BY d.id, ro.id, month " + - "ORDER BY d.id, ro.id, month"; - stmt.executeUpdate(create_views_stats_tmp); - logger.info("Created views_stats_tmp table"); -/* - logger.info("Dropping views_stats table"); - String drop_views_stats = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".views_stats"; - stmt.executeUpdate(drop_views_stats); - logger.info("Dropped views_stats table"); -*/ - logger.info("Creating views_stats table"); - String create_view_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + - "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp STORED AS PARQUET"; - stmt.executeUpdate(create_view_stats); - logger.info("Created views_stats table"); - - logger.info("Dropping pageviews_stats_tmp table"); - String drop_pageviews_stats_tmp = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".pageviews_stats_tmp"; - stmt.executeUpdate(drop_pageviews_stats_tmp); - logger.info("Dropped pageviews_stats_tmp table"); - - logger.info("Creating pageviews_stats_tmp table"); - String create_pageviews_stats_tmp = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".pageviews_stats_tmp AS SELECT " + - "'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, max(views) AS count " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".result_views_monthly_tmp p, " + - ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + - "WHERE p.source=" + ExecuteWorkflow.portalMatomoID + " AND p.source=d.piwik_id and p.id=ro.id \n" + - "GROUP BY d.id, ro.id, month " + - "ORDER BY d.id, ro.id, month"; - stmt.executeUpdate(create_pageviews_stats_tmp); - logger.info("Created pageviews_stats_tmp table"); - -/* logger.info("Droping pageviews_stats table"); - String drop_pageviews_stats = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".pageviews_stats"; - stmt.executeUpdate(drop_pageviews_stats); - logger.info("Dropped pageviews_stats table"); -*/ - logger.info("Creating pageviews_stats table"); - String create_pageviews_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".pageviews_stats " + - "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats_tmp STORED AS PARQUET"; - stmt.executeUpdate(create_pageviews_stats); - logger.info("Created pageviews_stats table"); - - stmt.close(); - ConnectDB.getHiveConnection().close(); - } - - private void downloadsStats() throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Dropping result_downloads_monthly_tmp view"); - String drop_result_downloads_monthly_tmp = "DROP VIEW IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".result_downloads_monthly_tmp"; - stmt.executeUpdate(drop_result_downloads_monthly_tmp); - logger.info("Dropped result_downloads_monthly_tmp view"); - - logger.info("Creating result_downloads_monthly_tmp view"); - String sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + ".result_downloads_monthly_tmp " + - "AS SELECT entity_id AS id, COUNT(entity_id) as downloads, " + - "SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) AS openaire_referrer, " + - "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp where action='download' " + - "AND (source_item_type='oaItem' OR source_item_type='repItem') " + - "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) , source " + - "ORDER BY source, entity_id, month"; - stmt.executeUpdate(sql); - logger.info("Created result_downloads_monthly_tmp view"); - - logger.info("Dropping downloads_stats_tmp table"); - String drop_views_stats = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".downloads_stats_tmp"; - stmt.executeUpdate(drop_views_stats); - logger.info("Dropped downloads_stats_tmp table"); - - logger.info("Creating downloads_stats_tmp table"); - sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp AS " + - "SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + - "max(downloads) AS count, max(openaire_referrer) AS openaire " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".result_downloads_monthly_tmp p, " + - ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + - "WHERE p.source=d.piwik_id and p.id=ro.oid " + - "GROUP BY d.id, ro.id, month " + - "ORDER BY d.id, ro.id, month"; - stmt.executeUpdate(sql); - logger.info("Created downloads_stats_tmp table"); -/* - logger.info("Dropping downloads_stats table"); - String drop_downloads_stats = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".downloads_stats"; - stmt.executeUpdate(drop_downloads_stats); - logger.info("Dropped downloads_stats table"); -*/ - logger.info("Creating downloads_stats table"); - String create_downloads_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats " + - "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp STORED AS PARQUET "; - stmt.executeUpdate(create_downloads_stats); - logger.info("Created downloads_stats table"); - - logger.info("Dropping result_downloads_monthly_tmp view"); - sql = "DROP VIEW IF EXISTS result_downloads_monthly_tmp"; - logger.info("Dropped result_downloads_monthly_tmp view"); - stmt.executeUpdate(sql); - - stmt.close(); - ConnectDB.getHiveConnection().close(); - } - - public void finalizeStats() throws Exception { - stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Dropping full_dates table"); - String dropFullDates = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".full_dates"; - stmt.executeUpdate(dropFullDates); - logger.info("Dropped full_dates table"); - - Calendar startCalendar = Calendar.getInstance(); - startCalendar.setTime(new SimpleDateFormat("yyyy-MM-dd").parse("2016-01-01")); - Calendar endCalendar = Calendar.getInstance(); - int diffYear = endCalendar.get(Calendar.YEAR) - startCalendar.get(Calendar.YEAR); - int diffMonth = diffYear * 12 + endCalendar.get(Calendar.MONTH) - startCalendar.get(Calendar.MONTH); - - logger.info("Creating full_dates table"); - String sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".full_dates AS " + - "SELECT from_unixtime(unix_timestamp(cast(add_months(from_date,i) AS DATE)), 'yyyy/MM') AS txn_date " + - "FROM (SELECT DATE '2016-01-01' AS from_date) p " + - "LATERAL VIEW " + - "posexplode(split(space(" + diffMonth + "),' ')) pe AS i,x"; - stmt.executeUpdate(sql); - logger.info("Created full_dates table"); - - logger.info("Creating downloads_stats table"); - String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".downloads_stats " + - "(`source` string, " + - "`repository_id` string, " + - "`result_id` string, " + - "`date` string, " + - "`count` bigint, " + - "`openaire` bigint)"; - stmt.executeUpdate(createDownloadsStats); - logger.info("Created downloads_stats table"); - - logger.info("Creating views_stats table"); - String createViewsStats = "CREATE TABLE IF NOT EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".views_stats " + - "(`source` string, " + - "`repository_id` string, " + - "`result_id` string, " + - "`date` string, " + - "`count` bigint, " + - "`openaire` bigint)"; - stmt.executeUpdate(createViewsStats); - logger.info("Created views_stats table"); - - logger.info("Inserting data to usage_stats"); - sql = "INSERT INTO "+ConnectDB.getUsageStatsDBSchema() + ".usage_stats " + - "SELECT coalesce(ds.source, vs.source) as source, " + - "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + - "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + - "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + - "coalesce(ds.openaire, 0) as openaire_downloads, " + - "coalesce(vs.openaire, 0) as openaire_views " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp AS ds FULL OUTER JOIN " + - ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp AS vs ON ds.source=vs.source " + - "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; - stmt.executeUpdate(sql); - logger.info("Inserted data to usage_stats"); - - - stmt.close(); - ConnectDB.getHiveConnection().close(); - } - - // Create repository Views statistics - private void repositoryViewsStats() throws Exception { - stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - -// String sql = "SELECT entity_id AS id , COUNT(entity_id) AS number_of_views, timestamp::date AS date, source INTO repo_view_stats FROM piwiklog WHERE source!='5' AND action=\'action\' AND source_item_type=\'repItem\' GROUP BY entity_id, date, source ORDER BY entity_id, date ASC, COUNT(entity_id) DESC;"; - String sql = "CREATE TABLE IF NOT EXISTS repo_view_stats AS SELECT entity_id AS id , COUNT(entity_id) AS number_of_views, timestamp::date AS date, source FROM piwiklog WHERE source!='5' AND action=\'action\' AND source_item_type=\'repItem\' GROUP BY entity_id, date, source ORDER BY entity_id, date ASC, COUNT(entity_id) DESC;"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_view_stats_id ON repo_view_stats USING btree (id)"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_view_stats_date ON repo_view_stats USING btree(date)"; - stmt.executeUpdate(sql); - -// sql = "SELECT roid.id, sum(number_of_views), extract('year' from date) ||'/'|| LPAD(CAST(extract('month' from date) AS VARCHAR), 2, '0') AS month, source INTO repo_view_stats_monthly_clean FROM repo_view_stats rvs, result_oids roid where rvs.id=roid.orid group by roid.id, month, source;"; - sql = "CREATE TABLE IF NOT EXISTS repo_view_stats_monthly_clean AS SELECT roid.id, sum(number_of_views), extract('year' from date) ||'/'|| LPAD(CAST(extract('month' from date) AS VARCHAR), 2, '0') AS month, source FROM repo_view_stats rvs, result_oids roid where rvs.id=roid.orid group by roid.id, month, source;"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_view_stats_monthly_clean_id ON repo_view_stats_monthly_clean USING btree (id)"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_view_stats_monthly_clean_month ON repo_view_stats_monthly_clean USING btree(month)"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_view_stats_monthly_clean_source ON repo_view_stats_monthly_clean USING btree(source)"; - stmt.executeUpdate(sql); - - Calendar startCalendar = Calendar.getInstance(); - startCalendar.setTime(new SimpleDateFormat("yyyy-MM-dd").parse("2016-01-01")); - Calendar endCalendar = Calendar.getInstance(); - int diffYear = endCalendar.get(Calendar.YEAR) - startCalendar.get(Calendar.YEAR); - int diffMonth = diffYear * 12 + endCalendar.get(Calendar.MONTH) - startCalendar.get(Calendar.MONTH); - - // sql="CREATE OR REPLACE view repo_view_stats_monthly AS select d.id, d.new_date AS month, case when rdm.sum is - // null then 0 else rdm.sum end, d.source from (select distinct rdsm.id, to_char(date_trunc('month', - // ('2016-01-01'::date + interval '1 month'*offs)), 'YYYY/MM') AS new_date, rdsm.source from generate_series(0, - // " + diffMonth +", 1) AS offs, repo_view_stats_monthly_clean rdsm) d LEFT JOIN (select id, month, sum, source - // from repo_view_stats_monthly_clean) rdm ON d.new_date=rdm.month and d.id=rdm.id and d.source=rdm.source order - // by d.id, d.new_date"; -// sql = "select d.id, d.new_date AS month, case when rdm.sum is null then 0 else rdm.sum end, d.source INTO repo_view_stats_monthly from (select distinct rdsm.id, to_char(date_trunc('month', ('2016-01-01'::date + interval '1 month'*offs)), 'YYYY/MM') AS new_date, rdsm.source from generate_series(0, " + diffMonth + ", 1) AS offs, repo_view_stats_monthly_clean rdsm) d LEFT JOIN (select id, month, sum, source from repo_view_stats_monthly_clean) rdm ON d.new_date=rdm.month and d.id=rdm.id and d.source=rdm.source order by d.id, d.new_date"; - sql = "CREATE TABLE IF NOT EXISTS repo_view_stats_monthly AS select d.id, d.new_date AS month, case when rdm.sum is null then 0 else rdm.sum end, d.source from (select distinct rdsm.id, to_char(date_trunc('month', ('2016-01-01'::date + interval '1 month'*offs)), 'YYYY/MM') AS new_date, rdsm.source from generate_series(0, " - + diffMonth - + ", 1) AS offs, repo_view_stats_monthly_clean rdsm) d LEFT JOIN (select id, month, sum, source from repo_view_stats_monthly_clean) rdm ON d.new_date=rdm.month and d.id=rdm.id and d.source=rdm.source order by d.id, d.new_date"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_view_stats_monthly_id ON repo_view_stats_monthly USING btree (id)"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_view_stats_monthly_month ON repo_view_stats_monthly USING btree(month)"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_view_stats_monthly_source ON repo_view_stats_monthly USING btree(source)"; - stmt.executeUpdate(sql); - - sql = "CREATE OR REPLACE view repo_view_stats_monthly_sushi AS SELECT id, sum(number_of_views), extract('year' from date) ||'-'|| LPAD(CAST(extract('month' from date) AS VARCHAR), 2, '0') ||'-01' AS month, source FROM repo_view_stats group by id, month, source;"; - stmt.executeUpdate(sql); - - stmt.close(); - ConnectDB.getHiveConnection().commit(); - ConnectDB.getHiveConnection().close(); - } - - // Create repository downloads statistics - private void repositoryDownloadsStats() throws Exception { - stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - -// String sql = "SELECT entity_id AS id, COUNT(entity_id) AS number_of_downloads, timestamp::date AS date, source INTO repo_download_stats FROM piwiklog WHERE source!='5' AND action=\'download\' AND source_item_type=\'repItem\' GROUP BY entity_id, date, source ORDER BY entity_id, date ASC, COUNT(entity_id) DESC;"; - String sql = "CREATE TABLE IF NOT EXISTS repo_download_stats AS SELECT entity_id AS id, COUNT(entity_id) AS number_of_downloads, timestamp::date AS date, source FROM piwiklog WHERE source!='5' AND action=\'download\' AND source_item_type=\'repItem\' GROUP BY entity_id, date, source ORDER BY entity_id, date ASC, COUNT(entity_id) DESC;"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_download_stats_id ON repo_download_stats USING btree (id)"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_download_stats_date ON repo_download_stats USING btree(date)"; - stmt.executeUpdate(sql); - -// sql = "SELECT roid.id, sum(number_of_downloads), extract('year' from date) ||'/'|| LPAD(CAST(extract('month' from date) AS VARCHAR), 2, '0') AS month, source INTO repo_download_stats_monthly_clean FROM repo_download_stats rvs, result_oids roid WHERE rvs.id=roid.orid GROUP BY roid.id, month, source;"; - sql = "CREATE TABLE IF NOT EXISTS repo_download_stats_monthly_clean AS SELECT roid.id, sum(number_of_downloads), extract('year' from date) ||'/'|| LPAD(CAST(extract('month' from date) AS VARCHAR), 2, '0') AS month, source FROM repo_download_stats rvs, result_oids roid WHERE rvs.id=roid.orid GROUP BY roid.id, month, source;"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_download_stats_monthly_clean_id ON repo_download_stats_monthly_clean USING btree (id)"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_download_stats_monthly_clean_month ON repo_download_stats_monthly_clean USING btree(month)"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_download_stats_monthly_clean_source ON repo_download_stats_monthly_clean USING btree(source)"; - stmt.executeUpdate(sql); - - Calendar startCalendar = Calendar.getInstance(); - startCalendar.setTime(new SimpleDateFormat("yyyy-MM-dd").parse("2016-01-01")); - Calendar endCalendar = Calendar.getInstance(); - int diffYear = endCalendar.get(Calendar.YEAR) - startCalendar.get(Calendar.YEAR); - int diffMonth = diffYear * 12 + endCalendar.get(Calendar.MONTH) - startCalendar.get(Calendar.MONTH); - - // sql="CREATE OR REPLACE view repo_download_stats_monthly AS select d.id, d.new_date AS month, case when - // rdm.sum is null then 0 else rdm.sum end, d.source from (select distinct rdsm.id, to_char(date_trunc('month', - // ('2016-01-01'::date + interval '1 month'*offs)), 'YYYY/MM') AS new_date, rdsm.source from generate_series(0, - // " + diffMonth +", 1) AS offs, repo_download_stats_monthly_clean rdsm) d LEFT JOIN (select id, month, sum, - // source from repo_download_stats_monthly_clean) rdm ON d.new_date=rdm.month and d.id=rdm.id and - // d.source=rdm.source order by d.id, d.new_date"; - // sql = "select d.id, d.new_date AS month, case when rdm.sum is null then 0 else rdm.sum end, d.source INTO - // repo_download_stats_monthly from (select distinct rdsm.id, to_char(date_trunc('month', ('2016-01-01'::date + - // interval '1 month'*offs)), 'YYYY/MM') AS new_date, rdsm.source from generate_series(0, " + diffMonth + ", 1) - // AS offs, repo_download_stats_monthly_clean rdsm) d LEFT JOIN (select id, month, sum, source from - // repo_download_stats_monthly_clean) rdm ON d.new_date=rdm.month and d.id=rdm.id and d.source=rdm.source order - // by d.id, d.new_date"; - sql = "CREATE TABLE IF NOT EXISTS repo_download_stats_monthly AS select d.id, d.new_date AS month, case when rdm.sum is null then 0 else rdm.sum end, d.source from (select distinct rdsm.id, to_char(date_trunc('month', ('2016-01-01'::date + interval '1 month'*offs)), 'YYYY/MM') AS new_date, rdsm.source from generate_series(0, " - + diffMonth - + ", 1) AS offs, repo_download_stats_monthly_clean rdsm) d LEFT JOIN (select id, month, sum, source from repo_download_stats_monthly_clean) rdm ON d.new_date=rdm.month and d.id=rdm.id and d.source=rdm.source order by d.id, d.new_date"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_download_stats_monthly_id ON repo_download_stats_monthly USING btree (id)"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_download_stats_monthly_month ON repo_download_stats_monthly USING btree(month)"; - stmt.executeUpdate(sql); - - sql = "CREATE INDEX repo_download_stats_monthly_source ON repo_download_stats_monthly USING btree(source)"; - stmt.executeUpdate(sql); - - sql = "CREATE OR REPLACE view repo_download_stats_monthly_sushi AS SELECT id, sum(number_of_downloads), extract('year' from date) ||'-'|| LPAD(CAST(extract('month' from date) AS VARCHAR), 2, '0') ||'-01' AS month, source FROM repo_download_stats group by id, month, source;"; - stmt.executeUpdate(sql); - - stmt.close(); - ConnectDB.getHiveConnection().commit(); - ConnectDB.getHiveConnection().close(); - } - public void processPortalLog() throws Exception { Statement stmt = ConnectDB.getHiveConnection().createStatement(); ConnectDB.getHiveConnection().setAutoCommit(false); @@ -1154,47 +793,17 @@ public class PiwikStatsDB { String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklog " + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; stmt.executeUpdate(sql); - - logger.info("Inserting data to views_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp"; - stmt.executeUpdate(sql); - - logger.info("Inserting data to downloads_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp"; - stmt.executeUpdate(sql); - - logger.info("Inserting data to pageviews_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats_tmp"; - stmt.executeUpdate(sql); - - logger.info("Creating usage_stats table"); - String createUsageStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats " + - "AS SELECT coalesce(ds.source, vs.source) as source, " + - "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + - "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + - "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + - "coalesce(ds.openaire, 0) as openaire_downloads, " + - "coalesce(vs.openaire, 0) as openaire_views " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats AS ds FULL OUTER JOIN " + - ConnectDB.getUsageStatsDBSchema() + ".views_stats AS vs ON ds.source=vs.source " + - "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; - stmt.executeUpdate(createUsageStats); - logger.info("Created usage_stats table"); - - /* - * logger.info("Dropping table views_stats_tmp"); sql = "DROP TABLE IF EXISTS " + - * ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp"; stmt.executeUpdate(sql); - * logger.info("Dropping table downloads_stats_tmp"); sql = "DROP TABLE IF EXISTS " + - * ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp"; stmt.executeUpdate(sql); - * logger.info("Dropping table pageviews_stats_tmp"); sql = "DROP TABLE IF EXISTS " + - * ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats_tmp"; stmt.executeUpdate(sql); - * logger.info("Dropping table process_portal_log_tmp"); sql = "DROP TABLE IF EXISTS " + - * ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp"; stmt.executeUpdate(sql); - */ + logger.info("Dropping piwiklogtmp"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; + stmt.executeUpdate(sql); + logger.info("Dropped piwiklogtmp"); + + logger.info("Dropping process_portal_log_tmp"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp"; + stmt.executeUpdate(sql); + logger.info("Dropped process_portal_log_tmp"); + stmt.close(); ConnectDB.getHiveConnection().close(); diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java index 54ed286cb..4ca20c52e 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java @@ -285,7 +285,7 @@ public class SarcStats { stmtHive = ConnectDB.getHiveConnection().createStatement(); ConnectDB.getHiveConnection().setAutoCommit(false); stmtImpala = ConnectDB.getImpalaConnection().createStatement(); - +/* logger.info("Creating downloads_stats table_tmp"); String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp " @@ -366,7 +366,7 @@ public class SarcStats { + "`count` int)"; stmtHive.executeUpdate(createSushilog); logger.info("Created sushilog table"); - +*/ // Insert into sushilog logger.info("Inserting into sushilog"); String insertSushiLog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java index c4ee7d63c..bf2187569 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java @@ -56,9 +56,14 @@ public class UsageStatsExporter { PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); logger.info("Re-creating database and tables"); - if (ExecuteWorkflow.recreateDbAndTables) + if (ExecuteWorkflow.recreateDbAndTables){ piwikstatsdb.recreateDBAndTables(); - ; + logger.info("DB-Tables-TmpTables are created "); + } +// else { +// piwikstatsdb.createTmpTables(); +// logger.info("TmpTables are created "); +// } logger.info("Initializing the download logs module"); PiwikDownloadLogs piwd = new PiwikDownloadLogs(ExecuteWorkflow.matomoBaseURL, ExecuteWorkflow.matomoAuthToken); @@ -77,7 +82,7 @@ public class UsageStatsExporter { ExecuteWorkflow.portalLogPath, ExecuteWorkflow.portalMatomoID); } logger.info("Downloaded piwik logs"); -/* + // Create DB tables, insert/update statistics String cRobotsUrl = "https://raw.githubusercontent.com/atmire/COUNTER-Robots/master/COUNTER_Robots_list.json"; piwikstatsdb.setCounterRobotsURL(cRobotsUrl); @@ -86,7 +91,7 @@ public class UsageStatsExporter { logger.info("Processing logs"); piwikstatsdb.processLogs(); } -*/ + logger.info("Creating LaReferencia tables"); LaReferenciaDownloadLogs lrf = new LaReferenciaDownloadLogs(ExecuteWorkflow.lareferenciaBaseURL, ExecuteWorkflow.lareferenciaAuthToken); @@ -101,7 +106,8 @@ public class UsageStatsExporter { lrf.GetLaReferenciaRepos(ExecuteWorkflow.lareferenciaLogPath); logger.info("Downloaded LaReferencia logs"); } -/* + + LaReferenciaStats lastats = new LaReferenciaStats(ExecuteWorkflow.lareferenciaLogPath); if (ExecuteWorkflow.processLaReferenciaLogs) { @@ -109,7 +115,8 @@ public class UsageStatsExporter { lastats.processLogs(); logger.info("LaReferencia logs done"); } -*/ + + IrusStats irusstats = new IrusStats(ExecuteWorkflow.irusUKBaseURL); if (ExecuteWorkflow.irusCreateTablesEmptyDirs) { logger.info("Creating Irus Stats tables"); @@ -124,12 +131,15 @@ public class UsageStatsExporter { if (ExecuteWorkflow.irusDownloadReports) { irusstats.getIrusRRReport(ExecuteWorkflow.irusUKReportPath); } -/* + + if (ExecuteWorkflow.irusProcessStats) { irusstats.processIrusStats(); logger.info("Irus done"); } -*/ + + + SarcStats sarcStats = new SarcStats(); if (ExecuteWorkflow.sarcCreateTablesEmptyDirs) { sarcStats.reCreateLogDirs(); @@ -137,13 +147,14 @@ public class UsageStatsExporter { if (ExecuteWorkflow.sarcDownloadReports) { sarcStats.getAndProcessSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); } -/* + + if (ExecuteWorkflow.sarcProcessStats) { sarcStats.processSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); sarcStats.finalizeSarcStats(); } logger.info("Sarc done"); -*/ + /* // finalize usagestats @@ -160,6 +171,7 @@ public class UsageStatsExporter { invalidateMetadata(); } */ + logger.info("End"); } diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml new file mode 100644 index 000000000..f400239f5 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -0,0 +1,79 @@ + + + + + + + + + dhp-workflows + eu.dnetlib.dhp + 1.1.7-SNAPSHOT + + 4.0.0 + dhp-usage-stats-build + + + UTF-8 + UTF-8 + 0.13.1-cdh5.2.1 + 2.5.0-cdh5.2.1 + + + + + org.apache.spark + spark-core_2.11 + 2.2.0 + + + org.apache.spark + spark-sql_2.11 + 2.4.5 + + + com.googlecode.json-simple + json-simple + 1.1.1 + + + org.json + json + 20180130 + jar + + + org.apache.hive + hive-jdbc + ${cdh.hive.version} + + + org.apache.hadoop + hadoop-common + ${cdh.hadoop.version} + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + c3p0 + c3p0 + 0.9.1.2 + jar + + + dhp-usage-stats-build + diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ConnectDB.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ConnectDB.java new file mode 100644 index 000000000..8f0f8eae7 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ConnectDB.java @@ -0,0 +1,130 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.sql.Connection; +import java.sql.DriverManager; +import java.sql.SQLException; +import java.sql.Statement; +import java.util.Properties; + +import org.apache.log4j.Logger; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +/** + * @author D. Pierrakos, S. Zoupanos + */ +import com.mchange.v2.c3p0.ComboPooledDataSource; + +public abstract class ConnectDB { + + public static Connection DB_HIVE_CONNECTION; + public static Connection DB_IMPALA_CONNECTION; + + private static String dbHiveUrl; + private static String dbImpalaUrl; + private static String usageRawDataDBSchema; + private static String usageStatsDBSchema; + private static String statsDBSchema; + private final static Logger log = Logger.getLogger(ConnectDB.class); + + static void init() throws ClassNotFoundException { + + dbHiveUrl = ExecuteWorkflow.dbHiveUrl; + dbImpalaUrl = ExecuteWorkflow.dbImpalaUrl; + usageStatsDBSchema = ExecuteWorkflow.usageStatsDBSchema; + statsDBSchema = ExecuteWorkflow.statsDBSchema; + usageRawDataDBSchema = ExecuteWorkflow.usageRawDataDBSchema; + + Class.forName("org.apache.hive.jdbc.HiveDriver"); + } + + public static Connection getHiveConnection() throws SQLException { + if (DB_HIVE_CONNECTION != null && !DB_HIVE_CONNECTION.isClosed()) { + return DB_HIVE_CONNECTION; + } else { + DB_HIVE_CONNECTION = connectHive(); + + return DB_HIVE_CONNECTION; + } + } + + public static Connection getImpalaConnection() throws SQLException { + if (DB_IMPALA_CONNECTION != null && !DB_IMPALA_CONNECTION.isClosed()) { + return DB_IMPALA_CONNECTION; + } else { + DB_IMPALA_CONNECTION = connectImpala(); + + return DB_IMPALA_CONNECTION; + } + } + + public static String getUsageRawDataDBSchema() { + return usageRawDataDBSchema; + } + + public static String getUsageStatsDBSchema() { + return ConnectDB.usageStatsDBSchema; + } + + public static String getStatsDBSchema() { + return ConnectDB.statsDBSchema; + } + + private static Connection connectHive() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbHiveUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbHiveUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(30); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + return cpds.getConnection(); + + } + + private static Connection connectImpala() throws SQLException { + /* + * Connection connection = DriverManager.getConnection(dbImpalaUrl); Statement stmt = + * connection.createStatement(); log.debug("Opened database successfully"); return connection; + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbImpalaUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); + + cpds.setAcquireRetryAttempts(30); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); + + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + + return cpds.getConnection(); + + } + +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ExecuteWorkflow.java new file mode 100644 index 000000000..3f958abba --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ExecuteWorkflow.java @@ -0,0 +1,172 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.text.SimpleDateFormat; +import java.util.Calendar; +import java.util.Date; + +import org.apache.commons.io.IOUtils; +import org.apache.log4j.BasicConfigurator; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class ExecuteWorkflow { + + static String matomoAuthToken; + static String matomoBaseURL; + static String repoLogPath; + static String portalLogPath; + static String portalMatomoID; + static String irusUKBaseURL; + static String irusUKReportPath; + static String sarcsReportPathArray; + static String sarcsReportPathNonArray; + static String lareferenciaLogPath; + static String lareferenciaBaseURL; + static String lareferenciaAuthToken; + static String dbHiveUrl; + static String dbImpalaUrl; + static String usageRawDataDBSchema; + static String usageStatsDBSchema; + static String statsDBSchema; + static boolean recreateDbAndTables; + + static boolean piwikEmptyDirs; + static boolean downloadPiwikLogs; + static boolean processPiwikLogs; + + static Calendar startingLogPeriod; + static Calendar endingLogPeriod; + static int numberOfPiwikIdsToDownload; + static int numberOfSiteIdsToDownload; + + static boolean laReferenciaEmptyDirs; + static boolean downloadLaReferenciaLogs; + static boolean processLaReferenciaLogs; + + static boolean irusCreateTablesEmptyDirs; + static boolean irusDownloadReports; + static boolean irusProcessStats; + static int irusNumberOfOpendoarsToDownload; + + static boolean sarcCreateTablesEmptyDirs; + static boolean sarcDownloadReports; + static boolean sarcProcessStats; + static int sarcNumberOfIssnToDownload; + + static boolean finalizeStats; + static boolean finalTablesVisibleToImpala; + + static int numberOfDownloadThreads; + + private static final Logger logger = LoggerFactory.getLogger(PiwikStatsDB.class); + + public static void main(String args[]) throws Exception { + + // Sending the logs to the console + BasicConfigurator.configure(); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + UsageStatsExporter.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json"))); + parser.parseArgument(args); + + // Setting up the initial parameters + matomoAuthToken = parser.get("matomoAuthToken"); + matomoBaseURL = parser.get("matomoBaseURL"); + repoLogPath = parser.get("repoLogPath"); + portalLogPath = parser.get("portalLogPath"); + portalMatomoID = parser.get("portalMatomoID"); + irusUKBaseURL = parser.get("irusUKBaseURL"); + irusUKReportPath = parser.get("irusUKReportPath"); + sarcsReportPathArray = parser.get("sarcsReportPathArray"); + sarcsReportPathNonArray = parser.get("sarcsReportPathNonArray"); + lareferenciaLogPath = parser.get("lareferenciaLogPath"); + lareferenciaBaseURL = parser.get("lareferenciaBaseURL"); + lareferenciaAuthToken = parser.get("lareferenciaAuthToken"); + + dbHiveUrl = parser.get("dbHiveUrl"); + dbImpalaUrl = parser.get("dbImpalaUrl"); + usageRawDataDBSchema = parser.get("usageRawDataDBSchema"); + usageStatsDBSchema = parser.get("usageStatsDBSchema"); + statsDBSchema = parser.get("statsDBSchema"); + + if (parser.get("processPiwikLogs").toLowerCase().equals("true")) { + processPiwikLogs = true; + } else { + processPiwikLogs = false; + } + + String startingLogPeriodStr = parser.get("startingLogPeriod"); + Date startingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(startingLogPeriodStr); + startingLogPeriod = startingLogPeriodStr(startingLogPeriodDate); + + String endingLogPeriodStr = parser.get("endingLogPeriod"); + Date endingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(endingLogPeriodStr); + endingLogPeriod = startingLogPeriodStr(endingLogPeriodDate); + + numberOfPiwikIdsToDownload = Integer.parseInt(parser.get("numberOfPiwikIdsToDownload")); + numberOfSiteIdsToDownload = Integer.parseInt(parser.get("numberOfSiteIdsToDownload")); + + if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) { + recreateDbAndTables = true; + } else { + recreateDbAndTables = false; + } + + if (parser.get("processLaReferenciaLogs").toLowerCase().equals("true")) { + processLaReferenciaLogs = true; + } else { + processLaReferenciaLogs = false; + } + + if (parser.get("irusProcessStats").toLowerCase().equals("true")) { + irusProcessStats = true; + } else { + irusProcessStats = false; + } + + irusNumberOfOpendoarsToDownload = Integer.parseInt(parser.get("irusNumberOfOpendoarsToDownload")); + + if (parser.get("sarcProcessStats").toLowerCase().equals("true")) { + sarcProcessStats = true; + } else { + sarcProcessStats = false; + } + sarcNumberOfIssnToDownload = Integer.parseInt(parser.get("sarcNumberOfIssnToDownload")); + + if (parser.get("finalizeStats").toLowerCase().equals("true")) { + finalizeStats = true; + } else { + finalizeStats = false; + } + if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) { + finalTablesVisibleToImpala = true; + } else { + numberOfDownloadThreads = Integer.parseInt(parser.get("numberOfDownloadThreads")); + } + + UsageStatsExporter usagestatsExport = new UsageStatsExporter(); + usagestatsExport.export(); + } + + private static Calendar startingLogPeriodStr(Date date) { + + Calendar calendar = Calendar.getInstance(); + calendar.setTime(date); + return calendar; + + } +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/IrusStats.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/IrusStats.java new file mode 100644 index 000000000..4f34adc04 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/IrusStats.java @@ -0,0 +1,71 @@ +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.io.*; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.List; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class IrusStats { + + private String irusUKURL; + + private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); + + public IrusStats() throws Exception { + } + + + public void processIrusStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + + logger.info("Creating irus_downloads_stats_tmp table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".irus_downloads_stats_tmp " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmt.executeUpdate(createDownloadsStats); + logger.info("Created irus_downloads_stats_tmp table"); + + logger.info("Inserting into irus_downloads_stats_tmp"); + String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_downloads_stats_tmp " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(YEAR(date), '/', LPAD(MONTH(date), 2, '0')) as date, s.count, '0' " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".sushilog s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE s.repository=d.oid AND s.rid=ro.oid AND metric_type='ft_total' AND s.source='IRUS-UK'"; + stmt.executeUpdate(insertDStats); + logger.info("Inserted into irus_downloads_stats_tmp"); + + stmt.close(); + //ConnectDB.getHiveConnection().close(); + } + + +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/LaReferenciaStats.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/LaReferenciaStats.java new file mode 100644 index 000000000..ea3ac5948 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/LaReferenciaStats.java @@ -0,0 +1,149 @@ + +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.io.*; +import java.net.URLDecoder; +import java.sql.Connection; +import java.sql.PreparedStatement; +import java.sql.SQLException; +import java.sql.Statement; +import java.sql.Timestamp; +import java.text.SimpleDateFormat; +import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocatedFileStatus; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.RemoteIterator; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class LaReferenciaStats { + + private static final Logger logger = LoggerFactory.getLogger(LaReferenciaStats.class); + + private String logRepoPath; + + private Statement stmt = null; + + private String CounterRobotsURL; + private ArrayList robotsList; + + public LaReferenciaStats() throws Exception { + } + + + + public void processLogs() throws Exception { + try { + logger.info("LaReferencia creating viewsStats"); + viewsStats(); + logger.info("LaReferencia created viewsStats"); + logger.info("LaReferencia creating downloadsStats"); + downloadsStats(); + logger.info("LaReferencia created downloadsStats"); + +// logger.info("LaReferencia updating Production Tables"); +// updateProdTables(); +// logger.info("LaReferencia updated Production Tables"); + + } catch (Exception e) { + logger.error("Failed to process logs: " + e); + throw new Exception("Failed to process logs: " + e.toString(), e); + } + } + + + public void viewsStats() throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating la_result_views_monthly_tmp view"); + String sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + ".la_result_views_monthly_tmp AS " + + + "SELECT entity_id AS id, COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' " + + "THEN 1 ELSE 0 END) AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".lareferencialog where action='action' and " + + "(source_item_type='oaItem' or source_item_type='repItem') " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), " + + "source ORDER BY source, entity_id"; + stmt.executeUpdate(sql); + logger.info("Created la_result_views_monthly_tmp view"); + + logger.info("Dropping la_views_stats_tmp table"); + sql = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".la_views_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Dropped la_views_stats_tmp table"); + + logger.info("Creating la_views_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".la_views_stats_tmp " + + "AS SELECT 'LaReferencia' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(views) AS count, max(openaire_referrer) AS openaire " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_result_views_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=d.oid AND p.id=ro.oid " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month"; + stmt.executeUpdate(sql); + logger.info("Created la_views_stats_tmp table"); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + } + + private void downloadsStats() throws Exception { + + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating la_result_downloads_monthly_tmp view"); + String sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + + ".la_result_downloads_monthly_tmp AS " + + "SELECT entity_id AS id, COUNT(entity_id) as downloads, SUM(CASE WHEN referrer_name LIKE '%openaire%' " + + "THEN 1 ELSE 0 END) AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".lareferencialog where action='download' and " + + "(source_item_type='oaItem' or source_item_type='repItem') " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), " + + "source ORDER BY source, entity_id"; + stmt.executeUpdate(sql); + logger.info("Created la_result_downloads_monthly_tmp view"); + + logger.info("Dropping la_downloads_stats_tmp table"); + sql = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".la_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Dropped la_downloads_stats_tmp table"); + + logger.info("Creating la_downloads_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".la_downloads_stats_tmp " + + "AS SELECT 'LaReferencia' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(downloads) AS count, max(openaire_referrer) AS openaire " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_result_downloads_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=d.oid AND p.id=ro.oid " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month"; + stmt.executeUpdate(sql); + logger.info("Created la_downloads_stats_tmp table"); + + stmt.close(); + //ConnectDB.getHiveConnection().close(); + } + + +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/PiwikStatsDB.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/PiwikStatsDB.java new file mode 100644 index 000000000..a165c6eab --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/PiwikStatsDB.java @@ -0,0 +1,345 @@ + +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.io.*; +import java.net.URLDecoder; +import java.sql.Connection; +import java.sql.SQLException; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.*; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocatedFileStatus; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.RemoteIterator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import java.sql.Timestamp; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class PiwikStatsDB { + + private String logPath; + + private Statement stmt = null; + + private static final Logger logger = LoggerFactory.getLogger(PiwikStatsDB.class); + + + public PiwikStatsDB() throws Exception { + + } + + + public void recreateDBAndTables() throws Exception { + this.createDatabase(); + // The piwiklog table is not needed since it is built + // on top of JSON files + ////////////this.createTmpTables(); + } + + private void createDatabase() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Dropping usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); + String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + " CASCADE"; + stmt.executeUpdate(dropDatabase); + } catch (Exception e) { + logger.error("Failed to drop database: " + e); + throw new Exception("Failed to drop database: " + e.toString(), e); + } + + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); + String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema(); + stmt.executeUpdate(createDatabase); + + } catch (Exception e) { + logger.error("Failed to create database: " + e); + throw new Exception("Failed to create database: " + e.toString(), e); + } + } + + + public void processLogs() throws Exception { + try { + + logger.info("ViewsStats processing starts at: "+new Timestamp(System.currentTimeMillis())); + viewsStats(); + logger.info("ViewsStats processing ends at: "+new Timestamp(System.currentTimeMillis())); + + logger.info("DownloadsStats processing starts at: "+new Timestamp(System.currentTimeMillis())); + downloadsStats(); + logger.info("DownloadsStats processing ends at: "+new Timestamp(System.currentTimeMillis())); + + } catch (Exception e) { + logger.error("Failed to process logs: " + e); + throw new Exception("Failed to process logs: " + e.toString(), e); + } + } + + + + public void viewsStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Dropping openaire_result_views_monthly_tmp view"); + String drop_result_views_monthly = "DROP VIEW IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_piwikresult_views_monthly_tmp"; + stmt.executeUpdate(drop_result_views_monthly); + logger.info("Dropped openaire_result_views_monthly_tmp view"); + + logger.info("Creating openaire_result_views_monthly_tmp view"); + String create_result_views_monthly = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + + ".openaire_result_views_monthly_tmp " + + "AS SELECT entity_id AS id, " + + "COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) " + + "AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + + ".piwiklog where action='action' and (source_item_type='oaItem' or " + + "source_item_type='repItem') " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), " + + "source ORDER BY source, entity_id"; + stmt.executeUpdate(create_result_views_monthly); + logger.info("Created openaire_result_views_monthly_tmp table"); + + logger.info("Dropping openaire_views_stats_tmp table"); + String drop_views_stats = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_views_stats_tmp"; + stmt.executeUpdate(drop_views_stats); + logger.info("Dropped openaire_views_stats_tmp table"); + + logger.info("Creating openaire_views_stats_tmp table"); + String create_views_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".openaire_views_stats_tmp " + + "AS SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(views) AS count, max(openaire_referrer) AS openaire " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_views_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=d.piwik_id AND p.id=ro.oid " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month "; + stmt.executeUpdate(create_views_stats); + logger.info("Created openaire_views_stats_tmp table"); + + logger.info("Creating openaire_pageviews_stats_tmp table"); + String create_pageviews_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".openaire_pageviews_stats_tmp AS SELECT " + + "'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, max(views) AS count " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_views_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=" + ExecuteWorkflow.portalMatomoID + " AND p.source=d.piwik_id and p.id=ro.id \n" + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month "; + stmt.executeUpdate(create_pageviews_stats); + logger.info("Created pageviews_stats table"); + + stmt.close(); + //ConnectDB.getHiveConnection().close(); + } + + private void downloadsStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Dropping openaire_result_downloads_monthly_tmp view"); + String drop_result_downloads_monthly = "DROP VIEW IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_result_downloads_monthly_tmp"; + stmt.executeUpdate(drop_result_downloads_monthly); + logger.info("Dropped openaire_result_downloads_monthly_tmp view"); + + logger.info("Creating openaire_result_downloads_monthly_tmp view"); + String sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_downloads_monthly_tmp " + + "AS SELECT entity_id AS id, COUNT(entity_id) as downloads, " + + "SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema()+ ".piwiklog where action='download' " + + "AND (source_item_type='oaItem' OR source_item_type='repItem') " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) , source " + + "ORDER BY source, entity_id, month"; + stmt.executeUpdate(sql); + logger.info("Created openaire_result_downloads_monthly_tmp view"); + + logger.info("Dropping openaire_downloads_stats_tmp table"); + String drop_views_stats = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_downloads_stats_tmp"; + stmt.executeUpdate(drop_views_stats); + logger.info("Dropped openaire_downloads_stats_tmp table"); + + logger.info("Creating openaire_downloads_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp AS " + + "SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(downloads) AS count, max(openaire_referrer) AS openaire " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_downloads_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=d.piwik_id and p.id=ro.oid " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month "; + stmt.executeUpdate(sql); + logger.info("Created downloads_stats table"); + + + logger.info("Dropping openaire_result_downloads_monthly_tmp view"); + sql = "DROP VIEW IF EXISTS "+ConnectDB.getUsageStatsDBSchema() + ".openaire_result_downloads_monthly_tmp"; + logger.info("Dropped openaire_result_downloads_monthly_tmp view "); + stmt.executeUpdate(sql); + + stmt.close(); + //ConnectDB.getHiveConnection().close(); + } + + public void finalizeStats() throws Exception { + stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + //Dropping views_stats table + logger.info("Dropping views_stats table"); + String sql = "DROP TABLE IF EXISTS "+ConnectDB.getUsageStatsDBSchema() + ".views_stats"; + logger.info("Dropped views_stats table "); + stmt.executeUpdate(sql); + + //Dropping downloads_stats table + logger.info("Dropping downloads_stats table"); + sql = "DROP TABLE IF EXISTS "+ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; + logger.info("Dropped downloads_stats table "); + stmt.executeUpdate(sql); + + //Dropping page_views_stats table + logger.info("Dropping pageviews_stats table"); + sql = "DROP TABLE IF EXISTS "+ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; + logger.info("Dropped pageviews_stats table "); + stmt.executeUpdate(sql); + + //Creating views_stats table + logger.info("Creating views_stats table"); + String createViewsStats = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".views_stats " + + "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_views_stats_tmp STORED AS PARQUET"; + stmt.executeUpdate(createViewsStats); + logger.info("Created views_stats table"); + + //Inserting OpenAIRE views stats + logger.info("Inserting Openaire data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_views_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Openaire views updated to views_stats"); + + //Inserting Lareferencia views stats + logger.info("Inserting LaReferencia data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_views_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("LaReferencia views updated to views_stats"); + + + logger.info("Creating downloads_stats table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats " + + "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp STORED AS PARQUET"; + stmt.executeUpdate(createDownloadsStats); + logger.info("Created downloads_stats table"); + + //Inserting OpenAIRE downloads stats + logger.info("Inserting OpenAIRE data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp"; + stmt.executeUpdate(sql); + + //Inserting Lareferencia downloads stats + logger.info("Inserting LaReferencia data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Lareferencia downloads updated to downloads_stats"); + + //Inserting IRUS downloads stats + logger.info("Inserting IRUS data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("IRUS downloads updated to downloads_stats"); + + //Inserting SARC-OJS downloads stats + logger.info("Inserting SARC data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("SARC-OJS downloads updated to downloads_stats"); + + + logger.info("Creating pageviews_stats table"); + String create_pageviews_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".pageviews_stats " + + "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_pageviews_stats_tmp STORED AS PARQUET"; + stmt.executeUpdate(create_pageviews_stats); + logger.info("Created pageviews_stats table"); + + //Inserting OpenAIRE views stats from Portal + logger.info("Inserting data to page_views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_pageviews_stats_tmp"; + stmt.executeUpdate(sql); + + logger.info("Dropping full_dates table"); + String dropFullDates = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".full_dates"; + stmt.executeUpdate(dropFullDates); + logger.info("Dropped full_dates table"); + + Calendar startCalendar = Calendar.getInstance(); + startCalendar.setTime(new SimpleDateFormat("yyyy-MM-dd").parse("2016-01-01")); + Calendar endCalendar = Calendar.getInstance(); + int diffYear = endCalendar.get(Calendar.YEAR) - startCalendar.get(Calendar.YEAR); + int diffMonth = diffYear * 12 + endCalendar.get(Calendar.MONTH) - startCalendar.get(Calendar.MONTH); + + logger.info("Creating full_dates table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".full_dates AS " + + "SELECT from_unixtime(unix_timestamp(cast(add_months(from_date,i) AS DATE)), 'yyyy/MM') AS txn_date " + + "FROM (SELECT DATE '2016-01-01' AS from_date) p " + + "LATERAL VIEW " + + "posexplode(split(space(" + diffMonth + "),' ')) pe AS i,x"; + stmt.executeUpdate(sql); + logger.info("Created full_dates table"); + + + logger.info("Inserting data to usage_stats"); + sql = "CREATE TABLE IF NOT EXISTS "+ConnectDB.getUsageStatsDBSchema() + ".usage_stats AS " + + "SELECT coalesce(ds.source, vs.source) as source, " + + "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + + "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + + "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + + "coalesce(ds.openaire, 0) as openaire_downloads, " + + "coalesce(vs.openaire, 0) as openaire_views " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats AS ds FULL OUTER JOIN " + + ConnectDB.getUsageStatsDBSchema() + ".views_stats AS vs ON ds.source=vs.source " + + "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; + stmt.executeUpdate(sql); + logger.info("Inserted data to usage_stats"); + + + stmt.close(); + ConnectDB.getHiveConnection().close(); + } + + + private Connection getConnection() throws SQLException { + return ConnectDB.getHiveConnection(); + } +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/SarcStats.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/SarcStats.java new file mode 100644 index 000000000..2d224075f --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/SarcStats.java @@ -0,0 +1,106 @@ +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.io.*; +// import java.io.BufferedReader; +// import java.io.InputStreamReader; +import java.net.URL; +import java.net.URLConnection; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.sql.Statement; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Calendar; +import java.util.Date; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class SarcStats { + + private Statement stmtHive = null; + private Statement stmtImpala = null; + + private static final Logger logger = LoggerFactory.getLogger(SarcStats.class); + + public SarcStats() throws Exception { +// createTables(); + } + + private void createTables() throws Exception { + try { + + stmtHive = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilog(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; + stmtHive.executeUpdate(sqlCreateTableSushiLog); + + // String sqlCopyPublicSushiLog="INSERT INTO sushilog SELECT * FROM public.sushilog;"; + // stmt.executeUpdate(sqlCopyPublicSushiLog); + String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " + + " ON INSERT TO sushilog " + + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," + + "sushilog.rid, sushilog.date " + + "FROM sushilog " + + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; + stmtHive.executeUpdate(sqlcreateRuleSushiLog); + String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; + stmtHive.executeUpdate(createSushiIndex); + + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + + public void processSarc() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating sarc_downloads_stats_tmp table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_downloads_stats_tmp " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmt.executeUpdate(createDownloadsStats); + logger.info("Created sarc_downloads_stats_tmp table"); + + logger.info("Inserting into sarc_downloads_stats_tmp"); + String insertSarcStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_downloads_stats_tmp " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(CAST(YEAR(`date`) AS STRING), '/', " + + "LPAD(CAST(MONTH(`date`) AS STRING), 2, '0')) AS `date`, s.count, '0' " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".sushilog s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".result_pids ro " + + "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND d.id like CONCAT('%', 'sarcservicod', '%') " + + "AND s.rid=ro.pid AND ro.type='Digital Object Identifier' AND s.metric_type='ft_total' AND s.source='SARC-OJS'"; + stmt.executeUpdate(insertSarcStats); + logger.info("Inserted into sarc_downloads_stats_tmp"); + + stmt.close(); + //ConnectDB.getHiveConnection().close(); + } + +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/UsageStatsExporter.java new file mode 100644 index 000000000..43abb1681 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/UsageStatsExporter.java @@ -0,0 +1,106 @@ +package eu.dnetlib.oa.graph.usagestatsbuild.export; + +import java.io.IOException; +import java.sql.SQLException; +import java.sql.Statement; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Main class for downloading and processing Usage statistics + * + * @author D. Pierrakos, S. Zoupanos + */ +public class UsageStatsExporter { + + public UsageStatsExporter() { + + } + + private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); + + public void export() throws Exception { + + logger.info("Initialising DB properties"); + ConnectDB.init(); + +// runImpalaQuery(); + PiwikStatsDB piwikstatsdb = new PiwikStatsDB(); + + logger.info("Re-creating database and tables"); + if (ExecuteWorkflow.recreateDbAndTables) { + piwikstatsdb.recreateDBAndTables(); + logger.info("DB-Tables are created "); + } +// else { +// piwikstatsdb.createTmpTables(); +// logger.info("TmpTables are created "); +// } + if (ExecuteWorkflow.processPiwikLogs) { + logger.info("Processing logs"); + piwikstatsdb.processLogs(); + } + + LaReferenciaStats lastats = new LaReferenciaStats(); + + if (ExecuteWorkflow.processLaReferenciaLogs) { + logger.info("Processing LaReferencia logs"); + lastats.processLogs(); + logger.info("LaReferencia logs done"); + } + + IrusStats irusstats = new IrusStats(); + + if (ExecuteWorkflow.irusProcessStats) { + logger.info("Processing IRUS"); + irusstats.processIrusStats(); + logger.info("Irus done"); + } + + SarcStats sarcStats = new SarcStats(); + + if (ExecuteWorkflow.sarcProcessStats) { + sarcStats.processSarc(); + } + logger.info("Sarc done"); + + // finalize usagestats + if (ExecuteWorkflow.finalizeStats) { + piwikstatsdb.finalizeStats(); + logger.info("Finalized stats"); + } + + // Make the tables available to Impala + if (ExecuteWorkflow.finalTablesVisibleToImpala) { + logger.info("Making tables visible to Impala"); + invalidateMetadata(); + } + + logger.info("End"); + } + + private void invalidateMetadata() throws SQLException { + Statement stmt = null; + + stmt = ConnectDB.getImpalaConnection().createStatement(); + + String sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + } +} diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json new file mode 100644 index 000000000..3f121288e --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json @@ -0,0 +1,237 @@ +[ + { + "paramName": "mat", + "paramLongName": "matomoAuthToken", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "mbu", + "paramLongName": "matomoBaseURL", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + }, + { + "paramName": "rlp", + "paramLongName": "repoLogPath", + "paramDescription": "nameNode of the source cluster", + "paramRequired": true + }, + { + "paramName": "plp", + "paramLongName": "portalLogPath", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "pmi", + "paramLongName": "portalMatomoID", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "iukbuw", + "paramLongName": "irusUKBaseURL", + "paramDescription": "working directory", + "paramRequired": true + }, + { + "paramName": "iukrp", + "paramLongName": "irusUKReportPath", + "paramDescription": "maximum number of map tasks used in the distcp process", + "paramRequired": true + }, + { + "paramName": "srpa", + "paramLongName": "sarcsReportPathArray", + "paramDescription": "memory for distcp action copying actionsets from remote cluster", + "paramRequired": true + }, + { + "paramName": "srpna", + "paramLongName": "sarcsReportPathNonArray", + "paramDescription": "timeout for distcp copying actions from remote cluster", + "paramRequired": true + }, + { + "paramName": "llp", + "paramLongName": "lareferenciaLogPath", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "lbu", + "paramLongName": "lareferenciaBaseURL", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "lat", + "paramLongName": "lareferenciaAuthToken", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbhu", + "paramLongName": "dbHiveUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbiu", + "paramLongName": "dbImpalaUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "urdbs", + "paramLongName": "usageRawDataDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "usdbs", + "paramLongName": "usageStatsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "sdbs", + "paramLongName": "statsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "rdbt", + "paramLongName": "recreateDbAndTables", + "paramDescription": "Re-create database and initial tables?", + "paramRequired": true + }, + { + "paramName": "pwed", + "paramLongName": "piwikEmptyDirs", + "paramDescription": "Empty piwik directories?", + "paramRequired": true + }, + { + "paramName": "ppwl", + "paramLongName": "processPiwikLogs", + "paramDescription": "Process the piwiklogs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "dpwl", + "paramLongName": "downloadPiwikLogs", + "paramDescription": "download piwik logs?", + "paramRequired": true + }, + { + "paramName": "slp", + "paramLongName": "startingLogPeriod", + "paramDescription": "Starting log period", + "paramRequired": true + }, + { + "paramName": "elp", + "paramLongName": "endingLogPeriod", + "paramDescription": "Ending log period", + "paramRequired": true + }, + { + "paramName": "npidd", + "paramLongName": "numberOfPiwikIdsToDownload", + "paramDescription": "Limit the number of the downloaded piwikids to the first numberOfPiwikIdsToDownload", + "paramRequired": true + }, + { + "paramName": "nsidd", + "paramLongName": "numberOfSiteIdsToDownload", + "paramDescription": "Limit the number of the downloaded siteids (La Referencia logs) to the first numberOfSiteIdsToDownload", + "paramRequired": true + }, + { + "paramName": "lerd", + "paramLongName": "laReferenciaEmptyDirs", + "paramDescription": "Empty LaReferencia directories?", + "paramRequired": true + }, + { + "paramName": "plrl", + "paramLongName": "processLaReferenciaLogs", + "paramDescription": "Process the La Referencia logs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "dlrl", + "paramLongName": "downloadLaReferenciaLogs", + "paramDescription": "download La Referencia logs?", + "paramRequired": true + }, + { + "paramName": "icted", + "paramLongName": "irusCreateTablesEmptyDirs", + "paramDescription": "Irus section: Create tables and empty JSON directories?", + "paramRequired": true + }, + { + "paramName": "idr", + "paramLongName": "irusDownloadReports", + "paramDescription": "Irus section: Download reports?", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "irusProcessStats", + "paramDescription": "Irus section: Process stats?", + "paramRequired": true + }, + { + "paramName": "inod", + "paramLongName": "irusNumberOfOpendoarsToDownload", + "paramDescription": "Limit the number of the downloaded Opendoars (Irus) to the first irusNumberOfOpendoarsToDownload", + "paramRequired": true + }, + { + "paramName": "icted", + "paramLongName": "sarcCreateTablesEmptyDirs", + "paramDescription": "Sarc section: Create tables and empty JSON directories?", + "paramRequired": true + }, + { + "paramName": "idr", + "paramLongName": "sarcDownloadReports", + "paramDescription": "Sarc section: Download reports?", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "sarcProcessStats", + "paramDescription": "Sarc section: Process stats?", + "paramRequired": true + }, + { + "paramName": "inod", + "paramLongName": "sarcNumberOfIssnToDownload", + "paramDescription": "Limit the number of the downloaded ISSN (Sarc) to the first sarcNumberOfIssnToDownload", + "paramRequired": true + }, + + { + "paramName": "fs", + "paramLongName": "finalizeStats", + "paramDescription": "Create the usage_stats table?", + "paramRequired": true + }, + { + "paramName": "ftvi", + "paramLongName": "finalTablesVisibleToImpala", + "paramDescription": "Make the usage_stats, views_stats and downloads_stats tables visible to Impala", + "paramRequired": true + }, + { + "paramName": "nodt", + "paramLongName": "numberOfDownloadThreads", + "paramDescription": "Number of download threads", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/config-default.xml b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/config-default.xml new file mode 100644 index 000000000..b5c807378 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/config-default.xml @@ -0,0 +1,38 @@ + + + jobTracker + ${jobTracker} + + + nameNode + ${nameNode} + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1 + + + impalaJdbcUrl + jdbc:hive2://iis-cdh5-test-gw.ocean.icm.edu.pl:21050/;auth=noSasl; + + + oozie.wf.workflow.notification.url + {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status + + + oozie.use.system.libpath + true + + diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/workflow.xml b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/workflow.xml new file mode 100644 index 000000000..37700539b --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/workflow.xml @@ -0,0 +1,91 @@ + + + + hiveMetastoreUris + Hive server metastore URIs + + + hiveJdbcUrl + Hive server jdbc url + + + impalaJdbcUrl + Impala server jdbc url + + + + + ${jobTracker} + ${nameNode} + + + hive.metastore.uris + ${hiveMetastoreUris} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + eu.dnetlib.oa.graph.usagestatsbuild.export.ExecuteWorkflow + --matomoAuthToken${matomoAuthToken} + --matomoBaseURL${matomoBaseURL} + --repoLogPath${repoLogPath} + --portalLogPath${portalLogPath} + --portalMatomoID${portalMatomoID} + --irusUKBaseURL${irusUKBaseURL} + --irusUKReportPath${irusUKReportPath} + --sarcsReportPathArray${sarcsReportPathArray} + --sarcsReportPathNonArray${sarcsReportPathNonArray} + --lareferenciaLogPath${lareferenciaLogPath} + --lareferenciaBaseURL${lareferenciaBaseURL} + --lareferenciaAuthToken${lareferenciaAuthToken} + --dbHiveUrl${hiveJdbcUrl} + --dbImpalaUrl${impalaJdbcUrl} + --usageRawDataDBSchema${usageRawDataDBSchema} + --usageStatsDBSchema${usageStatsDBSchema} + --statsDBSchema${statsDBSchema} + --recreateDbAndTables${recreateDbAndTables} + --piwikEmptyDirs${piwikEmptyDirs} + --downloadPiwikLogs${downloadPiwikLogs} + --processPiwikLogs${processPiwikLogs} + --startingLogPeriod${startingLogPeriod} + --endingLogPeriod${endingLogPeriod} + --numberOfPiwikIdsToDownload${numberOfPiwikIdsToDownload} + --numberOfSiteIdsToDownload${numberOfSiteIdsToDownload} + --laReferenciaEmptyDirs${laReferenciaEmptyDirs} + --downloadLaReferenciaLogs${downloadLaReferenciaLogs} + --processLaReferenciaLogs${processLaReferenciaLogs} + --irusCreateTablesEmptyDirs${irusCreateTablesEmptyDirs} + --irusDownloadReports${irusDownloadReports} + --irusProcessStats${irusProcessStats} + --irusNumberOfOpendoarsToDownload${irusNumberOfOpendoarsToDownload} + --sarcCreateTablesEmptyDirs${sarcCreateTablesEmptyDirs} + --sarcDownloadReports${sarcDownloadReports} + --sarcProcessStats${sarcProcessStats} + --sarcNumberOfIssnToDownload${sarcNumberOfIssnToDownload} + --finalizeStats${finalizeStats} + --finalTablesVisibleToImpala${finalTablesVisibleToImpala} + --numberOfDownloadThreads${numberOfDownloadThreads} + + + + + + + + From 57cac3689801929d651404fbe47c6a1cb7998f14 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 13:38:03 +0100 Subject: [PATCH 005/149] changed the workflow name --- .../dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml index 4c286e4a2..b809b58fb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml @@ -1,4 +1,4 @@ - + From 46ba3793f61084d59ed251a48b74aef1c157026c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 16:47:31 +0100 Subject: [PATCH 006/149] code, workflow and parameters for the dump of the results associated to funders --- .../dump/funderresults/FunderResults.java | 19 ++ .../SparkPrepareResultProject.java | 165 ++++++++++++++++ .../graph/dump/funder_result_parameters.json | 26 +++ .../oozie_app/config-default.xml | 30 +++ .../dump/funderresults/oozie_app/workflow.xml | 179 ++++++++++++++++++ 5 files changed, 419 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java new file mode 100644 index 000000000..18884a327 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java @@ -0,0 +1,19 @@ + +package eu.dnetlib.dhp.oa.graph.dump.funderresults; + +import java.io.Serializable; +import java.util.List; + +import eu.dnetlib.dhp.schema.dump.oaf.Result; + +public class FunderResults implements Serializable { + private List results; + + public List getResults() { + return results; + } + + public void setResults(List results) { + this.results = results; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java new file mode 100644 index 000000000..179c449f6 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java @@ -0,0 +1,165 @@ + +package eu.dnetlib.dhp.oa.graph.dump.funderresults; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.*; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.dump.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Relation; +import scala.Tuple2; + +/** + * Preparation of the Project information to be added to the dumped results. For each result associated to at least one + * Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the + * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to + */ +public class SparkPrepareResultProject implements Serializable { + private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkPrepareResultProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String communityMapPath = parser.get("communityMapPath"); + log.info("communityMapPath: {}", communityMapPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + prepareResultProjectList2(spark, inputPath, outputPath, communityMapPath); + }); + } + + private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath, + String communityMapPath) { + + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + + Dataset relation = Utils + .readPath(spark, inputPath + "/relation", Relation.class) + .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + + Dataset result = Utils + .readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class) + .union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class)) + .union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class)); + + result + .joinWith(relation, result.col("id").equalTo(relation.col("target"))) + .groupByKey( + (MapFunction, String>) value -> value + ._2() + .getSource() + .substring(3, 15), + Encoders.STRING()) + .mapGroups( + (MapGroupsFunction, Tuple2>) ( + s, it) -> { + Tuple2 first = it.next(); + FunderResults fr = new FunderResults(); + List resultList = new ArrayList<>(); + resultList.add(ResultMapper.map(first._1(), communityMap, true)); + it.forEachRemaining(c -> { + resultList.add(ResultMapper.map(c._1(), communityMap, true)); + + }); + fr.setResults(resultList); + return new Tuple2<>(s, fr); + }, Encoders.tuple(Encoders.STRING(), Encoders.bean(FunderResults.class))) + .foreach(t -> { + String funder = t._1(); + spark + .createDataFrame(t._2.getResults(), Result.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); + }); + + } + + private static void prepareResultProjectList2(SparkSession spark, String inputPath, String outputPath, + String communityMapPath) { + + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + + Dataset relation = Utils + .readPath(spark, inputPath + "/relation", Relation.class) + .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + + Dataset result = Utils + .readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class) + .union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class)) + .union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class)); + + result + .joinWith(relation, result.col("id").equalTo(relation.col("target"))) + .groupByKey( + (MapFunction, String>) value -> value + ._2() + .getSource() + .substring(3, 15), + Encoders.STRING()) + .mapGroups( + (MapGroupsFunction, String>) (s, it) -> { + Tuple2 first = it.next(); + List resultList = new ArrayList<>(); + resultList.add(ResultMapper.map(first._1(), communityMap, true)); + it.forEachRemaining(c -> { + resultList.add(ResultMapper.map(c._1(), communityMap, true)); + + }); + spark + .createDataFrame(resultList, Result.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + s); + + return new String(); + }, Encoders.STRING()); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json new file mode 100644 index 000000000..f5eb81983 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "cmp", + "paramLongName": "communityMapPath", + "paramDescription": "the community map path", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml new file mode 100644 index 000000000..e5ec3d0ae --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml new file mode 100644 index 000000000..5ddab3398 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -0,0 +1,179 @@ + + + + + sourcePath + the source path + + + isLookUpUrl + the isLookup service endpoint + + + outputPath + the output path + + + accessToken + the access token used for the deposition in Zenodo + + + connectionUrl + the connection url for Zenodo + + + metadata + the metadata associated to the deposition + + + depositionType + the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) + + + conceptRecordId + for new version, the id of the record for the old deposition + + + depositionId + the depositionId of a deposition open that has to be added content + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap + --outputPath${workingDir}/communityMap + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/result + --communityMapPath${workingDir}/communityMap + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS + --hdfsPath${outputPath} + --nameNode${nameNode} + --accessToken${accessToken} + --connectionUrl${connectionUrl} + --metadata${metadata} + --communityMapPath${workingDir}/communityMap + --conceptRecordId${conceptRecordId} + --depositionType${depositionType} + --depositionId${depositionId} + + + + + + + + \ No newline at end of file From a172a37ad1c8259d95c1fb7acb83701ea057763a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 16:55:07 +0100 Subject: [PATCH 007/149] fixed typo --- .../dhp/oa/graph/dump/community/SparkPrepareResultProject.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 39850b5b8..612af6d16 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -34,7 +34,7 @@ import scala.Tuple2; /** * Preparation of the Project information to be added to the dumped results. For each result associated to at least one - * Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the + * Project, a serialization of an instance af ResultProject class is done. ResultProject contains the resultId, and the * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to */ public class SparkPrepareResultProject implements Serializable { From 5402062ff52df8183016d248f70e4aa95f737dc3 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 16:58:20 +0100 Subject: [PATCH 008/149] changed parameter file with the ono associated to the job --- .../oa/graph/dump/funderresults/SparkPrepareResultProject.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java index 179c449f6..9b254088a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java @@ -38,7 +38,7 @@ public class SparkPrepareResultProject implements Serializable { .toString( SparkPrepareResultProject.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json")); + "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); From 906db690d2c4c1cfd69a05c5d5f5dc75db2229e9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 17:43:08 +0100 Subject: [PATCH 009/149] - --- .../SparkPrepareResultProject.java | 47 +------------------ 1 file changed, 1 insertion(+), 46 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java index 9b254088a..21b4f4dc7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java @@ -65,7 +65,7 @@ public class SparkPrepareResultProject implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - prepareResultProjectList2(spark, inputPath, outputPath, communityMapPath); + prepareResultProjectList(spark, inputPath, outputPath, communityMapPath); }); } @@ -115,51 +115,6 @@ public class SparkPrepareResultProject implements Serializable { .option("compression", "gzip") .json(outputPath + "/" + funder); }); - - } - - private static void prepareResultProjectList2(SparkSession spark, String inputPath, String outputPath, - String communityMapPath) { - - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - - Dataset relation = Utils - .readPath(spark, inputPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); - - Dataset result = Utils - .readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class) - .union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class)) - .union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class)); - - result - .joinWith(relation, result.col("id").equalTo(relation.col("target"))) - .groupByKey( - (MapFunction, String>) value -> value - ._2() - .getSource() - .substring(3, 15), - Encoders.STRING()) - .mapGroups( - (MapGroupsFunction, String>) (s, it) -> { - Tuple2 first = it.next(); - List resultList = new ArrayList<>(); - resultList.add(ResultMapper.map(first._1(), communityMap, true)); - it.forEachRemaining(c -> { - resultList.add(ResultMapper.map(c._1(), communityMap, true)); - - }); - spark - .createDataFrame(resultList, Result.class) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + s); - - return new String(); - }, Encoders.STRING()); - } } From fafb6888871367a18bebf3b9f1b1dff3dd369174 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 18 Nov 2020 18:56:48 +0100 Subject: [PATCH 010/149] - --- .../dump/funderresults/FunderResults.java | 13 +++-- ...oject.java => SparkDumpFunderResults.java} | 53 ++++++------------- .../dump/funderresults/oozie_app/workflow.xml | 2 +- 3 files changed, 23 insertions(+), 45 deletions(-) rename dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/{SparkPrepareResultProject.java => SparkDumpFunderResults.java} (66%) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java index 18884a327..c3d2d4c2c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java @@ -2,18 +2,17 @@ package eu.dnetlib.dhp.oa.graph.dump.funderresults; import java.io.Serializable; -import java.util.List; import eu.dnetlib.dhp.schema.dump.oaf.Result; -public class FunderResults implements Serializable { - private List results; +public class FunderResults extends Result implements Serializable { + private String funder_id; - public List getResults() { - return results; + public String getFunder_id() { + return funder_id; } - public void setResults(List results) { - this.results = results; + public void setFunder_id(String funder_id) { + this.funder_id = funder_id; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java similarity index 66% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 21b4f4dc7..f84a5fd11 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -9,7 +9,6 @@ import java.util.*; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -21,7 +20,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.dump.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; @@ -30,13 +28,13 @@ import scala.Tuple2; * Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to */ -public class SparkPrepareResultProject implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.class); +public class SparkDumpFunderResults implements Serializable { + private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( - SparkPrepareResultProject.class + SparkDumpFunderResults.class .getResourceAsStream( "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); @@ -65,12 +63,12 @@ public class SparkPrepareResultProject implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - prepareResultProjectList(spark, inputPath, outputPath, communityMapPath); + writeResultProjectList(spark, inputPath, outputPath, communityMapPath); }); } - private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath, - String communityMapPath) { + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, + String communityMapPath) { CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); @@ -85,36 +83,17 @@ public class SparkPrepareResultProject implements Serializable { .union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class)); result - .joinWith(relation, result.col("id").equalTo(relation.col("target"))) - .groupByKey( - (MapFunction, String>) value -> value - ._2() - .getSource() - .substring(3, 15), - Encoders.STRING()) - .mapGroups( - (MapGroupsFunction, Tuple2>) ( - s, it) -> { - Tuple2 first = it.next(); - FunderResults fr = new FunderResults(); - List resultList = new ArrayList<>(); - resultList.add(ResultMapper.map(first._1(), communityMap, true)); - it.forEachRemaining(c -> { - resultList.add(ResultMapper.map(c._1(), communityMap, true)); + .joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner") + .map((MapFunction, FunderResults>) value ->{ + FunderResults res = (FunderResults) ResultMapper.map(value._1(), communityMap, false); + res.setFunder_id(value._2().getSource().substring(3,15)); + return res; + }, Encoders.bean(FunderResults.class)) + .write() + .partitionBy("funder_id") + .mode(SaveMode.Overwrite) + .json(outputPath); - }); - fr.setResults(resultList); - return new Tuple2<>(s, fr); - }, Encoders.tuple(Encoders.STRING(), Encoders.bean(FunderResults.class))) - .foreach(t -> { - String funder = t._1(); - spark - .createDataFrame(t._2.getResults(), Result.class) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funder); - }); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml index 5ddab3398..aca8f9714 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -137,7 +137,7 @@ yarn cluster Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkPrepareResultProject + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults dhp-graph-mapper-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} From 24c56fa7a3584c4a258e9674e089ce36f23b7125 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 19 Nov 2020 19:15:39 +0100 Subject: [PATCH 011/149] new logic and workflow for dump of results with link to projects. In this implementation the result match the model of the communityresult. --- .../dump/funderresults/FunderResults.java | 4 +- .../funderresults/SparkDumpFunderResults.java | 41 +- .../SparkResultLinkedToProject.java | 82 ++++ .../dump/funderresults/oozie_app/workflow.xml | 365 +++++++++++++++++- .../graph/dump/input_parameters_link_prj.json | 36 ++ 5 files changed, 501 insertions(+), 27 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java index c3d2d4c2c..138e262e4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java @@ -3,9 +3,9 @@ package eu.dnetlib.dhp.oa.graph.dump.funderresults; import java.io.Serializable; -import eu.dnetlib.dhp.schema.dump.oaf.Result; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -public class FunderResults extends Result implements Serializable { +public class FunderResults extends CommunityResult implements Serializable { private String funder_id; public String getFunder_id() { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index f84a5fd11..d4e294735 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -17,9 +17,11 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.api.zenodo.Community; import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; @@ -53,8 +55,8 @@ public class SparkDumpFunderResults implements Serializable { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final String communityMapPath = parser.get("communityMapPath"); - log.info("communityMapPath: {}", communityMapPath); + final String relationPath = parser.get("relationPath"); + log.info("relationPath: {}", relationPath); SparkConf conf = new SparkConf(); @@ -63,36 +65,33 @@ public class SparkDumpFunderResults implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath, communityMapPath); + writeResultProjectList(spark, inputPath, outputPath); }); } - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, - String communityMapPath) { - - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); - Dataset result = Utils - .readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class) - .union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class)) - .union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class)); + Dataset result = Utils + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); result .joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner") - .map((MapFunction, FunderResults>) value ->{ - FunderResults res = (FunderResults) ResultMapper.map(value._1(), communityMap, false); - res.setFunder_id(value._2().getSource().substring(3,15)); - return res; - }, Encoders.bean(FunderResults.class)) - .write() - .partitionBy("funder_id") - .mode(SaveMode.Overwrite) - .json(outputPath); + .map((MapFunction, FunderResults>) value -> { + FunderResults res = (FunderResults) value._1(); + res.setFunder_id(value._2().getSource().substring(3, 15)); + return res; + }, Encoders.bean(FunderResults.class)) + .write() + .partitionBy("funder_id") + .mode(SaveMode.Overwrite) + .json(outputPath); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java new file mode 100644 index 000000000..456e44447 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -0,0 +1,82 @@ + +package eu.dnetlib.dhp.oa.graph.dump.funderresults; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class SparkResultLinkedToProject implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkResultLinkedToProject.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkResultLinkedToProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + final String relationPath = parser.get("relationPath"); + log.info("relationPath: {}", relationPath); + + Class inputClazz = (Class) Class.forName(resultClassName); + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultsLikedToProjects(spark, inputClazz, inputPath, outputPath, relationPath); + }); + } + + private static void writeResultsLikedToProjects(SparkSession spark, Class inputClazz, + String inputPath, String outputPath, String relationPath) { + + Dataset results = Utils.readPath(spark, inputPath, inputClazz); + Dataset relations = Utils + .readPath(spark, relationPath, Relation.class) + .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + relations + .joinWith( + results, relations.col("target").equalTo(results.col("id")), + "inner") + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml index aca8f9714..d0acdf051 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -127,10 +127,367 @@ --nameNode${nameNode} --isLookUpUrl${isLookUpUrl} - + + + + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/publication + --relationPath${sourcePath}/relation + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/dataset + --relationPath${sourcePath}/relation + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/otherresearchproduct + --relationPath${sourcePath}/relation + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/software + --relationPath${sourcePath}/relation + + + + + + + + + + + + + + + + + yarn + cluster + Dump table publication for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/result/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/dump/publication + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table dataset for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/result/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dump/dataset + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table ORP for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/result/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/dump/otherresearchproduct + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table software for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/result/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/dump/software + --communityMapPath${workingDir}/communityMap + + + + + + + + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + + + + + + + + + + + yarn + cluster + Extend dumped publications with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/publication + --outputPath${workingDir}/ext/publication + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped dataset with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/dataset + --outputPath${workingDir}/ext/dataset + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped ORP with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/otherresearchproduct + --outputPath${workingDir}/ext/orp + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped software with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/software + --outputPath${workingDir}/ext/software + --preparedInfoPath${workingDir}/preparedInfo + + + + + @@ -149,9 +506,9 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${sourcePath} - --outputPath${workingDir}/result - --communityMapPath${workingDir}/communityMap + --sourcePath${workingDir}/ext + --outputPath${outputPath} + --relationPath${sourcePath}/relation diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json new file mode 100644 index 000000000..b1f4c026a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -0,0 +1,36 @@ +[ + + { + "paramName":"cmp", + "paramLongName":"communityMapPath", + "paramDescription": "the path to the serialization of the community map", + "paramRequired": true + }, + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName":"tn", + "paramLongName":"resultTableName", + "paramDescription": "the name of the result table we are currently working on", + "paramRequired": true + } +] + + + From cf3f47563fbca758ba69e6a50a9096fc252c00f4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 19 Nov 2020 19:16:05 +0100 Subject: [PATCH 012/149] new parameter files --- .../dhp/oa/graph/dump/funder_result_parameters.json | 7 ++++++- .../dhp/oa/graph/dump/input_parameters_link_prj.json | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json index f5eb81983..2128c91e4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -22,5 +22,10 @@ "paramLongName": "communityMapPath", "paramDescription": "the community map path", "paramRequired": true - } + },{ + "paramName": "rp", + "paramLongName": "relationPath", + "paramDescription": "the relationPath", + "paramRequired": true +} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json index b1f4c026a..aab929e43 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -29,7 +29,12 @@ "paramLongName":"resultTableName", "paramDescription": "the name of the result table we are currently working on", "paramRequired": true - } + }, { + "paramName":"rp", + "paramLongName":"relationPath", + "paramDescription": "the path to the relations", + "paramRequired": true +} ] From 0a9db67eecb01753a9b144bf3dd98ff4ce17f06e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 20 Nov 2020 12:21:33 +0100 Subject: [PATCH 013/149] - --- .../dump/funderresults/SparkResultLinkedToProject.java | 5 +++++ .../dhp/oa/graph/dump/funder_result_parameters.json | 7 +------ .../dhp/oa/graph/dump/input_parameters_link_prj.json | 7 ------- 3 files changed, 6 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 456e44447..6d059567c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -8,7 +8,10 @@ import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; @@ -18,6 +21,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; +import scala.Tuple2; public class SparkResultLinkedToProject implements Serializable { @@ -74,6 +78,7 @@ public class SparkResultLinkedToProject implements Serializable { .joinWith( results, relations.col("target").equalTo(results.col("id")), "inner") + .map((MapFunction, R>) t2 -> t2._2(), Encoders.bean(inputClazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json index 2128c91e4..9a5a553b1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -17,12 +17,7 @@ "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false }, - { - "paramName": "cmp", - "paramLongName": "communityMapPath", - "paramDescription": "the community map path", - "paramRequired": true - },{ +{ "paramName": "rp", "paramLongName": "relationPath", "paramDescription": "the relationPath", diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json index aab929e43..5c4886741 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -1,11 +1,4 @@ [ - - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": true - }, { "paramName":"s", "paramLongName":"sourcePath", From 259c67ce365b58aa052ae2df85a20a4e526ccb2c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 20 Nov 2020 12:32:23 +0100 Subject: [PATCH 014/149] fixed issue in path name --- .../oa/graph/dump/funderresults/SparkDumpFunderResults.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index d4e294735..acafa968a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -65,14 +65,14 @@ public class SparkDumpFunderResults implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath); + writeResultProjectList(spark, inputPath, outputPath, relationPath); }); } - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, String relationPath) { Dataset relation = Utils - .readPath(spark, inputPath + "/relation", Relation.class) + .readPath(spark, relationPath + "/relation", Relation.class) .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); Dataset result = Utils From 73dbb79602aa2665b8238bf08feae98d09028545 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:36:15 +0100 Subject: [PATCH 015/149] removed the checl for the community name in the common version on MakeTar --- .../src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java index 4047fdca4..89fa09f3c 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java @@ -90,9 +90,9 @@ public class MakeTarArchive implements Serializable { String p_string = p.toString(); if (!p_string.endsWith("_SUCCESS")) { String name = p_string.substring(p_string.lastIndexOf("/") + 1); - if (name.trim().equalsIgnoreCase("communities_infrastructures")) { - name = "communities_infrastructures.json"; - } +// if (name.trim().equalsIgnoreCase("communities_infrastructures")) { +// name = "communities_infrastructures.json"; +// } TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name); entry.setSize(fileStatus.getLen()); current_size += fileStatus.getLen(); From 1832708c42bfddf065ac19db28cf39ce6a328c87 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:37:36 +0100 Subject: [PATCH 016/149] modified boolean variable with string one whcih specify the type of dump we are performing: complete, community or funder --- .../dhp/oa/graph/dump/DumpProducts.java | 22 ++++++++----------- .../dhp/oa/graph/dump/ResultMapper.java | 8 +++---- .../community/SparkDumpCommunityProducts.java | 10 ++++++++- 3 files changed, 22 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java index 1279ede53..d20a3036e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -11,17 +11,12 @@ import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; -import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; import eu.dnetlib.dhp.schema.oaf.*; /** @@ -33,7 +28,7 @@ public class DumpProducts implements Serializable { public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath, Class inputClazz, Class outputClazz, - boolean graph) { + String dumpType) { SparkConf conf = new SparkConf(); @@ -42,7 +37,7 @@ public class DumpProducts implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, graph); + execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); }); } @@ -53,13 +48,13 @@ public class DumpProducts implements Serializable { String communityMapPath, Class inputClazz, Class outputClazz, - boolean graph) { + String dumpType) { CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); Utils .readPath(spark, inputPath, inputClazz) - .map((MapFunction) value -> execMap(value, communityMap, graph), Encoders.bean(outputClazz)) + .map((MapFunction) value -> execMap(value, communityMap, dumpType), Encoders.bean(outputClazz)) .filter(Objects::nonNull) .write() .mode(SaveMode.Overwrite) @@ -70,18 +65,18 @@ public class DumpProducts implements Serializable { private static O execMap(I value, CommunityMap communityMap, - boolean graph) { + String dumpType) { Optional odInfo = Optional.ofNullable(value.getDataInfo()); if (odInfo.isPresent()) { - if (odInfo.get().getDeletedbyinference()) { + if (odInfo.get().getDeletedbyinference() || odInfo.get().getInvisible()) { return null; } } else { return null; } - if (!graph) { + if (Constants.DUMPTYPE.COMMUNITY.getType().equals(dumpType)) { Set communities = communityMap.keySet(); Optional> inputContext = Optional @@ -102,7 +97,8 @@ public class DumpProducts implements Serializable { return null; } } - return (O) ResultMapper.map(value, communityMap, graph); + + return (O) ResultMapper.map(value, communityMap, dumpType); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index 4c3bc0dd5..cb052ebaa 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -21,10 +21,10 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class ResultMapper implements Serializable { public static Result map( - E in, Map communityMap, boolean graph) { + E in, Map communityMap, String dumpType) { Result out; - if (graph) { + if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { out = new GraphResult(); } else { out = new CommunityResult(); @@ -217,7 +217,7 @@ public class ResultMapper implements Serializable { .ofNullable(input.getInstance()); if (oInst.isPresent()) { - if (graph) { + if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { ((GraphResult) out) .setInstance(oInst.get().stream().map(i -> getGraphInstance(i)).collect(Collectors.toList())); } else { @@ -296,7 +296,7 @@ public class ResultMapper implements Serializable { out.setType(input.getResulttype().getClassid()); } - if (!graph) { + if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { ((CommunityResult) out) .setCollectedfrom( input diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java index c4b89936f..63970d14b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java @@ -4,12 +4,15 @@ package eu.dnetlib.dhp.oa.graph.dump.community; import java.io.Serializable; import java.util.*; +import javax.swing.text.html.Option; + import org.apache.commons.io.IOUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Result; @@ -48,6 +51,11 @@ public class SparkDumpCommunityProducts implements Serializable { String communityMapPath = parser.get("communityMapPath"); + final String dumpType = Optional + .ofNullable(parser.get("dumpType")) + .map(String::valueOf) + .orElse("community"); + Class inputClazz = (Class) Class.forName(resultClassName); DumpProducts dump = new DumpProducts(); @@ -55,7 +63,7 @@ public class SparkDumpCommunityProducts implements Serializable { dump .run( isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, CommunityResult.class, - false); + dumpType); } From 44db258dc4324d03be64091e114a885c75a9a752 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:38:06 +0100 Subject: [PATCH 017/149] added enumerated for the dump type --- .../eu/dnetlib/dhp/oa/graph/dump/Constants.java | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index a466cf074..86a275ae2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -40,4 +40,18 @@ public class Constants { coarCodeLabelMap.put("c_14cb", "CLOSED"); coarCodeLabelMap.put("c_f1cf", "EMBARGO"); } + + public enum DUMPTYPE { + COMPLETE("complete"), COMMUNITY("community"), FUNDER("funder"); + + private String type; + + DUMPTYPE(String type) { + this.type = type; + } + + public String getType() { + return type; + } + } } From 00c377dac2b53380b24fe75fd908aed5676c15cb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:40:22 +0100 Subject: [PATCH 018/149] added specification of MapFunction types in map --- .../dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java index 1276d8495..2b80b1d86 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java @@ -8,6 +8,7 @@ import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -20,6 +21,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import scala.Tuple2; public class SparkUpdateProjectInfo implements Serializable { @@ -73,7 +75,7 @@ public class SparkUpdateProjectInfo implements Serializable { .joinWith( resultProject, result.col("id").equalTo(resultProject.col("resultId")), "left") - .map(value -> { + .map((MapFunction, CommunityResult>) value -> { CommunityResult r = value._1(); Optional.ofNullable(value._2()).ifPresent(rp -> { r.setProjects(rp.getProjectsList()); From 3319440c5348ec03399f7b4e77c7e165ee3de882 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:41:09 +0100 Subject: [PATCH 019/149] changed the direction of the relation between projects and result considered to select the results linked to projects --- .../graph/dump/community/SparkPrepareResultProject.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 612af6d16..2d43888b4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -76,16 +76,16 @@ public class SparkPrepareResultProject implements Serializable { private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + .filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'"); Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); projects - .joinWith(relation, projects.col("id").equalTo(relation.col("source"))) + .joinWith(relation, projects.col("id").equalTo(relation.col("target")), "inner") .groupByKey( (MapFunction, String>) value -> value ._2() - .getTarget(), + .getSource(), Encoders.STRING()) .mapGroups( (MapGroupsFunction, ResultProject>) (s, @@ -93,7 +93,7 @@ public class SparkPrepareResultProject implements Serializable { Set projectSet = new HashSet<>(); Tuple2 first = it.next(); ResultProject rp = new ResultProject(); - rp.setResultId(first._2().getTarget()); + rp.setResultId(s); eu.dnetlib.dhp.schema.oaf.Project p = first._1(); projectSet.add(p.getId()); Project ps = getProject(p); From 62928ef7a5a68c8c45fb9f7662b4bb25153b908d Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:42:41 +0100 Subject: [PATCH 020/149] changed to save the communities_infrastructures information as the other entity dumps: in a json.gz file --- .../dump/complete/CreateContextEntities.java | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java index 23224f8db..ccb84c713 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java @@ -1,22 +1,25 @@ package eu.dnetlib.dhp.oa.graph.dump.complete; -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; +import java.io.*; import java.nio.charset.StandardCharsets; import java.util.function.Consumer; import java.util.function.Function; +import org.apache.commons.crypto.utils.IoUtils; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FSDataOutputStream; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.apache.hadoop.io.compress.CompressionOutputStream; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; @@ -76,8 +79,11 @@ public class CreateContextEntities implements Serializable { } else { fsDataOutputStream = fileSystem.create(hdfsWritePath); } + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); - this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + this.writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), + StandardCharsets.UTF_8)); } From 7e940f1991c1755d2ec51b11e85675dee212b5f7 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:43:34 +0100 Subject: [PATCH 021/149] changed to consider the modification for the specification of the type of dump --- .../dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java index 773068dfb..36ced3a4a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java @@ -49,7 +49,7 @@ public class DumpGraphEntities implements Serializable { d .run( isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, GraphResult.class, - true); + eu.dnetlib.dhp.oa.graph.dump.Constants.DUMPTYPE.COMPLETE.getType()); break; case "40": runWithSparkSession( From b9b6bdb2e67f99d14abeaca83783d3450b015fb4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:44:53 +0100 Subject: [PATCH 022/149] fixing issue on previous implementation --- .../funderresults/SparkDumpFunderResults.java | 55 +++++++++++++------ .../SparkResultLinkedToProject.java | 19 +++++-- 2 files changed, 53 insertions(+), 21 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index acafa968a..740a4245d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -9,10 +9,7 @@ import java.util.*; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -22,6 +19,7 @@ import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Project; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; @@ -69,11 +67,12 @@ public class SparkDumpFunderResults implements Serializable { }); } - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, String relationPath) { + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, + String relationPath) { Dataset relation = Utils .readPath(spark, relationPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + .filter("dataInfo.deletedbyinference = false and relClass = 'isProducedBy'"); Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) @@ -81,18 +80,40 @@ public class SparkDumpFunderResults implements Serializable { .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - result - .joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner") - .map((MapFunction, FunderResults>) value -> { - FunderResults res = (FunderResults) value._1(); - res.setFunder_id(value._2().getSource().substring(3, 15)); - return res; - }, Encoders.bean(FunderResults.class)) - .write() - .partitionBy("funder_id") - .mode(SaveMode.Overwrite) - .json(outputPath); + List funderList = relation + .select("target") + .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) + .distinct() + .collectAsList(); + +// Dataset results = result +// .joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner") +// .map((MapFunction, CommunityResult>) value -> { +// return value._1(); +// }, Encoders.bean(CommunityResult.class)); + + funderList.forEach(funder -> writeFunderResult(funder, result, outputPath)); } + private static void writeFunderResult(String funder, Dataset results, String outputPath) { + + results.map((MapFunction) r -> { + if (!Optional.ofNullable(r.getProjects()).isPresent()) { + return null; + } + for (Project p : r.getProjects()) { + if (p.getId().startsWith(funder)) { + return r; + } + } + return null; + }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 6d059567c..e5d7e2254 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -10,6 +10,7 @@ import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -70,15 +71,25 @@ public class SparkResultLinkedToProject implements Serializable { private static void writeResultsLikedToProjects(SparkSession spark, Class inputClazz, String inputPath, String outputPath, String relationPath) { - Dataset results = Utils.readPath(spark, inputPath, inputClazz); + Dataset results = Utils + .readPath(spark, inputPath, inputClazz) + .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); Dataset relations = Utils .readPath(spark, relationPath, Relation.class) - .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + .filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'"); + relations .joinWith( - results, relations.col("target").equalTo(results.col("id")), + results, relations.col("source").equalTo(results.col("id")), "inner") - .map((MapFunction, R>) t2 -> t2._2(), Encoders.bean(inputClazz)) + .groupByKey( + (MapFunction, String>) value -> value + ._2() + .getId(), + Encoders.STRING()) + .mapGroups((MapGroupsFunction, R>) (k, it) -> { + return it.next()._2(); + }, Encoders.bean(inputClazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") From 35ecea8842886c9952a4b3abfdffdf4514e01b2f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:45:15 +0100 Subject: [PATCH 023/149] changed to consider the modification for the specification of the type of dump --- .../dnetlib/dhp/oa/graph/dump/DumpJobTest.java | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java index 54a610b9c..271ae8fc1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -8,7 +8,6 @@ import java.util.Arrays; import java.util.List; import org.apache.commons.io.FileUtils; -import org.apache.hadoop.yarn.webapp.hamlet.Hamlet; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -23,7 +22,6 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.Gson; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.dump.oaf.Result; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; import eu.dnetlib.dhp.schema.oaf.Dataset; @@ -155,7 +153,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -220,7 +218,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - GraphResult.class, true); + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -253,7 +251,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -285,7 +283,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -321,7 +319,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -357,7 +355,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -392,7 +390,7 @@ public class DumpJobTest { .run( // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, false); + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); From 54a309bb6bec5a7b7629c2257485579637e18b96 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:45:30 +0100 Subject: [PATCH 024/149] refactoring --- .../graph/dump/complete/CreateEntityTest.java | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index 411e6f4b0..702811549 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -3,13 +3,25 @@ package eu.dnetlib.dhp.oa.graph.dump.complete; import static org.mockito.Mockito.lenient; +import java.io.BufferedWriter; import java.io.IOException; +import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; +import java.nio.file.Files; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.function.Consumer; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; @@ -60,6 +72,8 @@ public class CreateEntityTest { private QueryInformationSystem queryInformationSystem; + private static String workingDir; + @BeforeEach public void setUp() throws ISLookUpException { lenient().when(isLookUpService.quickSearchProfile(XQUERY_ENTITY)).thenReturn(communityMap); @@ -67,6 +81,13 @@ public class CreateEntityTest { queryInformationSystem.setIsLookUp(isLookUpService); } + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.complete.CreateEntityTest.class.getSimpleName()) + .toString(); + } + @Test public void test1() throws ISLookUpException, IOException { List cInfoList = new ArrayList<>(); @@ -123,4 +144,30 @@ public class CreateEntityTest { riList.forEach(c -> System.out.println(new Gson().toJson(c))); } + + @Test + public void test2() throws IOException, ISLookUpException { + LocalFileSystem fs = FileSystem.getLocal(new Configuration()); + + Path hdfsWritePath = new Path(workingDir + "/prova"); + FSDataOutputStream fsDataOutputStream = null; + if (fs.exists(hdfsWritePath)) { + fsDataOutputStream = fs.append(hdfsWritePath); + } else { + fsDataOutputStream = fs.create(hdfsWritePath); + } + CompressionCodecFactory factory = new CompressionCodecFactory(fs.getConf()); + CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); + + BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), + StandardCharsets.UTF_8)); + + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + queryInformationSystem.getContextInformation(consumer); + + List riList = new ArrayList<>(); + cInfoList.forEach(cInfo -> riList.add(Process.getEntity(cInfo))); + + } } From c167a18057f3b5326c76f73ae144cb64c5347762 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:45:50 +0100 Subject: [PATCH 025/149] added new parameter for the dumpType --- .../eu/dnetlib/dhp/oa/graph/dump/input_parameters.json | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json index b1f4c026a..ca12ae3ec 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json @@ -29,7 +29,12 @@ "paramLongName":"resultTableName", "paramDescription": "the name of the result table we are currently working on", "paramRequired": true - } + },{ + "paramName":"dt", + "paramLongName":"dumpType", + "paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project", + "paramRequired": false +} ] From 7e14452a87ba88657abda8f41ea6731ee5751502 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:46:34 +0100 Subject: [PATCH 026/149] final versione of the wf to get the dump of results associated to at least one funder per funder --- .../dump/funderresults/oozie_app/workflow.xml | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml index d0acdf051..d258d4dd4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -182,7 +182,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/result/dataset --relationPath${sourcePath}/relation @@ -208,7 +208,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/result/otherresearchproduct --relationPath${sourcePath}/relation @@ -234,7 +234,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/result/software --relationPath${sourcePath}/relation @@ -269,9 +269,11 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/dump/publication --communityMapPath${workingDir}/communityMap + --dumpTypefunder @@ -295,9 +297,11 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/dump/dataset --communityMapPath${workingDir}/communityMap + --dumpTypefunder @@ -321,9 +325,11 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/dump/otherresearchproduct --communityMapPath${workingDir}/communityMap + --dumpTypefunder @@ -347,9 +353,11 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/dump/software --communityMapPath${workingDir}/communityMap + --dumpTypefunder @@ -508,7 +516,7 @@ --sourcePath${workingDir}/ext --outputPath${outputPath} - --relationPath${sourcePath}/relation + --relationPath${sourcePath} From 39f4a2087300f90bc64cbe928655c13bb0dcc2ff Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 14:47:32 +0100 Subject: [PATCH 027/149] chenged the path and the name for saving the communities_infrastructures dump file --- .../dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml index b809b58fb..8189e2594 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/oozie_app/workflow.xml @@ -368,7 +368,7 @@ eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities - --hdfsPath${workingDir}/collect/communities_infrastructures + --hdfsPath${workingDir}/collect/communities_infrastructures/communities_infrastructure.json.gz --nameNode${nameNode} --isLookUpUrl${isLookUpUrl} From 72bb0fe360747bed534890b72f4142f165a6e8e4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 24 Nov 2020 16:47:07 +0100 Subject: [PATCH 028/149] changed directory name --- .../dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 740a4245d..232459c19 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -77,7 +77,7 @@ public class SparkDumpFunderResults implements Serializable { Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); List funderList = relation From b37b9352d7cd96febbe2c9aab4a5f22aef43d675 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:41:08 +0100 Subject: [PATCH 029/149] added constant value for semantic relationship between projects and results --- .../dnetlib/dhp/oa/graph/dump/Constants.java | 2 ++ .../dump/funderresults/FunderResults.java | 18 ----------- .../ResultLinkedToProjectTest.java | 4 +++ .../dump/funderresult/SplitPerFunderTest.java | 4 +++ .../dump/funderresource/extendeddump/dataset | 0 .../dump/funderresource/extendeddump/orp | 0 .../funderresource/extendeddump/publication | 12 +++++++ .../dump/funderresource/extendeddump/relation | 8 +++++ .../dump/funderresource/extendeddump/software | 0 .../dump/funderresource/match/papers.json | 32 +++++++++++++++++++ .../dump/funderresource/match/relations.json | 30 +++++++++++++++++ .../dump/funderresource/nomatch/papers.json | 32 +++++++++++++++++++ .../funderresource/nomatch/relations.json | 30 +++++++++++++++++ 13 files changed, 154 insertions(+), 18 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/dataset create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/publication create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/software create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index 86a275ae2..c64554555 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -26,6 +26,8 @@ public class Constants { public static String ORCID = "orcid"; + public static String RESULT_PROJECT_IS_PRODUCED_BY = "isProducedBy"; + static { accessRightsCoarMap.put("OPEN", "c_abf2"); accessRightsCoarMap.put("RESTRICTED", "c_16ec"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java deleted file mode 100644 index 138e262e4..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/FunderResults.java +++ /dev/null @@ -1,18 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresults; - -import java.io.Serializable; - -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; - -public class FunderResults extends CommunityResult implements Serializable { - private String funder_id; - - public String getFunder_id() { - return funder_id; - } - - public void setFunder_id(String funder_id) { - this.funder_id = funder_id; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java new file mode 100644 index 000000000..3696db7f8 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -0,0 +1,4 @@ +package eu.dnetlib.dhp.oa.graph.dump.funderresult; + +public class ResultLinkedToProjectTest { +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java new file mode 100644 index 000000000..8e49b9fc6 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -0,0 +1,4 @@ +package eu.dnetlib.dhp.oa.graph.dump.funderresult; + +public class DumpResultPerFunderTest { +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/dataset b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/dataset new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/publication b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/publication new file mode 100644 index 000000000..901b34abc --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/publication @@ -0,0 +1,12 @@ +{"author":[{"fullname":"Eric A. Wright","name":"Eric A.","pid":{"id":{"scheme":"orcid","value":"0000-0001-8604-7026"}},"rank":1,"surname":"Wright"},{"fullname":"Christopher D. d’Esterre","name":"Christopher D.","rank":2,"surname":"d’Esterre"},{"fullname":"Laura B. Morrison","name":"Laura B.","rank":3,"surname":"Morrison"},{"fullname":"Neil Cockburn","name":"Neil","rank":4,"surname":"Cockburn"},{"fullname":"Michael Kovacs","name":"Michael","rank":5,"surname":"Kovacs"},{"fullname":"Ting-Yim Lee","name":"Ting-Yim","rank":6,"surname":"Lee"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},{"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed Central"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},{"key":"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c","value":"Europe PubMed Central"}],"context":[{"code":"ni","label":"Neuroinformatics","provenance":[{"provenance":"Inferred by OpenAIRE","trust":"0.8"}]}],"contributor":["Jiang, Quan"],"country":[],"coverage":[],"dateofcollection":"","description":["CT Perfusion (CTP) derived cerebral blood flow (CBF) thresholds have been proposed as the optimal parameter for distinguishing the infarct core prior to reperfusion. Previous threshold-derivation studies have been limited by uncertainties introduced by infarct expansion between the acute phase of stroke and follow-up imaging, or DWI lesion reversibility. In this study a model is proposed for determining infarction CBF thresholds at 3hr ischemia time by comparing contemporaneously acquired CTP derived CBF maps to 18F-FFMZ-PET imaging, with the objective of deriving a CBF threshold for infarction after 3 hours of ischemia. Endothelin-1 (ET-1) was injected into the brain of Duroc-Cross pigs (n = 11) through a burr hole in the skull. CTP images were acquired 10 and 30 minutes post ET-1 injection and then every 30 minutes for 150 minutes. 370 MBq of 18F-FFMZ was injected ~120 minutes post ET-1 injection and PET images were acquired for 25 minutes starting ~155-180 minutes post ET-1 injection. CBF maps from each CTP acquisition were co-registered and converted into a median CBF map. The median CBF map was co-registered to blood volume maps for vessel exclusion, an average CT image for grey/white matter segmentation, and 18F-FFMZ-PET images for infarct delineation. Logistic regression and ROC analysis were performed on infarcted and non-infarcted pixel CBF values for each animal that developed infarct. Six of the eleven animals developed infarction. The mean CBF value corresponding to the optimal operating point of the ROC curves for the 6 animals was 12.6 ± 2.8 mL·min-1·100g-1 for infarction after 3 hours of ischemia. The porcine ET-1 model of cerebral ischemia is easier to implement then other large animal models of stroke, and performs similarly as long as CBF is monitored using CTP to prevent reperfusion."],"format":[],"id":"50|dedup_wf_001::0017bb7bb6a0e2f5624db2721a1bc1a5","instance":[{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"http://creativecommons.org/licenses/by/4.0","publicationdate":"2016-06-27","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1371/journal.pone.0158157"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed Central"},"hostedby":{"key":"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c","value":"Europe PubMed Central"},"publicationdate":"2016-06-01","refereed":"UNKNOWN","type":"Article","url":["http://europepmc.org/articles/PMC4922566"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"license":"http://creativecommons.org/licenses/by/4.0/","publicationdate":"2016-06-27","refereed":"UNKNOWN","type":"Article","url":["http://dx.plos.org/10.1371/journal.pone.0158157","http://dx.doi.org/10.1371/journal.pone.0158157"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|doajarticles::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"license":"cc-by","refereed":"UNKNOWN","type":"Article","url":["https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0158157&type=printable"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|doajarticles::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"refereed":"UNKNOWN","type":"Article","url":["https://www.ncbi.nlm.nih.gov/pubmed/27347877","http://ui.adsabs.harvard.edu/abs/2016PLoSO..1158157W/abstract","https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158157","https://paperity.org/p/80470187/absolute-cerebral-blood-flow-infarction-threshold-for-3-hour-ischemia-time-determined","https://dx.plos.org/10.1371/journal.pone.0158157","https://academic.microsoft.com/#/detail/2460634846"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::830e55b42c4aaa815c19cfa4f2e5855e","value":"PLoS ONE"},"publicationdate":"2016-01-01","refereed":"UNKNOWN","type":"Article","url":["http://europepmc.org/articles/PMC4922566?pdf=render","https://doaj.org/toc/1932-6203"]},{"collectedfrom":{"key":"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c","value":"Europe PubMed Central"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2016-06-27T17:32:46Z","refereed":"UNKNOWN","type":"UNKNOWN","url":["https://dx.doi.org/10.1371/journal.pone.0158157"]}],"language":{"code":"UNKNOWN","label":"UNKNOWN"},"lastupdatetimestamp":1603727328518,"maintitle":"Absolute Cerebral Blood Flow Infarction Threshold for 3-Hour Ischemia Time Determined with CT Perfusion and 18F-FFMZ-PET Imaging in a Porcine Model of Cerebral Ischemia","originalId":["10.1371/journal.pone.0158157","oai:pubmedcentral.nih.gov:4922566","2460634846","oai:doaj.org/article:a0a0f971217e4277aae02c2ddb0243ed","27347877"],"pid":[{"scheme":"doi","value":"10.1371/journal.pone.0158157"},{"scheme":"pmc","value":"PMC4922566"},{"scheme":"pmid","value":"27347877"}],"projects":[{"code":"unidentified","funder":{"jurisdiction":"CA","name":"Canadian Institutes of Health Research","shortName":"CIHR"},"id":"40|cihr________::1e5e62235d094afd01cd56e65112fc63","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"unidentified"}],"publicationdate":"2016-06-27","publisher":"Public Library of Science (PLoS)","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Research Article"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine and Health Sciences"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Diagnostic Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Signs and Symptoms"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Infarction"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Pathology and Laboratory Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Critical Care and Emergency Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Reperfusion"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Research and Analysis Methods"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Imaging Techniques"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Neuroimaging"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Positron Emission Tomography"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Biology and Life Sciences"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Neuroscience"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Diagnostic Radiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Tomography"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Radiology and Imaging"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Neurology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Cerebral Ischemia"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Vascular Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Ischemia"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Cerebrovascular Diseases"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Stroke"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Ischemic Stroke"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Computed Axial Tomography"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Model Organisms"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Animal Models"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Pig Models"}},{"subject":{"scheme":"keywords","value":"General Biochemistry, Genetics and Molecular Biology"}},{"subject":{"scheme":"keywords","value":"General Agricultural and Biological Sciences"}},{"subject":{"scheme":"keywords","value":"General Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"R"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Science"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Q"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.8487"},"subject":{"scheme":"mesheuropmc","value":"cardiovascular system"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.7884"},"subject":{"scheme":"mesheuropmc","value":"cardiovascular diseases"}}],"type":"publication"} +{"author":[{"fullname":"NIOO-KNAW KNAW","name":"NIOO-KNAW","pid":{"id":{"scheme":"orcid","value":"0000-0002-3835-159X"}},"rank":1,"surname":"KNAW"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},{"key":"10|openaire____::fdb035c8b3e0540a8d9a561a6c44f4de","value":"NARCIS"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"}],"context":[{"code":"dh-ch","label":"Digital Humanities and Cultural Heritage","provenance":[{"provenance":"Inferred by OpenAIRE","trust":"0.8"}]}],"contributor":["Universidad de Alicante. Departamento de Ciencias Ambientales y Recursos Naturales","Universidad de Alicante. Centro Iberoamericano de la Biodiversidad","Biodiversidad y Biotecnología aplicadas a la Biología de la Conservación","Terrestrial Ecology (TE)"],"country":[{"code":"NL","label":"Netherlands","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"ES","label":"Spain","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2018-10-03T06:57:46.116Z","description":["Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.\nThis work and T.V.’s activities were supported by Spanish Ministry of Science and Innovation, (CGL2016-79054), the Open Technology Program of NWO (TTW-13848), and the STSM Cost Action FA1405 funded by the European Union. A.P. research activities were supported by the Netherlands Organisation for Scientific Research (NWO, project no. 870.15.080)."],"format":["application/pdf","application/octet-stream"],"id":"50|dedup_wf_001::01644aebfe64e809f593492e515bc070","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"hostedby":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"license":"Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.","publicationdate":"2018-09-26","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/10045/80968"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::70703810b20723fe33cba6ffd7128212","value":"Scientific 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(NWO)","shortName":"NWO"},"id":"40|nwo_________::dc69ada721bf21ed51055b6421850d73","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Exploring and exploiting phytochemicals to lure hyperparasitoids away from beneficial biocontrol agents"},{"code":"2300189714","funder":{"jurisdiction":"NL","name":"Netherlands Organisation for Scientific Research (NWO)","shortName":"NWO"},"id":"40|nwo_________::39d892199c3b3d3b5ae9869a79e5bba8","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Linking aboveground-belowground interactions and plant-soil feedback to improve pest control and sustainability in greenhouse cut-flowers"}],"publicationdate":"2018-09-26","publisher":"Springer Nature","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Plant-mediated interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Herbivores"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Feeding guilds"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Parasitism"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Belowground interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Zoología"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"R"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Science"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Q"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"international"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratorium voor Entomologie"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"PE&RC"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratory of Entomology"}},{"subject":{"scheme":"keywords","value":"Multidisciplinary"}}],"type":"publication"} +{"author":[{"fullname":"Bonnie Berger","name":"Bonnie","pid":{"id":{"scheme":"orcid","value":"0000-0002-2724-7228"}},"rank":1,"surname":"Berger"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|opendoar____::89f0fd5c927d466d6ec9a21b9ac34ffa","value":"eScholarship - University of California"},{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},{"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed Central"},{"key":"10|opendoar____::8f19793b2671094e63a15ab883d50137","value":"Digital Access to Scholarship at Harvard"},{"key":"10|opendoar____::2a38a4a9316c49e5a833517c45d31070","value":"DSpace@MIT"}],"context":[{"code":"dh-ch","label":"Digital Humanities and Cultural Heritage","provenance":[{"provenance":"Inferred by OpenAIRE","trust":"0.8"}]}],"contributor":["Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory","Massachusetts Institute of Technology. Department of Mathematics","Lipson, Mark","Loh, Po-Ru","Berger, Bonnie"],"country":[{"code":"DZ","label":"Algeria","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"US","label":"United States","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2020-09-12T07:56:34.334Z","description":["Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.","National Science Foundation (U.S.). Graduate Research Fellowship Program","Simons Foundation","National Institutes of Health (U.S.) (Grant R01GM108348)","National Institutes of Health (U.S.) (Training Grant 5T32HG004947-04)"],"format":["application/pdf"],"id":"50|dedup_wf_001::025dff86cc73c1c865ed35e5b7646e73","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},"hostedby":{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","publicationdate":"2014-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/11858/00-001M-0000-0024-1F46-B","http://hdl.handle.net/11858/00-001M-0000-0024-1F8F-7","http://hdl.handle.net/11858/00-001M-0000-0024-1F90-1"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},"hostedby":{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},"publicationdate":"2014-05-27","refereed":"nonPeerReviewed","type":"Preprint","url":["http://dx.doi.org/10.1101/005603"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown 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Due to the portability and relative inexpensiveness of electroencephalography, the N400 event-related potential component has been proposed as a clinically valid means to identify preserved linguistic function in non-communicative patients. Across three experiments, we show that changes in both stimuli and task demands significantly influence the probability of detecting statistically significant N400 effects — that is, the difference in N400 amplitudes caused by the experimental manipulation. In terms of task demands, passively heard linguistic stimuli were significantly less likely to elicit N400 effects than task-relevant stimuli. Due to the inability of the majority of patients with disorders of consciousness to follow task commands, the insensitivity of passive listening would impede the identification of residual language abilities even when such abilities exist. In terms of stimuli, passively heard normatively associated word pairs produced the highest detection rate of N400 effects (50% of the participants), compared with semantically-similar word pairs (0%) and high-cloze sentences (17%). This result is consistent with a prediction error account of N400 magnitude, with highly predictable targets leading to smaller N400 waves, and therefore larger N400 effects. Overall, our data indicate that non-repeating normatively associated word pairs provide the highest probability of detecting single-subject N400s during passive listening, and may thereby provide a clinically viable means of assessing residual linguistic function. 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New polyethers, such as iubol (2), 22-hydroxy-15(28)- dehydrovenustatriol (3), 1,2-dehydropseudodehydrothyrsiferol (4), and secodehydrothyrsiferol (5) have been isolated and characterized from this alga. The structures were determined through the interpretation of NMR spectroscopic data and the relative configuration was proposed on the basis of NOESY spectrum and biogenetic considerations. All new compounds exhibited significant cytotoxic activity against a panel of cancer cell lines. © 2011 by the authors.","Financial support was provided by the grants MAREX (FP 7; KBBE-3-245137) (EU), CTQ2008-06754-C04-01 and SAF2008-02251 (MICINN); C2008000145 and EXMAR (ACISII); RD06/0020/1037 from Red Temática de Investigación Cooperativa en Cáncer, Instituto de Salud Carlos III, co-funded by the Fondo Europeo de Desarrollo Regional of the European Union, and Junta de Castilla y León (CSI052A11-2, and GR15-Experimental Therapeutics and Translational Oncology Program). 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The validity and utility of standard measures of childhood maltreatment requires clarification in order to inform the design of future studies investigating the mental health consequences of maltreatment. The present study assessed agreement between prospective informant-reports and retrospective self-reports of childhood maltreatment, as well as the comparative utility of both reports for predicting a range of psychiatric problems at age 18. Data were obtained from the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally-representative birth cohort of 2232 children followed to 18 years of age (with 93% retention). Childhood maltreatment was assessed in two ways: (i) prospective informant-reports from caregivers, researchers, and clinicians when children were aged 5, 7, 10 and 12; and (ii) retrospective self-reports of maltreatment experiences occurring up to age 12, obtained at age 18 using the Childhood Trauma Questionnaire. Participants were privately interviewed at age 18 concerning several psychiatric problems including depression, anxiety, self-injury, alcohol/cannabis dependence, and conduct disorder. There was only slight to fair agreement between prospective and retrospective reports of childhood maltreatment (all Kappa's ≤ 0.31). Both prospective and retrospective reports of maltreatment were associated with age-18 psychiatric problems, though the strongest associations were found when maltreatment was retrospectively self-reported. These findings indicate that prospective and retrospective reports of childhood maltreatment capture largely non-overlapping groups of individuals. Young adults who recall being maltreated have a particularly elevated risk for psychopathology."],"format":["application/pdf","text"],"id":"50|dedup_wf_001::085f9efc74e1192abca87031fb573d70","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research Portal"},"hostedby":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research 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Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.\r\nThe ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses."],"format":[],"id":"50|dedup_wf_001::09e54cbad6670d8f40a7de2704e2d2a4","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"license":"http://doi.wiley.com/10.1002/tdm_license_1.1","publicationdate":"2018-02-09","refereed":"UNKNOWN","type":"Article","url":["https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fnph.15014","http://onlinelibrary.wiley.com/wol1/doi/10.1111/nph.15014/fullpdf","http://dx.doi.org/10.1111/nph.15014"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.15014"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15014","https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014","http://onlinelibrary.wiley.com/doi/10.1111/nph.15014/abstract","https://aperto.unito.it/handle/2318/1660820","https://academic.microsoft.com/#/detail/2793208206"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"hostedby":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"publicationdate":"2018-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/2318/1660820"]},{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2018-12-01","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1111/nph.15014"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Native soils with their microbiotas elicit a state of alert in tomato plants","originalId":["10.1111/nph.15014","2793208206","oai:iris.unito.it:2318/1660820"],"pid":[{"scheme":"doi","value":"10.1111/nph.15014"},{"scheme":"pmid","value":"29424928"}],"projects":[{"acronym":"TomRes","code":"727929","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::94c4a066401e22002c4811a301bb4655","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"A NOVEL AND INTEGRATED APPROACH TO INCREASE MULTIPLE AND COMBINED STRESS TOLERANCE IN PLANTS USING TOMATO AS A MODEL"}],"publicationdate":"2018-12-01","publisher":"Wiley","subjects":[{"subject":{"scheme":"keywords","value":"Plant Science"}},{"subject":{"scheme":"keywords","value":"Physiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"food and beverages"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"fungi"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.8739"},"subject":{"scheme":"mesheuropmc","value":"complex mixtures"}}],"type":"publication"} +{"author":[{"fullname":"K.P. 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This study focuses on estimating the evapotranspiration and crop coefficients of table grapes vineyards trained on overhead “tendone” systems in the Apulia region (Italy). Maximum vineyard transpiration was estimated by adopting the “direct” methodology for ETp proposed by the Food and Agriculture Organization in Irrigation and Drainage Paper No. 56, with crop parameters estimated from Landsat 8 and RapidEye satellite data in combination with ground-based meteorological data. The modeling results of two growing seasons (2013 and 2014) indicated that canopy growth, seasonal and 10-day sums evapotranspiration values were strictly related to thermal requirements and rainfall events. The estimated values of mean seasonal daily evapotranspiration ranged between 4.2 and 4.1 mm·d−1, while midseason estimated values of crop coefficients ranged from 0.88 to 0.93 in 2013, and 1.02 to 1.04 in 2014, respectively. The experimental evapotranspiration values calculated represent the maximum value in absence of stress, so the resulting crop coefficients should be used with some caution. It is concluded that the retrieval of crop parameters and evapotranspiration derived from remotely-sensed data could be helpful for downscaling to the field the local weather conditions and agronomic practices and thus may be the basis for supporting grape growers and irrigation managers."],"format":["application/pdf"],"id":"50|dedup_wf_001::0bc332de35b4eb0cc3d0c54b3ff22dd3","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::a8db6f6b2ce4fe72e8b2314a9a93e7d9","value":"Sygma"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"https://creativecommons.org/licenses/by/4.0/","refereed":"UNKNOWN","type":"Article","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"https://creativecommons.org/licenses/by/4.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708/pdf","http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"cc-by","refereed":"UNKNOWN","type":"Article","url":["https://www.mdpi.com/2072-4292/7/11/14708/pdf"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"refereed":"UNKNOWN","type":"Article","url":["https://dblp.uni-trier.de/db/journals/remotesensing/remotesensing7.html#VaninoPNMBD15","https://doi.org/10.3390/rs71114708","https://core.ac.uk/display/55147144","http://doi.org/10.3390/rs71114708","https://academic.microsoft.com/#/detail/2149946514"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::c2cdfa5866e03cdd07d313cbc8fb8311","value":"Multidisciplinary Digital Publishing Institute"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"http://creativecommons.org/licenses/by/3.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"publicationdate":"2015-11-01","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708","https://doaj.org/toc/2072-4292"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::d8c24ca8f23c562a5600876ca2a550ce","value":"Archivio della ricerca - 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::a30b9a45766293af38951d767e77a471","subRelType":"participation","target":"40|aka_________::b733217d1cd609001dd3c75af419d872"} +{"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::a30b9a45766293af38951d767e77a471","subRelType":"participation","target":"40|aka_________::c33dee8231ad0374caf93e52c5a473e5"} \ No newline at end of file From bde6d337dd9178c51a9fdd5028b3d42683bfef52 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:42:01 +0100 Subject: [PATCH 030/149] test classes for dump of results related to funders --- .../ResultLinkedToProjectTest.java | 129 ++++++++++++++++ .../dump/funderresult/SplitPerFunderTest.java | 140 +++++++++++++++++- 2 files changed, 268 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index 3696db7f8..b7ee5b122 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -1,4 +1,133 @@ package eu.dnetlib.dhp.oa.graph.dump.funderresult; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + public class ResultLinkedToProjectTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + + private static HashMap map = new HashMap<>(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testNoMatch() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); + + final String relationPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json") + .getPath(); + + SparkResultLinkedToProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-relationPath", relationPath + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Result.class)); + + Assertions.assertEquals(0, verificationDataset.count()); + + } + + @Test + public void testMatchOne() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") + .getPath(); + + final String relationPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json") + .getPath(); + + SparkResultLinkedToProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-relationPath", relationPath + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 8e49b9fc6..3381dabe1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -1,4 +1,142 @@ package eu.dnetlib.dhp.oa.graph.dump.funderresult; -public class DumpResultPerFunderTest { +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +public class SplitPerFunderTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SplitPerFunderTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void test1() throws Exception { + + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") + .getPath(); + + + SparkDumpFunderResults.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath, + "-relationPath", sourcePath + + }); + + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + // FP7 3 + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/split/EC_FP7") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(3, verificationDataset.count()); + + Assertions + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + + + // CIHR 2 + tmp = sc + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(2, tmp.count()); + + //NWO 1 + tmp = sc + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); + + //NIH 3 + tmp = sc + .textFile(workingDir.toString() + "/split/NIH") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(2, tmp.count()); + + //NSF 1 + tmp = sc + .textFile(workingDir.toString() + "/split/NSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); + + //SNSF 1 + tmp = sc + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); + + //NHMRC 1 + tmp = sc + .textFile(workingDir.toString() + "/split/NHMRC") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); + + //H2020 3 + tmp = sc + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(3, tmp.count()); + + } } From 21ce175d176f76283cf4f0754842bd967e8f5d68 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:42:31 +0100 Subject: [PATCH 031/149] added FilterFunction specification if filter operation --- .../eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index 6be1befce..55f075e95 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -9,6 +9,7 @@ import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; @@ -54,7 +55,7 @@ public class CommunitySplit implements Serializable { private static void printResult(String c, Dataset result, String outputPath) { Dataset community_products = result - .filter(r -> containsCommunity(r, c)); + .filter((FilterFunction) r -> containsCommunity(r, c)); try { community_products.first(); From 305e3d0c9c13b74d99f4dfcc547dae5df68af826 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:43:41 +0100 Subject: [PATCH 032/149] added resource file for relation with relClass = isProducedBy --- .../dhp/oa/graph/dump/funderresource/extendeddump/relation | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation index 3cb855c1a..3ed91f451 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation @@ -1,7 +1,7 @@ {"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"40|cihr________::1e5e62235d094afd01cd56e65112fc63"} {"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::5ac587eb28411c351c2e357eb097fd3d","subRelType":"provision","target":"40|nwo_________::dc69ada721bf21ed51055b6421850d73"} 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{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::b566fa319c3923454e1e8eb886ab62d2","subRelType":"provision","target":"40|nhmrc_______::4e6c928fef9851b37ec73f4f6daca35b"} From e7e418e444cab97084faa167c0fe3057b09a9de0 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:44:10 +0100 Subject: [PATCH 033/149] added decision node to verify if to upload in Zenodo --- .../dump/funderresults/oozie_app/workflow.xml | 30 +++++++++++++++++-- 1 file changed, 27 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml index d258d4dd4..d310390b7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -1,6 +1,11 @@ + + upload + false + true to upload the dump for the funders in Zenodo + sourcePath the source path @@ -116,7 +121,7 @@ - + @@ -515,12 +520,31 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/ext - --outputPath${outputPath} + --outputPath${workingDir}/resultperfunder --relationPath${sourcePath} - + + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath} + --nameNode${nameNode} + + --sourcePath/user/miriam.baglioni/graph_dump_whole_production_funder_results + + + + + + + + ${wf:conf('upload') eq true} + + + From 87a9f616ae3d38062c136d1533c258dbbb68ac4f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:45:41 +0100 Subject: [PATCH 034/149] refactoring and addition of the funder nsp first part as nome for the dump insteasd of the whole nsp --- .../funderresults/SparkDumpFunderResults.java | 26 +++++++++++++------ 1 file changed, 18 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 232459c19..e2d8d7cb1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.*; +import eu.dnetlib.dhp.oa.graph.dump.Constants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -72,7 +73,7 @@ public class SparkDumpFunderResults implements Serializable { Dataset relation = Utils .readPath(spark, relationPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and relClass = 'isProducedBy'"); + .filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + Constants.RESULT_PROJECT_IS_PRODUCED_BY.toLowerCase()+ "'"); Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) @@ -86,13 +87,22 @@ public class SparkDumpFunderResults implements Serializable { .distinct() .collectAsList(); -// Dataset results = result -// .joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner") -// .map((MapFunction, CommunityResult>) value -> { -// return value._1(); -// }, Encoders.bean(CommunityResult.class)); - funderList.forEach(funder -> writeFunderResult(funder, result, outputPath)); + funderList.forEach(funder -> { + String fundernsp = funder.substring(3); + String funderdump; + if (fundernsp.startsWith("corda")){ + funderdump = "EC_"; + if(fundernsp.endsWith("h2020")){ + funderdump += "H2020"; + }else{ + funderdump += "FP7"; + } + }else{ + funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); + } + writeFunderResult(funder, result, outputPath + "/" + funderdump); + }); } @@ -113,7 +123,7 @@ public class SparkDumpFunderResults implements Serializable { .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(outputPath + "/" + funder); + .json(outputPath); } } From e758d5d9b4f6253a1b5deb65a35689705ffff2ce Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 13:46:39 +0100 Subject: [PATCH 035/149] refactoring --- .../dump/funderresults/SparkResultLinkedToProject.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index e5d7e2254..8c91fbf1f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -6,9 +6,9 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; +import eu.dnetlib.dhp.oa.graph.dump.Constants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -64,19 +64,19 @@ public class SparkResultLinkedToProject implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultsLikedToProjects(spark, inputClazz, inputPath, outputPath, relationPath); + writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, relationPath); }); } - private static void writeResultsLikedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String relationPath) { + private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, + String inputPath, String outputPath, String relationPath) { Dataset results = Utils .readPath(spark, inputPath, inputClazz) .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); Dataset relations = Utils .readPath(spark, relationPath, Relation.class) - .filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'"); + .filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + Constants.RESULT_PROJECT_IS_PRODUCED_BY.toLowerCase() + "'"); relations .joinWith( From 1f130cdf92ea2335824d77d81888e00aedbdd24e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 14:04:26 +0100 Subject: [PATCH 036/149] changed the relation (produces -> isProducedBy) due to the change in the code --- .../graph/dump/resultProject/match/relation | 16 +-- .../dump/resultProject/match_one/relation | 16 +-- .../dump/resultProject/no_match/relation | 119 +++--------------- 3 files changed, 35 insertions(+), 116 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match/relation b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match/relation index e23eebcc6..b1c793e2a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match/relation +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match/relation @@ -1,8 +1,8 @@ -{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395831891,"properties":[],"relClass":"produces","relType":"resultProject","source":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","subRelType":"outcome","target":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb"} -{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395831891,"properties":[],"relClass":"produces","relType":"resultProject","source":"40|aka_________::03376222b28a3aebf2730ac514818d04","subRelType":"outcome","target":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb"} 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b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one/relation @@ -1,8 +1,8 @@ -{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395831891,"properties":[],"relClass":"produces","relType":"resultProject","source":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","subRelType":"outcome","target":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb"} 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+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.72"},"lastupdatetimestamp":1590395830521,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|anr_________::01703d216eb2d01f73e9f476302cd341","subRelType":"outcome","source":"50|dedup_wf_001::d4b9ca4bf332403c15abb47d21963ddc"} +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.72"},"lastupdatetimestamp":1590395830521,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|anr_________::01703d216eb2d01f73e9f476302cd341","subRelType":"outcome","source":"50|dedup_wf_001::d4b9ca4bf332403c15abb47d21963ddc"} +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.72"},"lastupdatetimestamp":1590395828850,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|anr_________::0229a330cb3e72e8f976a93bef7e0982","subRelType":"outcome","source":"50|od________18::0fa23557cd83522c7db8ccfefad1f12e"} +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:project:semrel","classname":"Propagation of result to project through semantic relation","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"trust":"0.85"},"lastupdatetimestamp":null,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|anr_________::7f0f296b5e4ec1a1d61cfe4da63406c7","subRelType":"outcome","source":"50|dedup_wf_001::595ab3bf9261fbd616fb0240fb78add2"} +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.72"},"lastupdatetimestamp":1590395837446,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|anr_________::a7322657c4ea4c9a3dc7cb77deb51620","subRelType":"outcome","source":"50|od_______166::953fd0631804ebda31b415fea855d570"} \ No newline at end of file From b2c455f8837ef82e39cf2af8444b02ed61bccc0f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 14:08:09 +0100 Subject: [PATCH 037/149] added java doc --- .../oa/graph/dump/funderresults/SparkDumpFunderResults.java | 5 ++--- .../graph/dump/funderresults/SparkResultLinkedToProject.java | 5 +++++ 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index e2d8d7cb1..7049bdacf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -25,9 +25,8 @@ import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; /** - * Preparation of the Project information to be added to the dumped results. For each result associated to at least one - * Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the - * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to + * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC + * for the EC it specifies also the fundingStream (FP7 or H2020) */ public class SparkDumpFunderResults implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 8c91fbf1f..4c72cd526 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -24,6 +24,11 @@ import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; import scala.Tuple2; +/** + * Selects the results linked to projects. Only for these results the dump will be performed. + * The code to perform the dump and to expend the dumped results with the informaiton related to projects + * is the one used for the dump of the community products + */ public class SparkResultLinkedToProject implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkResultLinkedToProject.class); From 90d4369fd207663e6baadeb2e0b3a4858910387e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 14:34:58 +0100 Subject: [PATCH 038/149] added test to verify the compression in writing community info on hdfs --- .../graph/dump/complete/CreateEntityTest.java | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index 702811549..4a3c6ed20 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -20,10 +20,7 @@ import org.apache.hadoop.fs.LocalFileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; @@ -146,6 +143,7 @@ public class CreateEntityTest { } @Test + @Disabled public void test2() throws IOException, ISLookUpException { LocalFileSystem fs = FileSystem.getLocal(new Configuration()); @@ -166,8 +164,16 @@ public class CreateEntityTest { final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.getContextInformation(consumer); - List riList = new ArrayList<>(); - cInfoList.forEach(cInfo -> riList.add(Process.getEntity(cInfo))); + //List riList = new ArrayList<>(); + cInfoList.forEach(cInfo -> { + try { + writer.write(new Gson().toJson(Process.getEntity(cInfo))); + } catch (IOException e) { + e.printStackTrace(); + } + }); + + writer.close(); } } From 66c0e3e574d79da701b9cdf45f9d2c0616113675 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 17:52:17 +0100 Subject: [PATCH 039/149] changed because of https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2489 --- .../src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java index 89fa09f3c..76017d5b7 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java @@ -90,9 +90,6 @@ public class MakeTarArchive implements Serializable { String p_string = p.toString(); if (!p_string.endsWith("_SUCCESS")) { String name = p_string.substring(p_string.lastIndexOf("/") + 1); -// if (name.trim().equalsIgnoreCase("communities_infrastructures")) { -// name = "communities_infrastructures.json"; -// } TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name); entry.setSize(fileStatus.getLen()); current_size += fileStatus.getLen(); From 1df94b85b4f037b400498f1b0e462c2ccc9f03d5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 17:57:43 +0100 Subject: [PATCH 040/149] changed because of https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2491 --- .../eu/dnetlib/dhp/oa/graph/dump/Constants.java | 1 - .../funderresults/SparkDumpFunderResults.java | 16 +++++++++------- .../SparkResultLinkedToProject.java | 9 ++++++--- 3 files changed, 15 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index c64554555..eb01ebf32 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -26,7 +26,6 @@ public class Constants { public static String ORCID = "orcid"; - public static String RESULT_PROJECT_IS_PRODUCED_BY = "isProducedBy"; static { accessRightsCoarMap.put("OPEN", "c_abf2"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 7049bdacf..826b4be8c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -6,7 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.*; -import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -16,6 +16,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.api.zenodo.Community; +import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; @@ -72,7 +73,9 @@ public class SparkDumpFunderResults implements Serializable { Dataset relation = Utils .readPath(spark, relationPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + Constants.RESULT_PROJECT_IS_PRODUCED_BY.toLowerCase()+ "'"); + .filter( + "dataInfo.deletedbyinference = false and lower(relClass) = '" + + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) @@ -86,18 +89,17 @@ public class SparkDumpFunderResults implements Serializable { .distinct() .collectAsList(); - funderList.forEach(funder -> { String fundernsp = funder.substring(3); String funderdump; - if (fundernsp.startsWith("corda")){ + if (fundernsp.startsWith("corda")) { funderdump = "EC_"; - if(fundernsp.endsWith("h2020")){ + if (fundernsp.endsWith("h2020")) { funderdump += "H2020"; - }else{ + } else { funderdump += "FP7"; } - }else{ + } else { funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); } writeFunderResult(funder, result, outputPath + "/" + funderdump); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 4c72cd526..07e289cbd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -6,7 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; -import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -19,6 +19,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; @@ -74,14 +75,16 @@ public class SparkResultLinkedToProject implements Serializable { } private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String relationPath) { + String inputPath, String outputPath, String relationPath) { Dataset results = Utils .readPath(spark, inputPath, inputClazz) .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); Dataset relations = Utils .readPath(spark, relationPath, Relation.class) - .filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + Constants.RESULT_PROJECT_IS_PRODUCED_BY.toLowerCase() + "'"); + .filter( + "dataInfo.deletedbyinference = false and lower(relClass) = '" + + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); relations .joinWith( From f5e5e92a101feca613bc5a1232e43eb17d3edca2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 17:58:53 +0100 Subject: [PATCH 041/149] changed because of https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2493 --- .../oa/graph/dump/funderresults/oozie_app/workflow.xml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml index d310390b7..650b972fa 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml @@ -121,7 +121,7 @@ - + @@ -274,7 +274,6 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/dump/publication --communityMapPath${workingDir}/communityMap @@ -302,7 +301,6 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/dump/dataset --communityMapPath${workingDir}/communityMap @@ -330,7 +328,6 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/dump/otherresearchproduct --communityMapPath${workingDir}/communityMap @@ -358,7 +355,6 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/result/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/dump/software --communityMapPath${workingDir}/communityMap @@ -532,8 +528,7 @@ eu.dnetlib.dhp.oa.graph.dump.MakeTar --hdfsPath${outputPath} --nameNode${nameNode} - - --sourcePath/user/miriam.baglioni/graph_dump_whole_production_funder_results + --sourcePath${workingDir}/resultperfunder From d4ddde2ef2d5b6d8d2d50b36882a8e6e0b005cae Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 18:01:01 +0100 Subject: [PATCH 042/149] changed because of https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2503 --- .../eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java | 1 - 1 file changed, 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index 4a3c6ed20..f179e9de5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -164,7 +164,6 @@ public class CreateEntityTest { final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.getContextInformation(consumer); - //List riList = new ArrayList<>(); cInfoList.forEach(cInfo -> { try { writer.write(new Gson().toJson(Process.getEntity(cInfo))); From ed01e5a5e1feef7ba37ee7568290b75c31e74ede Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 18:09:34 +0100 Subject: [PATCH 043/149] https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2507 --- .../dnetlib/dhp/oa/graph/dump/input_parameters.json | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json index ca12ae3ec..1d986fc26 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json @@ -29,12 +29,13 @@ "paramLongName":"resultTableName", "paramDescription": "the name of the result table we are currently working on", "paramRequired": true - },{ - "paramName":"dt", - "paramLongName":"dumpType", - "paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project", - "paramRequired": false -} + }, + { + "paramName":"dt", + "paramLongName":"dumpType", + "paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project", + "paramRequired": false + } ] From 5fbe54ef54b68e4ec972666ea112a6c81494a1c6 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 18:10:28 +0100 Subject: [PATCH 044/149] https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2509 --- .../oa/graph/dump/input_parameters_link_prj.json | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json index 5c4886741..fdd9492fe 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -22,12 +22,13 @@ "paramLongName":"resultTableName", "paramDescription": "the name of the result table we are currently working on", "paramRequired": true - }, { - "paramName":"rp", - "paramLongName":"relationPath", - "paramDescription": "the path to the relations", - "paramRequired": true -} + }, + { + "paramName":"rp", + "paramLongName":"relationPath", + "paramDescription": "the path to the relations", + "paramRequired": true + } ] From 1a89f8211c6ec589305a77188a84b54268ff30d6 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 18:12:40 +0100 Subject: [PATCH 045/149] https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/61#issuecomment-2505 --- .../dhp/oa/graph/dump/complete/CreateEntityTest.java | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index f179e9de5..20c578738 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -164,14 +164,9 @@ public class CreateEntityTest { final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.getContextInformation(consumer); - cInfoList.forEach(cInfo -> { - try { - writer.write(new Gson().toJson(Process.getEntity(cInfo))); - } catch (IOException e) { - e.printStackTrace(); - } - }); - + for(ContextInfo cInfo: cInfoList){ + writer.write(new Gson().toJson(Process.getEntity(cInfo))); + } writer.close(); } From 124591a7f32d58b70166b22a6d1ad297c67d6c36 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 25 Nov 2020 18:23:28 +0100 Subject: [PATCH 046/149] refactoring --- .../dnetlib/dhp/oa/graph/dump/Constants.java | 1 - .../funderresults/SparkDumpFunderResults.java | 2 +- .../SparkResultLinkedToProject.java | 2 +- .../graph/dump/complete/CreateEntityTest.java | 2 +- .../ResultLinkedToProjectTest.java | 172 +++++++-------- .../dump/funderresult/SplitPerFunderTest.java | 195 +++++++++--------- 6 files changed, 188 insertions(+), 186 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index eb01ebf32..86a275ae2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -26,7 +26,6 @@ public class Constants { public static String ORCID = "orcid"; - static { accessRightsCoarMap.put("OPEN", "c_abf2"); accessRightsCoarMap.put("RESTRICTED", "c_16ec"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 826b4be8c..00f604b14 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.*; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -20,6 +19,7 @@ import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; import eu.dnetlib.dhp.schema.oaf.Relation; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 07e289cbd..1a28a21f4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -21,6 +20,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; import scala.Tuple2; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index 20c578738..3ecbd1894 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -164,7 +164,7 @@ public class CreateEntityTest { final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.getContextInformation(consumer); - for(ContextInfo cInfo: cInfoList){ + for (ContextInfo cInfo : cInfoList) { writer.write(new Gson().toJson(Process.getEntity(cInfo))); } writer.close(); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index b7ee5b122..dbe3db6fe 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -1,9 +1,11 @@ + package eu.dnetlib.dhp.oa.graph.dump.funderresult; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -17,117 +19,119 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; public class ResultLinkedToProjectTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); - private static HashMap map = new HashMap<>(); + private static HashMap map = new HashMap<>(); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - public void testNoMatch() throws Exception { + @Test + public void testNoMatch() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); - final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json") - .getPath(); + final String relationPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json") + .getPath(); - SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-relationPath", relationPath + SparkResultLinkedToProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-relationPath", relationPath - }); + }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Result.class)); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Result.class)); - Assertions.assertEquals(0, verificationDataset.count()); + Assertions.assertEquals(0, verificationDataset.count()); - } + } - @Test - public void testMatchOne() throws Exception { + @Test + public void testMatchOne() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") + .getPath(); - final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json") - .getPath(); + final String relationPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json") + .getPath(); - SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-relationPath", relationPath + SparkResultLinkedToProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-relationPath", relationPath - }); + }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - Assertions.assertEquals(1, verificationDataset.count()); + Assertions.assertEquals(1, verificationDataset.count()); - } + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 3381dabe1..71bf5d942 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -1,11 +1,10 @@ + package eu.dnetlib.dhp.oa.graph.dump.funderresult; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -19,124 +18,124 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; public class SplitPerFunderTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class); + private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(SplitPerFunderTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(SplitPerFunderTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - public void test1() throws Exception { + @Test + public void test1() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") + .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") - .getPath(); + SparkDumpFunderResults.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath, + "-relationPath", sourcePath + }); - SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath, - "-relationPath", sourcePath + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - }); + // FP7 3 + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/split/EC_FP7") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + Assertions.assertEquals(3, verificationDataset.count()); - // FP7 3 - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + // CIHR 2 + tmp = sc + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(2, tmp.count()); - Assertions.assertEquals(3, verificationDataset.count()); + // NWO 1 + tmp = sc + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + // NIH 3 + tmp = sc + .textFile(workingDir.toString() + "/split/NIH") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(2, tmp.count()); + // NSF 1 + tmp = sc + .textFile(workingDir.toString() + "/split/NSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); - // CIHR 2 - tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(2, tmp.count()); + // SNSF 1 + tmp = sc + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); - //NWO 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); + // NHMRC 1 + tmp = sc + .textFile(workingDir.toString() + "/split/NHMRC") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); - //NIH 3 - tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(2, tmp.count()); + // H2020 3 + tmp = sc + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(3, tmp.count()); - //NSF 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - //SNSF 1 - tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - //NHMRC 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - //H2020 3 - tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(3, tmp.count()); - - } + } } From db36e119127a88930892e9dd5ad7a61aad91baed Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 30 Nov 2020 20:14:23 +0100 Subject: [PATCH 047/149] classes test classes and resources for production of the actionset to include bipFinder score in results --- .../bipfinder/BipDeserialize.java | 23 + .../dhp/actionmanager/bipfinder/BipScore.java | 25 + .../dhp/actionmanager/bipfinder/KeyValue.java | 25 + .../bipfinder/PreparedResult.java | 24 + .../dhp/actionmanager/bipfinder/Score.java | 26 + .../bipfinder/SparkAtomicActionScoreJob.java | 203 +++ .../bipfinder/input_parameters.json | 32 + .../SparkAtomicActionScoreJobTest.java | 160 +++ .../actionmanager/bipfinder/bip_scores.json | 1101 +++++++++++++++++ .../actionmanager/bipfinder/publication.json | 18 + 10 files changed, 1637 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java new file mode 100644 index 000000000..e68b912b2 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java @@ -0,0 +1,23 @@ +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; + + +public class BipDeserialize extends HashMap> implements Serializable { + + public BipDeserialize(){ + super(); + } + + public List get(String key) { + + if (super.get(key) == null) { + return new ArrayList<>(); + } + return super.get(key); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java new file mode 100644 index 000000000..b1e381955 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java @@ -0,0 +1,25 @@ +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; +import java.util.List; + +public class BipScore implements Serializable { + private String id; + private List scoreList; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getScoreList() { + return scoreList; + } + + public void setScoreList(List scoreList) { + this.scoreList = scoreList; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java new file mode 100644 index 000000000..1fadae6fe --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java @@ -0,0 +1,25 @@ +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; + +public class KeyValue implements Serializable { + + private String key; + private String value; + + public String getKey() { + return key; + } + + public void setKey(String key) { + this.key = key; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java new file mode 100644 index 000000000..bb7648f0c --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java @@ -0,0 +1,24 @@ +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; + +public class PreparedResult implements Serializable { + private String id; //openaire id + private String value; //doi + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java new file mode 100644 index 000000000..b14d971cd --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java @@ -0,0 +1,26 @@ +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; +import java.util.List; + +public class Score implements Serializable { + + private String id; + private List unit; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getUnit() { + return unit; + } + + public void setUnit(List unit) { + this.unit = unit; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java new file mode 100644 index 000000000..658555e05 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -0,0 +1,203 @@ +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.hdfs.qjournal.protocol.QJournalProtocolProtos; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import scala.Tuple2; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class SparkAtomicActionScoreJob implements Serializable { + + private static String DOI = "doi"; + private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJob.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + SparkAtomicActionScoreJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("inputPath"); + log.info("inputPath {}: ", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + final String bipScorePath = parser.get("bipScorePath"); + log.info("bipScorePath: {}", bipScorePath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + Class inputClazz = (Class) Class.forName(resultClassName); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz); + }); + } + + private static void prepareResults(SparkSession spark, String inputPath, String outputPath, + String bipScorePath, Class inputClazz) { + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD bipDeserializeJavaRDD = sc.textFile(bipScorePath) + .map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class)); + + + Dataset bipScores = spark.createDataset(bipDeserializeJavaRDD.flatMap(entry -> + entry.keySet().stream().map(key -> { + BipScore bs = new BipScore(); + bs.setId(key); + bs.setScoreList(entry.get(key)); + return bs; + }).collect(Collectors.toList()).iterator() + ).rdd(), Encoders.bean(BipScore.class)); + + System.out.println(bipScores.count()); + + Dataset results = readPath(spark, inputPath, inputClazz); + + results.createOrReplaceTempView("result"); + + Dataset preparedResult = spark.sql("select pIde.value value, id " + + "from result " + + "lateral view explode (pid) p as pIde " + + "where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'") + .as(Encoders.bean(PreparedResult.class)); + + Dataset tmp = bipScores.joinWith(preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")), + "inner") + .map((MapFunction, BipScore>) value -> { + BipScore ret = value._1(); + ret.setId(value._2().getId()); + return ret; + }, Encoders.bean(BipScore.class)); + + tmp.groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, it) -> + { + Result ret = inputClazz.newInstance(); + BipScore first = it.next(); + ret.setId(first.getId()); + + ret.setMeasures(getMeasure(first)); + it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value))); + + return (I)ret; + }, Encoders.bean(inputClazz)) + .toJavaRDD() + .map(p -> new AtomicAction(inputClazz, p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + ; + } + + public static Dataset getBipScoreDataset(Dataset bipdeserialized){ + return bipdeserialized.flatMap((FlatMapFunction) bip -> + bip.keySet().stream().map(key -> { + BipScore bs = new BipScore(); + bs.setId(key); + bs.setScoreList(bip.get(key)); + return bs; + }).collect(Collectors.toList()).iterator() + , Encoders.bean(BipScore.class)); + } + + private static List getMeasure(BipScore value) { + return value.getScoreList() + .stream() + .map(score -> { + Measure m = new Measure(); + m.setId(score.getId()); + m.setUnit(score.getUnit().stream() + .map(unit -> { + KeyValue kv = new KeyValue(); + kv.setValue(unit.getValue()); + kv.setKey(unit.getKey()); + kv.setDataInfo(getDataInfo()); + return kv; + }).collect(Collectors.toList())); + return m; + }).collect(Collectors.toList()); + } + + + + private static DataInfo getDataInfo() { + DataInfo di = new DataInfo(); + di.setInferred(false); + di.setInvisible(false); + di.setDeletedbyinference(false); + di.setTrust(""); + Qualifier qualifier = new Qualifier(); + qualifier.setClassid("sysimport:actionset"); + qualifier.setClassname("Harvested"); + qualifier.setSchemename("dnet:provenanceActions"); + qualifier.setSchemeid("dnet:provenanceActions"); + di.setProvenanceaction(qualifier); + return di; + } + + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json new file mode 100644 index 000000000..ae844a0c9 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false +}, +{ +"paramName": "ip", +"paramLongName": "inputPath", +"paramDescription": "the URL from where to get the programme file", +"paramRequired": true +}, +{ +"paramName": "o", +"paramLongName": "outputPath", +"paramDescription": "the path of the new ActionSet", +"paramRequired": true +}, + { + "paramName": "rtn", + "paramLongName": "resultTableName", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + }, + { + "paramName": "bsp", + "paramLongName": "bipScorePath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java new file mode 100644 index 000000000..64518234e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java @@ -0,0 +1,160 @@ +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import scala.Tuple2; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.stream.Collectors; + +public class SparkAtomicActionScoreJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(SparkAtomicActionScoreJobTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SparkAtomicActionScoreJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SparkAtomicActionScoreJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void numberDistinctProjectTest() throws Exception { + String bipScoresPath = getClass().getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json").getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json") + .getPath(); + + SparkAtomicActionScoreJob.main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); + + Assertions.assertTrue(tmp.count() == 1); + +// Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); +// verificationDataset.createOrReplaceTempView("project"); + +// Dataset execverification = spark +// .sql( +// "SELECT id, class classification, h2020topiccode, h2020topicdescription FROM project LATERAL VIEW EXPLODE(h2020classification) c as class "); +// +// Assertions +// .assertEquals( +// "H2020-EU.3.4.7.", +// execverification +// .filter("id = '40|corda__h2020::2c7298913008865ba784e5c1350a0aa5'") +// .select("classification.h2020Programme.code") +// .collectAsList() +// .get(0) +// .getString(0)); + + + + + } + + private static List getMeasure(BipScore value) { + return value.getScoreList() + .stream() + .map(score -> { + Measure m = new Measure(); + m.setId(score.getId()); + m.setUnit(score.getUnit().stream() + .map(unit -> { + eu.dnetlib.dhp.schema.oaf.KeyValue kv = new KeyValue(); + kv.setValue(unit.getValue()); + kv.setKey(unit.getKey()); + kv.setDataInfo(getDataInfo()); + return kv; + }).collect(Collectors.toList())); + return m; + }).collect(Collectors.toList()); + } + + + private static DataInfo getDataInfo() { + DataInfo di = new DataInfo(); + di.setInferred(false); + di.setInvisible(false); + di.setDeletedbyinference(false); + di.setTrust(""); + Qualifier qualifier = new Qualifier(); + qualifier.setClassid("sysimport:actionset"); + qualifier.setClassname("Harvested"); + qualifier.setSchemename("dnet:provenanceActions"); + qualifier.setSchemeid("dnet:provenanceActions"); + di.setProvenanceaction(qualifier); + return di; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json new file mode 100644 index 000000000..a4f3fa8b8 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json @@ -0,0 +1,1101 @@ +{"10.1001/10-v4n2-hsf10003": [{"id": "influence", "unit": [{"value": "1.62759106106e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.22519296", "key": "score"}]}]} +{"10.1001/2012.jama.10456": [{"id": "influence", "unit": [{"value": "1.66083991022e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.8690688", "key": "score"}]}]} +{"10.1001/2013.jamadermatol.729": [{"id": "influence", "unit": [{"value": "2.0769133069e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.0279936", "key": "score"}]}]} +{"10.1001/archderm.107.6.853": [{"id": "influence", "unit": [{"value": "1.95361113607e-08", "key": "score"}]}, {"id": "popularity", "unit": 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. However, this method is inherently non-robust to modelling errors and input saturations. Moreover, obtaining a quantifiable guarantee of the attained stability domain in a nonlinear control context is not a very straightforward task. Unlike standard NDI approaches, our methodology can be viewed as a generalized nonlinear compensation framework which allows to incorporate uncertainties and input saturations in the design process. Paralleling anti-windup strategies, the controller can be computed through a single multichannel optimization problem or through a simple two-step process. Within this framework, linear fractional transformations of the nonlinear closed-loop can be easily derived for robust stability analysis using standard tools for linear systems. The proposed method is tested for the flight control of a delta wing type reentry vehicle at hypersonic, transonic and subsonic phases of the atmospheric reentry. For this thesis work, a Flight Mechanics simulator including diverse external factors and modelling errors was developed in Simulink."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|artemis___fr::630e47d8b572e3df0e91327d6d8f036d","instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|driver______::66c20c26ac26136628f5207819ae1abc","value":"Archives des thèses et mémoires de l’ISAE (ArTeMIS)"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2012-09-21"},"distributionlocation":"","hostedby":{"key":"10|driver______::66c20c26ac26136628f5207819ae1abc","value":"Archives des thèses et mémoires de l’ISAE 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atmosphérique"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"A generalized framework for robust nonlinear compensation : application to an atmospheric reentry control problem"}]} \ No newline at end of file From e819155eb2e5493e1d233a73aa96ce70366d48cd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 1 Dec 2020 09:51:58 +0100 Subject: [PATCH 048/149] added implements Seriaiazable --- .../src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java index c0c14d10d..78a4c6801 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; +import java.io.Serializable; import java.util.List; import com.google.common.base.Objects; @@ -8,7 +9,7 @@ import com.google.common.base.Objects; /** * Represent a measure, must be further described by a system available resource providing name and descriptions. */ -public class Measure { +public class Measure implements Serializable { /** * Unique measure identifier. @@ -16,7 +17,7 @@ public class Measure { private String id; /** - * List of units associated with this measure. KeyValue provides a pair to store the laber (key) and the value, plus + * List of units associated with this measure. KeyValue provides a pair to store the label (key) and the value, plus * common provenance information. */ private List unit; From 719da15f04356d550ce162e8328644fd4fb021bc Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 1 Dec 2020 12:42:30 +0100 Subject: [PATCH 049/149] added test resources --- .../actionmanager/bipfinder/publication_2.json | 18 ++++++++++++++++++ .../actionmanager/bipfinder/publication_3.json | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json new file mode 100644 index 000000000..f849811ab --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json @@ -0,0 +1,18 @@ +{"author":[{"fullname":"Niskala, Eino","name":"Eino","pid":[],"rank":1,"surname":"Niskala"}],"bestaccessright":{"classid":"RESTRICTED","classname":"Restricted","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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reentry"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"value":"629.8"}],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Cadre de travail généralisé de compensation non-linéaire robuste : application à la rentrée atmosphérique"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"A generalized framework for robust nonlinear compensation : application to an atmospheric reentry control problem"}]} \ No newline at end of file From 0051ebede575a5effa945e8ec9813c52f3ff6356 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 1 Dec 2020 12:43:03 +0100 Subject: [PATCH 050/149] extending test --- .../SparkAtomicActionScoreJobTest.java | 196 ++++++++++++++---- 1 file changed, 150 insertions(+), 46 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java index 64518234e..3b360f6ed 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java @@ -16,6 +16,7 @@ import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.Assertions; @@ -71,7 +72,7 @@ public class SparkAtomicActionScoreJobTest { } @Test - public void numberDistinctProjectTest() throws Exception { + public void matchOne() throws Exception { String bipScoresPath = getClass().getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json").getPath(); String inputPath = getClass() .getResource( @@ -102,59 +103,162 @@ public class SparkAtomicActionScoreJobTest { Assertions.assertTrue(tmp.count() == 1); -// Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); -// verificationDataset.createOrReplaceTempView("project"); + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); -// Dataset execverification = spark -// .sql( -// "SELECT id, class classification, h2020topiccode, h2020topicdescription FROM project LATERAL VIEW EXPLODE(h2020classification) c as class "); -// -// Assertions -// .assertEquals( -// "H2020-EU.3.4.7.", -// execverification -// .filter("id = '40|corda__h2020::2c7298913008865ba784e5c1350a0aa5'") -// .select("classification.h2020Programme.code") -// .collectAsList() -// .get(0) -// .getString(0)); + Dataset execVerification = spark.sql("Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); + + Assertions.assertEquals(2, execVerification.count()); + + Assertions.assertEquals("50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", + execVerification.select("oaid").collectAsList().get(0).getString(0)); + + Assertions.assertEquals("1.47565045883e-08", + execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0)); + + Assertions.assertEquals("0.227515392", + execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0)); + + } + + @Test + public void matchOneWithTwo() throws Exception { + String bipScoresPath = getClass().getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json").getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json") + .getPath(); + + SparkAtomicActionScoreJob.main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); + + Assertions.assertTrue(tmp.count() == 1); + + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); + + Dataset execVerification = spark.sql("Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); + + Assertions.assertEquals(4, execVerification.count()); + + + Assertions.assertEquals("50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", + execVerification.select("oaid").collectAsList().get(0).getString(0)); + + Assertions.assertEquals(2, + execVerification.filter("id = 'influence'").count()); + + Assertions.assertEquals(2, + execVerification.filter("id = 'popularity'").count()); + + List tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList(); + String tmp_influence = tmp_ds.get(0).getString(0); + Assertions.assertTrue("1.47565045883e-08".equals(tmp_influence)|| + "1.98956540239e-08".equals(tmp_influence) ); + + tmp_influence = tmp_ds.get(1).getString(0); + Assertions.assertTrue("1.47565045883e-08".equals(tmp_influence)|| + "1.98956540239e-08".equals(tmp_influence) ); + + Assertions.assertTrue(!tmp_ds.get(0).getString(0).equals(tmp_ds.get(1).getString(0))); } - private static List getMeasure(BipScore value) { - return value.getScoreList() - .stream() - .map(score -> { - Measure m = new Measure(); - m.setId(score.getId()); - m.setUnit(score.getUnit().stream() - .map(unit -> { - eu.dnetlib.dhp.schema.oaf.KeyValue kv = new KeyValue(); - kv.setValue(unit.getValue()); - kv.setKey(unit.getKey()); - kv.setDataInfo(getDataInfo()); - return kv; - }).collect(Collectors.toList())); - return m; - }).collect(Collectors.toList()); - } + @Test + public void matchTwo() throws Exception { + String bipScoresPath = getClass().getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json").getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json") + .getPath(); + + SparkAtomicActionScoreJob.main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); - private static DataInfo getDataInfo() { - DataInfo di = new DataInfo(); - di.setInferred(false); - di.setInvisible(false); - di.setDeletedbyinference(false); - di.setTrust(""); - Qualifier qualifier = new Qualifier(); - qualifier.setClassid("sysimport:actionset"); - qualifier.setClassname("Harvested"); - qualifier.setSchemename("dnet:provenanceActions"); - qualifier.setSchemeid("dnet:provenanceActions"); - di.setProvenanceaction(qualifier); - return di; + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); + + Assertions.assertTrue(tmp.count() == 2); + + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); + + Dataset execVerification = spark.sql("Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); + + Assertions.assertEquals(4, execVerification.count()); + + + Assertions.assertEquals(2, + execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count()); + + Assertions.assertEquals(2, + execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count()); + + + Assertions.assertEquals(2, + execVerification.filter("id = 'influence'").count()); + + Assertions.assertEquals(2, + execVerification.filter("id = 'popularity'").count()); + + Assertions.assertEquals("1.47565045883e-08" , + execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + + "and id = 'influence'").select("value").collectAsList().get(0).getString(0)); + + Assertions.assertEquals( + "1.98956540239e-08", execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + + "and id = 'influence'").select("value").collectAsList().get(0).getString(0)); + + Assertions.assertEquals( + "0.282046161584", execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + + "and id = 'popularity'").select("value").collectAsList().get(0).getString(0)); + + Assertions.assertEquals("0.227515392" , + execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + + "and id = 'popularity'").select("value").collectAsList().get(0).getString(0)); + } + } From 45d06c45c7a9bea15dcfeeb93eac217ba0de36de Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 1 Dec 2020 14:29:18 +0100 Subject: [PATCH 051/149] collecting all the atoic actions for result type and save them all in the AS path --- .../bipfinder/CollectAndSave.java | 85 +++++++++ .../bipfinder/input_actionset_parameter.json | 32 ++++ .../bipfinder/oozie_app/config-default.xml | 58 +++++++ .../bipfinder/oozie_app/workflow.xml | 163 ++++++++++++++++++ 4 files changed, 338 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java new file mode 100644 index 000000000..7164fc5ed --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java @@ -0,0 +1,85 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class CollectAndSave implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + CollectAndSave.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("inputPath"); + log.info("inputPath {}: ", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + collectAndSave(spark, inputPath, outputPath); + }); + } + + private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + sc + .sequenceFile(inputPath + "/publication", Text.class, Text.class) + .union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)) + .union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)) + .union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class)) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + ; + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json new file mode 100644 index 000000000..ae844a0c9 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false +}, +{ +"paramName": "ip", +"paramLongName": "inputPath", +"paramDescription": "the URL from where to get the programme file", +"paramRequired": true +}, +{ +"paramName": "o", +"paramLongName": "outputPath", +"paramDescription": "the path of the new ActionSet", +"paramRequired": true +}, + { + "paramName": "rtn", + "paramLongName": "resultTableName", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + }, + { + "paramName": "bsp", + "paramLongName": "bipScorePath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/config-default.xml new file mode 100644 index 000000000..a1755f329 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/config-default.xml @@ -0,0 +1,58 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + + + oozie.launcher.mapreduce.user.classpath.first + true + + + sparkExecutorNumber + 4 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + sparkDriverMemory + 15G + + + sparkExecutorMemory + 6G + + + sparkExecutorCores + 1 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml new file mode 100644 index 000000000..c710c8b55 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml @@ -0,0 +1,163 @@ + + + + projectFileURL + the url where to get the projects file + + + + programmeFileURL + the url where to get the programme file + + + + topicFileURL + the url where to get the topic file + + + outputPath + path where to store the action set + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV + --hdfsNameNode${nameNode} + --fileURL${projectFileURL} + --hdfsPath${workingDir}/projects + --classForNameeu.dnetlib.dhp.actionmanager.project.utils.CSVProject + + + + + + + + eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV + --hdfsNameNode${nameNode} + --fileURL${programmeFileURL} + --hdfsPath${workingDir}/programme + --classForNameeu.dnetlib.dhp.actionmanager.project.utils.CSVProgramme + + + + + + + + eu.dnetlib.dhp.actionmanager.project.utils.ReadExcel + --hdfsNameNode${nameNode} + --fileURL${topicFileURL} + --hdfsPath${workingDir}/topic + --classForNameeu.dnetlib.dhp.actionmanager.project.utils.EXCELTopic + + + + + + + + eu.dnetlib.dhp.actionmanager.project.ReadProjectsFromDB + --hdfsPath${workingDir}/dbProjects + --hdfsNameNode${nameNode} + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + + + + + + + + yarn + cluster + PrepareProgramme + eu.dnetlib.dhp.actionmanager.project.PrepareProgramme + dhp-aggregation-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --programmePath${workingDir}/programme + --outputPath${workingDir}/preparedProgramme + + + + + + + + yarn + cluster + PrepareProjects + eu.dnetlib.dhp.actionmanager.project.PrepareProjects + dhp-aggregation-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --projectPath${workingDir}/projects + --outputPath${workingDir}/preparedProjects + --dbProjectPath${workingDir}/dbProjects + + + + + + + + yarn + cluster + ProjectProgrammeAS + eu.dnetlib.dhp.actionmanager.project.SparkAtomicActionJob + dhp-aggregation-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --projectPath${workingDir}/preparedProjects + --programmePath${workingDir}/preparedProgramme + --topicPath${workingDir}/topic + --outputPath${outputPath} + + + + + + + \ No newline at end of file From 62ff4999e336b1524aaccfa80757baabb0deb634 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 1 Dec 2020 14:30:56 +0100 Subject: [PATCH 052/149] added workflow and last step of collection and save --- .../bipfinder/input_actionset_parameter.json | 14 +- .../bipfinder/oozie_app/workflow.xml | 178 +++++++++--------- 2 files changed, 94 insertions(+), 98 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json index ae844a0c9..67911eef1 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json @@ -16,17 +16,5 @@ "paramLongName": "outputPath", "paramDescription": "the path of the new ActionSet", "paramRequired": true -}, - { - "paramName": "rtn", - "paramLongName": "resultTableName", - "paramDescription": "the path of the new ActionSet", - "paramRequired": true - }, - { - "paramName": "bsp", - "paramLongName": "bipScorePath", - "paramDescription": "the path of the new ActionSet", - "paramRequired": true - } +} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml index c710c8b55..6f74146f1 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml @@ -1,22 +1,17 @@ - + - projectFileURL - the url where to get the projects file + inputPath + the input path of the resources to be extended - programmeFileURL - the url where to get the programme file - - - - topicFileURL - the url where to get the topic file + bipScorePath + the path where to find the bipFinder scores outputPath - path where to store the action set + the path where to store the actionset @@ -31,128 +26,141 @@ - + - - - eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV - --hdfsNameNode${nameNode} - --fileURL${projectFileURL} - --hdfsPath${workingDir}/projects - --classForNameeu.dnetlib.dhp.actionmanager.project.utils.CSVProject - - - - + + + + + + - - - eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV - --hdfsNameNode${nameNode} - --fileURL${programmeFileURL} - --hdfsPath${workingDir}/programme - --classForNameeu.dnetlib.dhp.actionmanager.project.utils.CSVProgramme - - - - - - - - eu.dnetlib.dhp.actionmanager.project.utils.ReadExcel - --hdfsNameNode${nameNode} - --fileURL${topicFileURL} - --hdfsPath${workingDir}/topic - --classForNameeu.dnetlib.dhp.actionmanager.project.utils.EXCELTopic - - - - - - - - eu.dnetlib.dhp.actionmanager.project.ReadProjectsFromDB - --hdfsPath${workingDir}/dbProjects - --hdfsNameNode${nameNode} - --postgresUrl${postgresURL} - --postgresUser${postgresUser} - --postgresPassword${postgresPassword} - - - - - - + yarn cluster - PrepareProgramme - eu.dnetlib.dhp.actionmanager.project.PrepareProgramme + Produces the atomic action with the bip finder scores for publications + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob dhp-aggregation-${projectVersion}.jar - --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=3840 + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --programmePath${workingDir}/programme - --outputPath${workingDir}/preparedProgramme + --inputPath${inputPath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/publication + --bipScorePath${bipScorePath} - + - + yarn cluster - PrepareProjects - eu.dnetlib.dhp.actionmanager.project.PrepareProjects + Produces the atomic action with the bip finder scores for datasets + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob dhp-aggregation-${projectVersion}.jar - --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=3840 + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --projectPath${workingDir}/projects - --outputPath${workingDir}/preparedProjects - --dbProjectPath${workingDir}/dbProjects + --inputPath${inputPath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/otherresearchproduct + --bipScorePath${bipScorePath} - + - + yarn cluster - ProjectProgrammeAS - eu.dnetlib.dhp.actionmanager.project.SparkAtomicActionJob + Produces the atomic action with the bip finder scores for orp + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob dhp-aggregation-${projectVersion}.jar - --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=3840 + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --projectPath${workingDir}/preparedProjects - --programmePath${workingDir}/preparedProgramme - --topicPath${workingDir}/topic + --inputPath${inputPath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/otherresearchproduct + --bipScorePath${bipScorePath} + + + + + + + + yarn + cluster + Produces the atomic action with the bip finder scores for software + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/software + --bipScorePath${bipScorePath} + + + + + + + + + + yarn + cluster + saves all the aa produced for the several types of results in the as output path + eu.dnetlib.dhp.actionmanager.bipfinder.CollectAndSave + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${workingDir} --outputPath${outputPath} From 5b3ed70808422c8fc34cf20562f01b3f9cbb3d9e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 1 Dec 2020 14:31:34 +0100 Subject: [PATCH 053/149] refactoring --- .../bipfinder/BipDeserialize.java | 22 +- .../dhp/actionmanager/bipfinder/BipScore.java | 29 +- .../dhp/actionmanager/bipfinder/KeyValue.java | 29 +- .../bipfinder/PreparedResult.java | 29 +- .../dhp/actionmanager/bipfinder/Score.java | 29 +- .../bipfinder/SparkAtomicActionScoreJob.java | 306 ++++++------ .../SparkAtomicActionScoreJobTest.java | 437 ++++++++++-------- 7 files changed, 480 insertions(+), 401 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java index e68b912b2..2ec3679ce 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.actionmanager.bipfinder; import java.io.Serializable; @@ -5,19 +6,18 @@ import java.util.ArrayList; import java.util.HashMap; import java.util.List; +public class BipDeserialize extends HashMap> implements Serializable { -public class BipDeserialize extends HashMap> implements Serializable { + public BipDeserialize() { + super(); + } - public BipDeserialize(){ - super(); - } + public List get(String key) { - public List get(String key) { - - if (super.get(key) == null) { - return new ArrayList<>(); - } - return super.get(key); - } + if (super.get(key) == null) { + return new ArrayList<>(); + } + return super.get(key); + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java index b1e381955..3aa2488cd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java @@ -1,25 +1,26 @@ + package eu.dnetlib.dhp.actionmanager.bipfinder; import java.io.Serializable; import java.util.List; public class BipScore implements Serializable { - private String id; - private List scoreList; + private String id; + private List scoreList; - public String getId() { - return id; - } + public String getId() { + return id; + } - public void setId(String id) { - this.id = id; - } + public void setId(String id) { + this.id = id; + } - public List getScoreList() { - return scoreList; - } + public List getScoreList() { + return scoreList; + } - public void setScoreList(List scoreList) { - this.scoreList = scoreList; - } + public void setScoreList(List scoreList) { + this.scoreList = scoreList; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java index 1fadae6fe..6909a9634 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java @@ -1,25 +1,26 @@ + package eu.dnetlib.dhp.actionmanager.bipfinder; import java.io.Serializable; public class KeyValue implements Serializable { - private String key; - private String value; + private String key; + private String value; - public String getKey() { - return key; - } + public String getKey() { + return key; + } - public void setKey(String key) { - this.key = key; - } + public void setKey(String key) { + this.key = key; + } - public String getValue() { - return value; - } + public String getValue() { + return value; + } - public void setValue(String value) { - this.value = value; - } + public void setValue(String value) { + this.value = value; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java index bb7648f0c..3e55ec6bc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java @@ -1,24 +1,25 @@ + package eu.dnetlib.dhp.actionmanager.bipfinder; import java.io.Serializable; public class PreparedResult implements Serializable { - private String id; //openaire id - private String value; //doi + private String id; // openaire id + private String value; // doi - public String getId() { - return id; - } + public String getId() { + return id; + } - public void setId(String id) { - this.id = id; - } + public void setId(String id) { + this.id = id; + } - public String getValue() { - return value; - } + public String getValue() { + return value; + } - public void setValue(String value) { - this.value = value; - } + public void setValue(String value) { + this.value = value; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java index b14d971cd..17423fe96 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.actionmanager.bipfinder; import java.io.Serializable; @@ -5,22 +6,22 @@ import java.util.List; public class Score implements Serializable { - private String id; - private List unit; + private String id; + private List unit; - public String getId() { - return id; - } + public String getId() { + return id; + } - public void setId(String id) { - this.id = id; - } + public void setId(String id) { + this.id = id; + } - public List getUnit() { - return unit; - } + public List getUnit() { + return unit; + } - public void setUnit(List unit) { - this.unit = unit; - } + public void setUnit(List unit) { + this.unit = unit; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 658555e05..1628fca39 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -1,11 +1,13 @@ + package eu.dnetlib.dhp.actionmanager.bipfinder; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.schema.action.AtomicAction; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.KeyValue; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + import org.apache.commons.io.IOUtils; import org.apache.hadoop.hdfs.qjournal.protocol.QJournalProtocolProtos; import org.apache.hadoop.io.Text; @@ -22,182 +24,188 @@ import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.KeyValue; import scala.Tuple2; -import java.io.Serializable; -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - public class SparkAtomicActionScoreJob implements Serializable { - private static String DOI = "doi"; - private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJob.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static String DOI = "doi"; + private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJob.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkAtomicActionScoreJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json")); + String jsonConfiguration = IOUtils + .toString( + SparkAtomicActionScoreJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("inputPath"); - log.info("inputPath {}: ", inputPath); + final String inputPath = parser.get("inputPath"); + log.info("inputPath {}: ", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath {}: ", outputPath); + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); - final String bipScorePath = parser.get("bipScorePath"); - log.info("bipScorePath: {}", bipScorePath); + final String bipScorePath = parser.get("bipScorePath"); + log.info("bipScorePath: {}", bipScorePath); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); - Class inputClazz = (Class) Class.forName(resultClassName); + Class inputClazz = (Class) Class.forName(resultClassName); - SparkConf conf = new SparkConf(); + SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - removeOutputDir(spark, outputPath); - prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz); - }); - } + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz); + }); + } - private static void prepareResults(SparkSession spark, String inputPath, String outputPath, - String bipScorePath, Class inputClazz) { + private static void prepareResults(SparkSession spark, String inputPath, String outputPath, + String bipScorePath, Class inputClazz) { - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - JavaRDD bipDeserializeJavaRDD = sc.textFile(bipScorePath) - .map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class)); + JavaRDD bipDeserializeJavaRDD = sc + .textFile(bipScorePath) + .map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class)); + Dataset bipScores = spark + .createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> { + BipScore bs = new BipScore(); + bs.setId(key); + bs.setScoreList(entry.get(key)); + return bs; + }).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class)); - Dataset bipScores = spark.createDataset(bipDeserializeJavaRDD.flatMap(entry -> - entry.keySet().stream().map(key -> { - BipScore bs = new BipScore(); - bs.setId(key); - bs.setScoreList(entry.get(key)); - return bs; - }).collect(Collectors.toList()).iterator() - ).rdd(), Encoders.bean(BipScore.class)); + System.out.println(bipScores.count()); - System.out.println(bipScores.count()); + Dataset results = readPath(spark, inputPath, inputClazz); - Dataset results = readPath(spark, inputPath, inputClazz); + results.createOrReplaceTempView("result"); - results.createOrReplaceTempView("result"); + Dataset preparedResult = spark + .sql( + "select pIde.value value, id " + + "from result " + + "lateral view explode (pid) p as pIde " + + "where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'") + .as(Encoders.bean(PreparedResult.class)); - Dataset preparedResult = spark.sql("select pIde.value value, id " + - "from result " + - "lateral view explode (pid) p as pIde " + - "where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'") - .as(Encoders.bean(PreparedResult.class)); + Dataset tmp = bipScores + .joinWith( + preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")), + "inner") + .map((MapFunction, BipScore>) value -> { + BipScore ret = value._1(); + ret.setId(value._2().getId()); + return ret; + }, Encoders.bean(BipScore.class)); - Dataset tmp = bipScores.joinWith(preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")), - "inner") - .map((MapFunction, BipScore>) value -> { - BipScore ret = value._1(); - ret.setId(value._2().getId()); - return ret; - }, Encoders.bean(BipScore.class)); + tmp + .groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, it) -> { + Result ret = inputClazz.newInstance(); + BipScore first = it.next(); + ret.setId(first.getId()); - tmp.groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, it) -> - { - Result ret = inputClazz.newInstance(); - BipScore first = it.next(); - ret.setId(first.getId()); + ret.setMeasures(getMeasure(first)); + it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value))); - ret.setMeasures(getMeasure(first)); - it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value))); + return (I) ret; + }, Encoders.bean(inputClazz)) + .toJavaRDD() + .map(p -> new AtomicAction(inputClazz, p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + ; + } - return (I)ret; - }, Encoders.bean(inputClazz)) - .toJavaRDD() - .map(p -> new AtomicAction(inputClazz, p)) - .mapToPair( - aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); - ; - } + public static Dataset getBipScoreDataset(Dataset bipdeserialized) { + return bipdeserialized + .flatMap((FlatMapFunction) bip -> bip.keySet().stream().map(key -> { + BipScore bs = new BipScore(); + bs.setId(key); + bs.setScoreList(bip.get(key)); + return bs; + }).collect(Collectors.toList()).iterator(), Encoders.bean(BipScore.class)); + } - public static Dataset getBipScoreDataset(Dataset bipdeserialized){ - return bipdeserialized.flatMap((FlatMapFunction) bip -> - bip.keySet().stream().map(key -> { - BipScore bs = new BipScore(); - bs.setId(key); - bs.setScoreList(bip.get(key)); - return bs; - }).collect(Collectors.toList()).iterator() - , Encoders.bean(BipScore.class)); - } + private static List getMeasure(BipScore value) { + return value + .getScoreList() + .stream() + .map(score -> { + Measure m = new Measure(); + m.setId(score.getId()); + m + .setUnit( + score + .getUnit() + .stream() + .map(unit -> { + KeyValue kv = new KeyValue(); + kv.setValue(unit.getValue()); + kv.setKey(unit.getKey()); + kv.setDataInfo(getDataInfo()); + return kv; + }) + .collect(Collectors.toList())); + return m; + }) + .collect(Collectors.toList()); + } - private static List getMeasure(BipScore value) { - return value.getScoreList() - .stream() - .map(score -> { - Measure m = new Measure(); - m.setId(score.getId()); - m.setUnit(score.getUnit().stream() - .map(unit -> { - KeyValue kv = new KeyValue(); - kv.setValue(unit.getValue()); - kv.setKey(unit.getKey()); - kv.setDataInfo(getDataInfo()); - return kv; - }).collect(Collectors.toList())); - return m; - }).collect(Collectors.toList()); - } + private static DataInfo getDataInfo() { + DataInfo di = new DataInfo(); + di.setInferred(false); + di.setInvisible(false); + di.setDeletedbyinference(false); + di.setTrust(""); + Qualifier qualifier = new Qualifier(); + qualifier.setClassid("sysimport:actionset"); + qualifier.setClassname("Harvested"); + qualifier.setSchemename("dnet:provenanceActions"); + qualifier.setSchemeid("dnet:provenanceActions"); + di.setProvenanceaction(qualifier); + return di; + } + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } - - private static DataInfo getDataInfo() { - DataInfo di = new DataInfo(); - di.setInferred(false); - di.setInvisible(false); - di.setDeletedbyinference(false); - di.setTrust(""); - Qualifier qualifier = new Qualifier(); - qualifier.setClassid("sysimport:actionset"); - qualifier.setClassname("Harvested"); - qualifier.setSchemename("dnet:provenanceActions"); - qualifier.setSchemeid("dnet:provenanceActions"); - di.setProvenanceaction(qualifier); - return di; - } - - - private static void removeOutputDir(SparkSession spark, String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } - - public static Dataset readPath( - SparkSession spark, String inputPath, Class clazz) { - return spark - .read() - .textFile(inputPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); - } - + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java index 3b360f6ed..4b02e7485 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java @@ -1,9 +1,12 @@ + package eu.dnetlib.dhp.actionmanager.bipfinder; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.action.AtomicAction; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.KeyValue; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.stream.Collectors; + import org.apache.commons.io.FileUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.SequenceFileOutputFormat; @@ -24,241 +27,305 @@ import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import scala.Tuple2; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; -import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import scala.Tuple2; public class SparkAtomicActionScoreJobTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(SparkAtomicActionScoreJobTest.class); + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(SparkAtomicActionScoreJobTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(SparkAtomicActionScoreJobTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(SparkAtomicActionScoreJobTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(SparkAtomicActionScoreJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(SparkAtomicActionScoreJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - public void matchOne() throws Exception { - String bipScoresPath = getClass().getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json").getPath(); - String inputPath = getClass() - .getResource( - "/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json") - .getPath(); + @Test + public void matchOne() throws Exception { + String bipScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") + .getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json") + .getPath(); - SparkAtomicActionScoreJob.main( - new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-inputPath", - inputPath, - "-bipScorePath", - bipScoresPath, - "-resultTableName", - "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", - workingDir.toString() + "/actionSet" - }); + SparkAtomicActionScoreJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); - JavaRDD tmp = sc - .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) - .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) - .map(aa -> ((Publication) aa.getPayload())); + Assertions.assertTrue(tmp.count() == 1); - Assertions.assertTrue(tmp.count() == 1); + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); - Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - verificationDataset.createOrReplaceTempView("publication"); + Dataset execVerification = spark + .sql( + "Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); - Dataset execVerification = spark.sql("Select p.id oaid, mes.id, mUnit.value from publication p " + - "lateral view explode(measures) m as mes " + - "lateral view explode(mes.unit) u as mUnit "); + Assertions.assertEquals(2, execVerification.count()); - Assertions.assertEquals(2, execVerification.count()); + Assertions + .assertEquals( + "50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", + execVerification.select("oaid").collectAsList().get(0).getString(0)); - Assertions.assertEquals("50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", - execVerification.select("oaid").collectAsList().get(0).getString(0)); + Assertions + .assertEquals( + "1.47565045883e-08", + execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0)); - Assertions.assertEquals("1.47565045883e-08", - execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0)); + Assertions + .assertEquals( + "0.227515392", + execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0)); - Assertions.assertEquals("0.227515392", - execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0)); + } - } + @Test + public void matchOneWithTwo() throws Exception { + String bipScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") + .getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json") + .getPath(); - @Test - public void matchOneWithTwo() throws Exception { - String bipScoresPath = getClass().getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json").getPath(); - String inputPath = getClass() - .getResource( - "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json") - .getPath(); + SparkAtomicActionScoreJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); - SparkAtomicActionScoreJob.main( - new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-inputPath", - inputPath, - "-bipScorePath", - bipScoresPath, - "-resultTableName", - "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", - workingDir.toString() + "/actionSet" - }); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + Assertions.assertTrue(tmp.count() == 1); - JavaRDD tmp = sc - .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) - .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) - .map(aa -> ((Publication) aa.getPayload())); + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); - Assertions.assertTrue(tmp.count() == 1); + Dataset execVerification = spark + .sql( + "Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); - Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - verificationDataset.createOrReplaceTempView("publication"); + Assertions.assertEquals(4, execVerification.count()); - Dataset execVerification = spark.sql("Select p.id oaid, mes.id, mUnit.value from publication p " + - "lateral view explode(measures) m as mes " + - "lateral view explode(mes.unit) u as mUnit "); + Assertions + .assertEquals( + "50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", + execVerification.select("oaid").collectAsList().get(0).getString(0)); - Assertions.assertEquals(4, execVerification.count()); + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'influence'").count()); + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'popularity'").count()); - Assertions.assertEquals("50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", - execVerification.select("oaid").collectAsList().get(0).getString(0)); + List tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList(); + String tmp_influence = tmp_ds.get(0).getString(0); + Assertions + .assertTrue( + "1.47565045883e-08".equals(tmp_influence) || + "1.98956540239e-08".equals(tmp_influence)); - Assertions.assertEquals(2, - execVerification.filter("id = 'influence'").count()); + tmp_influence = tmp_ds.get(1).getString(0); + Assertions + .assertTrue( + "1.47565045883e-08".equals(tmp_influence) || + "1.98956540239e-08".equals(tmp_influence)); - Assertions.assertEquals(2, - execVerification.filter("id = 'popularity'").count()); + Assertions.assertTrue(!tmp_ds.get(0).getString(0).equals(tmp_ds.get(1).getString(0))); - List tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList(); - String tmp_influence = tmp_ds.get(0).getString(0); - Assertions.assertTrue("1.47565045883e-08".equals(tmp_influence)|| - "1.98956540239e-08".equals(tmp_influence) ); + } - tmp_influence = tmp_ds.get(1).getString(0); - Assertions.assertTrue("1.47565045883e-08".equals(tmp_influence)|| - "1.98956540239e-08".equals(tmp_influence) ); + @Test + public void matchTwo() throws Exception { + String bipScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") + .getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json") + .getPath(); - Assertions.assertTrue(!tmp_ds.get(0).getString(0).equals(tmp_ds.get(1).getString(0))); + SparkAtomicActionScoreJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - } + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); - @Test - public void matchTwo() throws Exception { - String bipScoresPath = getClass().getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json").getPath(); - String inputPath = getClass() - .getResource( - "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json") - .getPath(); + Assertions.assertTrue(tmp.count() == 2); - SparkAtomicActionScoreJob.main( - new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-inputPath", - inputPath, - "-bipScorePath", - bipScoresPath, - "-resultTableName", - "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", - workingDir.toString() + "/actionSet" - }); + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); + Dataset execVerification = spark + .sql( + "Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + Assertions.assertEquals(4, execVerification.count()); - JavaRDD tmp = sc - .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) - .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) - .map(aa -> ((Publication) aa.getPayload())); + Assertions + .assertEquals( + 2, + execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count()); - Assertions.assertTrue(tmp.count() == 2); + Assertions + .assertEquals( + 2, + execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count()); - Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - verificationDataset.createOrReplaceTempView("publication"); + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'influence'").count()); - Dataset execVerification = spark.sql("Select p.id oaid, mes.id, mUnit.value from publication p " + - "lateral view explode(measures) m as mes " + - "lateral view explode(mes.unit) u as mUnit "); + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'popularity'").count()); - Assertions.assertEquals(4, execVerification.count()); + Assertions + .assertEquals( + "1.47565045883e-08", + execVerification + .filter( + "oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + + "and id = 'influence'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + Assertions + .assertEquals( + "1.98956540239e-08", + execVerification + .filter( + "oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + + "and id = 'influence'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); - Assertions.assertEquals(2, - execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count()); + Assertions + .assertEquals( + "0.282046161584", + execVerification + .filter( + "oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + + "and id = 'popularity'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); - Assertions.assertEquals(2, - execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count()); + Assertions + .assertEquals( + "0.227515392", + execVerification + .filter( + "oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + + "and id = 'popularity'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); - - Assertions.assertEquals(2, - execVerification.filter("id = 'influence'").count()); - - Assertions.assertEquals(2, - execVerification.filter("id = 'popularity'").count()); - - Assertions.assertEquals("1.47565045883e-08" , - execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + - "and id = 'influence'").select("value").collectAsList().get(0).getString(0)); - - Assertions.assertEquals( - "1.98956540239e-08", execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + - "and id = 'influence'").select("value").collectAsList().get(0).getString(0)); - - Assertions.assertEquals( - "0.282046161584", execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + - "and id = 'popularity'").select("value").collectAsList().get(0).getString(0)); - - Assertions.assertEquals("0.227515392" , - execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + - "and id = 'popularity'").select("value").collectAsList().get(0).getString(0)); - - } + } } From 17680296b97a3e70c758fed78508cd789dc4209c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 1 Dec 2020 15:02:31 +0100 Subject: [PATCH 054/149] removed unnecessary variable and unused method --- .../bipfinder/SparkAtomicActionScoreJob.java | 18 ++++-------------- 1 file changed, 4 insertions(+), 14 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 1628fca39..ddf1b3049 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -8,6 +8,7 @@ import java.util.List; import java.util.Optional; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.common.ModelSupport; import org.apache.commons.io.IOUtils; import org.apache.hadoop.hdfs.qjournal.protocol.QJournalProtocolProtos; import org.apache.hadoop.io.Text; @@ -115,7 +116,7 @@ public class SparkAtomicActionScoreJob implements Serializable { "where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'") .as(Encoders.bean(PreparedResult.class)); - Dataset tmp = bipScores + bipScores .joinWith( preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")), "inner") @@ -123,9 +124,7 @@ public class SparkAtomicActionScoreJob implements Serializable { BipScore ret = value._1(); ret.setId(value._2().getId()); return ret; - }, Encoders.bean(BipScore.class)); - - tmp + }, Encoders.bean(BipScore.class)) .groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) .mapGroups((MapGroupsFunction) (k, it) -> { Result ret = inputClazz.newInstance(); @@ -143,18 +142,9 @@ public class SparkAtomicActionScoreJob implements Serializable { aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), new Text(OBJECT_MAPPER.writeValueAsString(aa)))) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); - ; + } - public static Dataset getBipScoreDataset(Dataset bipdeserialized) { - return bipdeserialized - .flatMap((FlatMapFunction) bip -> bip.keySet().stream().map(key -> { - BipScore bs = new BipScore(); - bs.setId(key); - bs.setScoreList(bip.get(key)); - return bs; - }).collect(Collectors.toList()).iterator(), Encoders.bean(BipScore.class)); - } private static List getMeasure(BipScore value) { return value From 3d62d99d5dadf3a9f96e829bec637de3c1dcb08c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 1 Dec 2020 15:02:49 +0100 Subject: [PATCH 055/149] fixed issue in workflow variable --- .../dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml index 6f74146f1..ea2e9f58a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml @@ -82,7 +82,7 @@ --inputPath${inputPath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/otherresearchproduct + --outputPath${workingDir}/dataset --bipScorePath${bipScorePath} From 888175baf7f751826a13d622f0699353eb9f7612 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 1 Dec 2020 18:36:29 +0100 Subject: [PATCH 056/149] added java doc --- .../dhp/actionmanager/bipfinder/BipDeserialize.java | 5 +++++ .../eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java | 8 ++++++-- .../dhp/actionmanager/bipfinder/CollectAndSave.java | 8 ++++---- .../dhp/actionmanager/bipfinder/PreparedResult.java | 3 +++ .../eu/dnetlib/dhp/actionmanager/bipfinder/Score.java | 3 +++ .../bipfinder/SparkAtomicActionScoreJob.java | 7 +++---- 6 files changed, 24 insertions(+), 10 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java index 2ec3679ce..d5b2ced7c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java @@ -6,6 +6,11 @@ import java.util.ArrayList; import java.util.HashMap; import java.util.List; +/** + * Class that maps the model of the bipFinder! input data. + * Only needed for deserialization purposes + */ + public class BipDeserialize extends HashMap> implements Serializable { public BipDeserialize() { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java index 3aa2488cd..da9a4bd0c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java @@ -4,9 +4,13 @@ package eu.dnetlib.dhp.actionmanager.bipfinder; import java.io.Serializable; import java.util.List; +/** + * Rewriting of the bipFinder input data by extracting the identifier of the result (doi) + */ + public class BipScore implements Serializable { - private String id; - private List scoreList; + private String id; //doi + private List scoreList; //unit as given in the inputfile public String getId() { return id; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java index 7164fc5ed..0bebe2fb0 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java @@ -10,11 +10,7 @@ import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -25,6 +21,10 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.oaf.Result; +/** + * Just collects all the atomic actions produced for the different results and saves them in + * outputpath for the ActionSet + */ public class CollectAndSave implements Serializable { private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java index 3e55ec6bc..493e94417 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java @@ -3,6 +3,9 @@ package eu.dnetlib.dhp.actionmanager.bipfinder; import java.io.Serializable; +/** + * Subset of the information of the generic results that are needed to create the atomic action + */ public class PreparedResult implements Serializable { private String id; // openaire id private String value; // doi diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java index 17423fe96..7cc21b44d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java @@ -4,6 +4,9 @@ package eu.dnetlib.dhp.actionmanager.bipfinder; import java.io.Serializable; import java.util.List; +/** + * represents the score in the input file + */ public class Score implements Serializable { private String id; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index ddf1b3049..23764f38e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -8,20 +8,16 @@ import java.util.List; import java.util.Optional; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.common.ModelSupport; import org.apache.commons.io.IOUtils; -import org.apache.hadoop.hdfs.qjournal.protocol.QJournalProtocolProtos; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -35,6 +31,9 @@ import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.KeyValue; import scala.Tuple2; +/** + * created the Atomic Action for each tipe of results + */ public class SparkAtomicActionScoreJob implements Serializable { private static String DOI = "doi"; From d5efa6963a1fd8af983fe5fa71ffc4cd7d18d8ac Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 2 Dec 2020 11:20:26 +0100 Subject: [PATCH 057/149] using constants in ModelCOnstants --- .../dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java index aeaa8a3c1..4989e09d1 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java @@ -7,6 +7,7 @@ import java.nio.file.Path; import com.cloudera.org.codehaus.jackson.map.jsontype.impl.ClassNameIdResolver; import eu.dnetlib.dhp.PropagationConstant; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -169,7 +170,7 @@ public class OrcidPropagationJobTest { .filter( "id = '50|dedup_wf_001::95b033c0c3961f6a1cdcd41a99a9632e' " + "and name = 'Vajinder' and surname = 'Kumar' and pidType = '" + - PropagationConstant.PROPAGATION_AUTHOR_PID_CLASSID +"'") + ModelConstants.ORCID_PENDING + "'") .count()); Assertions.assertEquals(1, propagatedAuthors.filter("pid = '0000-0002-8825-3517'").count()); From 4c58bd1c93297bfc0e99b6e82268fa86f3d83067 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 3 Dec 2020 11:24:00 +0100 Subject: [PATCH 058/149] merge with upstream --- .../dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java | 1 - 1 file changed, 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java index 1bfb79dca..238375197 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java @@ -5,7 +5,6 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; - import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; From ea88dc3401e656682c8c13343684fa05a5e5e692 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 3 Dec 2020 11:24:23 +0100 Subject: [PATCH 059/149] fixed issue in property name --- .../dhp/oa/graph/dump/community/oozie_app/workflow.xml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/workflow.xml index 161fd2dec..fcef2547a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/community/oozie_app/workflow.xml @@ -26,8 +26,8 @@ the metadata associated to the deposition - newDeposition - true if it is a brand new depositon. false for new version of an old deposition + depositionType + one among {new, update, version} conceptRecordId @@ -419,6 +419,7 @@ --metadata${metadata} --communityMapPath${workingDir}/communityMap --conceptRecordId${conceptRecordId} + --depositionId${depositionId} --depositionType${depositionType} From 026ad4063304e31ea3e169cf40d93693912dccbb Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 7 Dec 2020 13:50:01 +0100 Subject: [PATCH 060/149] disabled test --- .../oa/provision/XmlRecordFactoryTest.java | 33 +------------------ 1 file changed, 1 insertion(+), 32 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index e84f97836..992ab26e8 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -5,31 +5,23 @@ import static org.junit.jupiter.api.Assertions.*; import java.io.IOException; import java.io.StringReader; -import java.util.List; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.io.SAXReader; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; -import org.mockito.Mock; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.OafMapperUtils; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; //TODO to enable it we need to update the joined_entity.json test file -//@Disabled +@Disabled public class XmlRecordFactoryTest { private static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource"; @@ -43,27 +35,6 @@ public class XmlRecordFactoryTest { JoinedEntity je = new ObjectMapper().readValue(json, JoinedEntity.class); assertNotNull(je); - Document doc = buildXml(je); - //// TODO specific test assertion on doc - } - - @Test - void testBologna() throws IOException, DocumentException { - final String json = IOUtils.toString(getClass().getResourceAsStream("oaf-bologna.json")); - Publication oaf = new ObjectMapper().readValue(json, Publication.class); - assertNotNull(oaf); - JoinedEntity je = new JoinedEntity(); - je.setEntity(oaf); - assertNotNull(je); - - Document doc = buildXml(je); - // TODO specific test assertion on doc - - System.out.println(doc.asXML()); - - } - - private Document buildXml(JoinedEntity je) throws DocumentException { ContextMapper contextMapper = new ContextMapper(); XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, @@ -78,7 +49,5 @@ public class XmlRecordFactoryTest { assertNotNull(doc); // TODO add assertions based of values extracted from the XML record - - return doc; } } From 5de8a7276fc8018848bf5cd80c2475049b5b47ad Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 7 Dec 2020 14:56:06 +0100 Subject: [PATCH 061/149] wf to partition opendoar events --- .../broker/oa/PartitionEventsByDsIdJob.java | 28 +++++++-- .../dhp/broker/oa/od_partitions_params.json | 14 +++++ .../oozie_app/config-default.xml | 0 .../oozie_app/workflow.xml | 59 ++----------------- 4 files changed, 42 insertions(+), 59 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json rename dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/{partial => opendoarPartition}/oozie_app/config-default.xml (100%) rename dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/{partial => opendoarPartition}/oozie_app/workflow.xml (61%) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index da2c5bb78..65d5e6f94 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -4,8 +4,13 @@ package eu.dnetlib.dhp.broker.oa; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.IOException; +import java.util.Arrays; +import java.util.HashSet; import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; +import org.apache.commons.codec.digest.DigestUtils; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.conf.Configuration; @@ -29,15 +34,14 @@ import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; public class PartitionEventsByDsIdJob { private static final Logger log = LoggerFactory.getLogger(PartitionEventsByDsIdJob.class); - private static final String OPENDOAR_NSPREFIX = "opendoar____::"; + private static final String OPENDOAR_NSPREFIX = "10|opendoar____::"; public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - PartitionEventsByDsIdJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); + .toString(PartitionEventsByDsIdJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -54,13 +58,25 @@ public class PartitionEventsByDsIdJob { final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId"; log.info("partitionPath: {}", partitionPath); + final String opendoarIds = parser.get("opendoarIds"); + log.info("opendoarIds: {}", opendoarIds); + + final Set validOpendoarIds = new HashSet<>(); + if (!opendoarIds.trim().equals("-")) { + validOpendoarIds.addAll(Arrays.stream(opendoarIds.split(",")) + .map(String::trim) + .filter(StringUtils::isNotBlank) + .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) + .collect(Collectors.toSet())); + } + runWithSparkSession(conf, isSparkSessionManaged, spark -> { ClusterUtils .readPath(spark, eventsPath, Event.class) .filter(e -> StringUtils.isNotBlank(e.getMap().getTargetDatasourceId())) - .filter(e -> e.getMap().getTargetDatasourceId().contains(OPENDOAR_NSPREFIX)) - .limit(10000) + .filter(e -> e.getMap().getTargetDatasourceId().startsWith(OPENDOAR_NSPREFIX)) + .filter(e -> validOpendoarIds.contains(e.getMap().getTargetDatasourceId())) .map(e -> messageFromNotification(e), Encoders.bean(ShortEventMessageWithGroupId.class)) .coalesce(1) .write() diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json new file mode 100644 index 000000000..10ba926ab --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json @@ -0,0 +1,14 @@ +[ + { + "paramName": "o", + "paramLongName": "workingPath", + "paramDescription": "the path where the temporary data will be stored", + "paramRequired": true + }, + { + "paramName": "list", + "paramLongName": "opendoarIds", + "paramDescription": "the opendoar IDs whitelist (comma separated)", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/config-default.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/config-default.xml rename to dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml similarity index 61% rename from dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml rename to dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index 8bae626f1..dba3c9f73 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -1,60 +1,13 @@ - + - graphInputPath - the path where the graph is stored + opendoarIds + the opendoar IDs whitelist (comma separated) workingPath the path where the the generated data will be stored - - - datasourceIdWhitelist - - - a white list (comma separeted, - for empty list) of datasource ids - - - datasourceTypeWhitelist - - - a white list (comma separeted, - for empty list) of datasource types - - - datasourceIdBlacklist - - - a black list (comma separeted, - for empty list) of datasource ids - - - esEventIndexName - the elasticsearch index name for events - - - esNotificationsIndexName - the elasticsearch index name for notifications - - - esIndexHost - the elasticsearch host - - - maxIndexedEventsForDsAndTopic - the max number of events for each couple (ds/topic) - - - brokerApiBaseUrl - the url of the broker service api - - - brokerDbUrl - the url of the broker database - - - brokerDbUser - the user of the broker database - - - brokerDbPassword - the password of the broker database sparkDriverMemory @@ -111,13 +64,13 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + yarn cluster @@ -134,8 +87,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --graphPath${graphInputPath} --workingPath${workingPath} + --opendoarIds${opendoarIds} From 302baab67b3de2e8f186a001ebc69e712058649a Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Mon, 7 Dec 2020 19:59:33 +0100 Subject: [PATCH 062/149] fixed doiboost mapping and workflows --- .../eu/dnetlib/dhp/schema/orcid/OrcidDOI.java | 29 ++++---- .../doiboost/SparkGenerateDoiBoost.scala | 2 +- .../mag/SparkImportMagIntoDataset.scala | 14 ++-- .../doiboost/mag/SparkPreProcessMAG.scala | 42 ++++++------ .../dnetlib/doiboost/orcid/ORCIDToOAF.scala | 27 +++++--- .../orcid/SparkConvertORCIDToOAF.scala | 66 +++++++++++++++---- .../intersection/oozie_app/workflow.xml | 9 +-- .../dhp/doiboost/mag/oozie_app/workflow.xml | 19 ++++-- .../doiboost/mag/preprocess_mag_params.json | 3 +- .../orcid/MappingORCIDToOAFTest.scala | 27 ++++++++ 10 files changed, 163 insertions(+), 75 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java index 11bce26c8..cf372c12a 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java @@ -1,24 +1,25 @@ + package eu.dnetlib.dhp.schema.orcid; import java.util.List; public class OrcidDOI { - private String doi; - private List authors; + private String doi; + private List authors; - public String getDoi() { - return doi; - } + public String getDoi() { + return doi; + } - public void setDoi(String doi) { - this.doi = doi; - } + public void setDoi(String doi) { + this.doi = doi; + } - public List getAuthors() { - return authors; - } + public List getAuthors() { + return authors; + } - public void setAuthors(List authors) { - this.authors = authors; - } + public void setAuthors(List authors) { + this.authors = authors; + } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index a29809fc0..860254527 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -62,7 +62,7 @@ object SparkGenerateDoiBoost { val orcidPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/orcidPublication").as[Publication].map(p => (p.getId, p)) fj.joinWith(orcidPublication, fj("_1").equalTo(orcidPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/secondJoin") - logger.info("Phase 3) Join Result with MAG") + logger.info("Phase 4) Join Result with MAG") val sj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/secondJoin").as[Publication].map(p => (p.getId, p)) val magPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/magPublication").as[Publication].map(p => (p.getId, p)) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala index f291a92f9..88fee72b7 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala @@ -21,15 +21,17 @@ object SparkImportMagIntoDataset { val stream = Map( - "Affiliations" -> Tuple2("mag/Affiliations.txt", Seq("AffiliationId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "GridId:string", "OfficialPage:string", "WikiPage:string", "PaperCount:long", "CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")), - "Authors" -> Tuple2("mag/Authors.txt", Seq("AuthorId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "LastKnownAffiliationId:long?", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), - "ConferenceInstances" -> Tuple2("mag/ConferenceInstances.txt", Seq("ConferenceInstanceId:long", "NormalizedName:string", "DisplayName:string", "ConferenceSeriesId:long", "Location:string", "OfficialUrl:string", "StartDate:DateTime?", "EndDate:DateTime?", "AbstractRegistrationDate:DateTime?", "SubmissionDeadlineDate:DateTime?", "NotificationDueDate:DateTime?", "FinalVersionDueDate:DateTime?", "PaperCount:long", "CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")), + "Affiliations" -> Tuple2("mag/Affiliations.txt", Seq("AffiliationId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "GridId:string", "OfficialPage:string", "WikiPage:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "Iso3166Code:string", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")), + "AuthorExtendedAttributes" -> Tuple2("mag/AuthorExtendedAttributes.txt", Seq("AuthorId:long", "AttributeType:int", "AttributeValue:string")), + "Authors" -> Tuple2("mag/Authors.txt", Seq("AuthorId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "LastKnownAffiliationId:long?", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")), + "ConferenceInstances" -> Tuple2("mag/ConferenceInstances.txt", Seq("ConferenceInstanceId:long", "NormalizedName:string", "DisplayName:string", "ConferenceSeriesId:long", "Location:string", "OfficialUrl:string", "StartDate:DateTime?", "EndDate:DateTime?", "AbstractRegistrationDate:DateTime?", "SubmissionDeadlineDate:DateTime?", "NotificationDueDate:DateTime?", "FinalVersionDueDate:DateTime?", "PaperCount:long", "PaperFamilyCount:long" ,"CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")), "ConferenceSeries" -> Tuple2("mag/ConferenceSeries.txt", Seq("ConferenceSeriesId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), "EntityRelatedEntities" -> Tuple2("advanced/EntityRelatedEntities.txt", Seq("EntityId:long", "EntityType:string", "RelatedEntityId:long", "RelatedEntityType:string", "RelatedType:int", "Score:float")), "FieldOfStudyChildren" -> Tuple2("advanced/FieldOfStudyChildren.txt", Seq("FieldOfStudyId:long", "ChildFieldOfStudyId:long")), "FieldOfStudyExtendedAttributes" -> Tuple2("advanced/FieldOfStudyExtendedAttributes.txt", Seq("FieldOfStudyId:long", "AttributeType:int", "AttributeValue:string")), - "FieldsOfStudy" -> Tuple2("advanced/FieldsOfStudy.txt", Seq("FieldOfStudyId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "MainType:string", "Level:int", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), - "Journals" -> Tuple2("mag/Journals.txt", Seq("JournalId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "Issn:string", "Publisher:string", "Webpage:string", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")), + // ['FieldOfStudyId:long', 'Rank:uint', 'NormalizedName:string', 'DisplayName:string', 'MainType:string', 'Level:int', 'PaperCount:long', 'PaperFamilyCount:long', 'CitationCount:long', 'CreatedDate:DateTime'] + "FieldsOfStudy" -> Tuple2("advanced/FieldsOfStudy.txt", Seq("FieldOfStudyId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "MainType:string", "Level:int", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")), + "Journals" -> Tuple2("mag/Journals.txt", Seq("JournalId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "Issn:string", "Publisher:string", "Webpage:string", "PaperCount:long", "PaperFamilyCount:long" ,"CitationCount:long", "CreatedDate:DateTime")), "PaperAbstractsInvertedIndex" -> Tuple2("nlp/PaperAbstractsInvertedIndex.txt.*", Seq("PaperId:long", "IndexedAbstract:string")), "PaperAuthorAffiliations" -> Tuple2("mag/PaperAuthorAffiliations.txt", Seq("PaperId:long", "AuthorId:long", "AffiliationId:long?", "AuthorSequenceNumber:uint", "OriginalAuthor:string", "OriginalAffiliation:string")), "PaperCitationContexts" -> Tuple2("nlp/PaperCitationContexts.txt", Seq("PaperId:long", "PaperReferenceId:long", "CitationContext:string")), @@ -39,7 +41,7 @@ object SparkImportMagIntoDataset { "PaperReferences" -> Tuple2("mag/PaperReferences.txt", Seq("PaperId:long", "PaperReferenceId:long")), "PaperResources" -> Tuple2("mag/PaperResources.txt", Seq("PaperId:long", "ResourceType:int", "ResourceUrl:string", "SourceUrl:string", "RelationshipType:int")), "PaperUrls" -> Tuple2("mag/PaperUrls.txt", Seq("PaperId:long", "SourceType:int?", "SourceUrl:string", "LanguageCode:string")), - "Papers" -> Tuple2("mag/Papers.txt", Seq("PaperId:long", "Rank:uint", "Doi:string", "DocType:string", "PaperTitle:string", "OriginalTitle:string", "BookTitle:string", "Year:int?", "Date:DateTime?", "Publisher:string", "JournalId:long?", "ConferenceSeriesId:long?", "ConferenceInstanceId:long?", "Volume:string", "Issue:string", "FirstPage:string", "LastPage:string", "ReferenceCount:long", "CitationCount:long", "EstimatedCitation:long", "OriginalVenue:string", "FamilyId:long?", "CreatedDate:DateTime")), + "Papers" -> Tuple2("mag/Papers.txt", Seq("PaperId:long", "Rank:uint", "Doi:string", "DocType:string", "PaperTitle:string", "OriginalTitle:string", "BookTitle:string", "Year:int?", "Date:DateTime?", "OnlineDate:DateTime?", "Publisher:string", "JournalId:long?", "ConferenceSeriesId:long?", "ConferenceInstanceId:long?", "Volume:string", "Issue:string", "FirstPage:string", "LastPage:string", "ReferenceCount:long", "CitationCount:long", "EstimatedCitation:long", "OriginalVenue:string", "FamilyId:long?", "FamilyRank:uint?", "CreatedDate:DateTime")), "RelatedFieldOfStudy" -> Tuple2("advanced/RelatedFieldOfStudy.txt", Seq("FieldOfStudyId1:long", "Type1:string", "FieldOfStudyId2:long", "Type2:string", "Rank:float")) ) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala index a24f0e6bb..02dc4979a 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala @@ -26,12 +26,15 @@ object SparkPreProcessMAG { .master(parser.get("master")).getOrCreate() val sourcePath = parser.get("sourcePath") + val workingPath = parser.get("workingPath") + val targetPath = parser.get("targetPath") + import spark.implicits._ implicit val mapEncoderPubs: Encoder[Publication] = org.apache.spark.sql.Encoders.kryo[Publication] implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs) logger.info("Phase 1) make uninque DOI in Papers:") - val d: Dataset[MagPapers] = spark.read.load(s"${parser.get("sourcePath")}/Papers").as[MagPapers] + val d: Dataset[MagPapers] = spark.read.load(s"$sourcePath/Papers").as[MagPapers] // Filtering Papers with DOI, and since for the same DOI we have multiple version of item with different PapersId we get the last one val result: RDD[MagPapers] = d.where(col("Doi").isNotNull) @@ -41,11 +44,12 @@ object SparkPreProcessMAG { .map(_._2) val distinctPaper: Dataset[MagPapers] = spark.createDataset(result) - distinctPaper.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/Papers_distinct") + + distinctPaper.write.mode(SaveMode.Overwrite).save(s"$workingPath/Papers_distinct") logger.info("Phase 0) Enrich Publication with description") - val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract] - pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract") + val pa = spark.read.load(s"$sourcePath/PaperAbstractsInvertedIndex").as[MagPaperAbstract] + pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"$workingPath/PaperAbstract") logger.info("Phase 3) Group Author by PaperId") val authors = spark.read.load(s"$sourcePath/Authors").as[MagAuthor] @@ -64,24 +68,24 @@ object SparkPreProcessMAG { } else mpa }).groupBy("PaperId").agg(collect_list(struct($"author", $"affiliation")).as("authors")) - .write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_1_paper_authors") + .write.mode(SaveMode.Overwrite).save(s"$workingPath/merge_step_1_paper_authors") logger.info("Phase 4) create First Version of publication Entity with Paper Journal and Authors") val journals = spark.read.load(s"$sourcePath/Journals").as[MagJournal] - val papers = spark.read.load((s"${parser.get("targetPath")}/Papers_distinct")).as[MagPapers] + val papers = spark.read.load((s"$workingPath/Papers_distinct")).as[MagPapers] - val paperWithAuthors = spark.read.load(s"${parser.get("targetPath")}/merge_step_1_paper_authors").as[MagPaperWithAuthorList] + val paperWithAuthors = spark.read.load(s"$workingPath/merge_step_1_paper_authors").as[MagPaperWithAuthorList] val firstJoin = papers.joinWith(journals, papers("JournalId").equalTo(journals("JournalId")), "left") firstJoin.joinWith(paperWithAuthors, firstJoin("_1.PaperId").equalTo(paperWithAuthors("PaperId")), "left") .map { a => ConversionUtil.createOAFFromJournalAuthorPaper(a) } - .write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2") + .write.mode(SaveMode.Overwrite).save(s"$workingPath/merge_step_2") var magPubs: Dataset[(String, Publication)] = - spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication] + spark.read.load(s"$workingPath/merge_step_2").as[Publication] .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] @@ -95,10 +99,10 @@ object SparkPreProcessMAG { .map(item => ConversionUtil.updatePubsWithConferenceInfo(item)) .write .mode(SaveMode.Overwrite) - .save(s"${parser.get("targetPath")}/merge_step_2_conference") + .save(s"$workingPath/merge_step_2_conference") - magPubs= spark.read.load(s"${parser.get("targetPath")}/merge_step_2_conference").as[Publication] + magPubs= spark.read.load(s"$workingPath/merge_step_2_conference").as[Publication] .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl] @@ -108,27 +112,27 @@ object SparkPreProcessMAG { magPubs.joinWith(paperUrlDataset, col("_1").equalTo(paperUrlDataset("PaperId")), "left") .map { a: ((String, Publication), MagUrl) => ConversionUtil.addInstances((a._1._2, a._2)) } .write.mode(SaveMode.Overwrite) - .save(s"${parser.get("targetPath")}/merge_step_3") + .save(s"$workingPath/merge_step_3") // logger.info("Phase 6) Enrich Publication with description") // val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract] // pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract") - val paperAbstract = spark.read.load((s"${parser.get("targetPath")}/PaperAbstract")).as[MagPaperAbstract] + val paperAbstract = spark.read.load((s"$workingPath/PaperAbstract")).as[MagPaperAbstract] - magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_3").as[Publication] + magPubs = spark.read.load(s"$workingPath/merge_step_3").as[Publication] .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] magPubs.joinWith(paperAbstract, col("_1").equalTo(paperAbstract("PaperId")), "left") .map(item => ConversionUtil.updatePubsWithDescription(item) - ).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_4") + ).write.mode(SaveMode.Overwrite).save(s"$workingPath/merge_step_4") logger.info("Phase 7) Enrich Publication with FieldOfStudy") - magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_4").as[Publication] + magPubs = spark.read.load(s"$workingPath/merge_step_4").as[Publication] .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] val fos = spark.read.load(s"$sourcePath/FieldsOfStudy").select($"FieldOfStudyId".alias("fos"), $"DisplayName", $"MainType") @@ -144,14 +148,14 @@ object SparkPreProcessMAG { .equalTo(paperField("PaperId")), "left") .map(item => ConversionUtil.updatePubsWithSubject(item)) .write.mode(SaveMode.Overwrite) - .save(s"${parser.get("targetPath")}/mag_publication") + .save(s"$workingPath/mag_publication") - val s:RDD[Publication] = spark.read.load(s"${parser.get("targetPath")}/mag_publication").as[Publication] + val s:RDD[Publication] = spark.read.load(s"$workingPath/mag_publication").as[Publication] .map(p=>Tuple2(p.getId, p)).rdd.reduceByKey((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b)) .map(_._2) - spark.createDataset(s).as[Publication].write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/mag_publication_u") + spark.createDataset(s).as[Publication].write.mode(SaveMode.Overwrite).save(s"$targetPath/magPublication") } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala index f230c604f..f7255e559 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala @@ -1,6 +1,7 @@ package eu.dnetlib.doiboost.orcid -import eu.dnetlib.dhp.schema.oaf.{Author, Publication} +import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication} +import eu.dnetlib.dhp.schema.orcid.OrcidDOI import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier} import org.apache.commons.lang.StringUtils @@ -43,16 +44,19 @@ object ORCIDToOAF { } - def convertTOOAF(input:ORCIDElement) :Publication = { - val doi = input.doi + def convertTOOAF(input:OrcidDOI) :Publication = { + val doi = input.getDoi val pub:Publication = new Publication - pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava) + pub.setPid(List(createSP(doi.toLowerCase, "doi", PID_TYPES)).asJava) pub.setDataInfo(generateDataInfo()) pub.setId(generateIdentifier(pub, doi.toLowerCase)) try{ - pub.setAuthor(input.authors.map(a=> { - generateAuthor(a.name, a.surname, a.creditName, a.oid) - }).asJava) + + val l:List[Author]= input.getAuthors.asScala.map(a=> { + generateAuthor(a.getName, a.getSurname, a.getCreditName, a.getOid) + })(collection.breakOut) + + pub.setAuthor(l.asJava) pub.setCollectedfrom(List(DoiBoostMappingUtil.createORIDCollectedFrom()).asJava) pub.setDataInfo(DoiBoostMappingUtil.generateDataInfo()) pub @@ -63,6 +67,13 @@ object ORCIDToOAF { } } + def generateOricPIDDatainfo():DataInfo = { + val di =DoiBoostMappingUtil.generateDataInfo("0.91") + di.getProvenanceaction.setClassid("sysimport:crosswalk:entityregistry") + di.getProvenanceaction.setClassname("Harvested") + di + } + def generateAuthor(given: String, family: String, fullName:String, orcid: String): Author = { val a = new Author a.setName(given) @@ -72,7 +83,7 @@ object ORCIDToOAF { else a.setFullname(s"$given $family") if (StringUtils.isNotBlank(orcid)) - a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava) + a.setPid(List(createSP(orcid, ORCID, PID_TYPES, generateOricPIDDatainfo())).asJava) a } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala index 1cd9ba4d4..f1c7c58b4 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala @@ -1,21 +1,72 @@ package eu.dnetlib.doiboost.orcid +import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper} import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.oa.merge.AuthorMerger import eu.dnetlib.dhp.schema.oaf.Publication +import eu.dnetlib.dhp.schema.orcid.OrcidDOI import eu.dnetlib.doiboost.mag.ConversionUtil import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.rdd.RDD +import org.apache.spark.sql.expressions.Aggregator import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} object SparkConvertORCIDToOAF { + val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass) + + def getPublicationAggregator(): Aggregator[(String, Publication), Publication, Publication] = new Aggregator[(String, Publication), Publication, Publication]{ + + override def zero: Publication = new Publication() + + override def reduce(b: Publication, a: (String, Publication)): Publication = { + b.mergeFrom(a._2) + b.setAuthor(AuthorMerger.mergeAuthor(a._2.getAuthor, b.getAuthor)) + if (b.getId == null) + b.setId(a._2.getId) + b + } + override def merge(wx: Publication, wy: Publication): Publication = { + wx.mergeFrom(wy) + wx.setAuthor(AuthorMerger.mergeAuthor(wy.getAuthor, wx.getAuthor)) + if(wx.getId == null && wy.getId.nonEmpty) + wx.setId(wy.getId) + wx + } + override def finish(reduction: Publication): Publication = reduction + + override def bufferEncoder: Encoder[Publication] = + Encoders.kryo(classOf[Publication]) + + override def outputEncoder: Encoder[Publication] = + Encoders.kryo(classOf[Publication]) + } + +def run(spark:SparkSession,sourcePath:String, targetPath:String):Unit = { + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] + implicit val mapOrcid: Encoder[OrcidDOI] = Encoders.kryo[OrcidDOI] + implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs) + + val mapper = new ObjectMapper() + mapper.getDeserializationConfig.withFeatures(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES) + + val dataset:Dataset[OrcidDOI] = spark.createDataset(spark.sparkContext.textFile(sourcePath).map(s => mapper.readValue(s,classOf[OrcidDOI]))) + + logger.info("Converting ORCID to OAF") + dataset.map(o => ORCIDToOAF.convertTOOAF(o)).filter(p=>p!=null) + .map(d => (d.getId, d)) + .groupByKey(_._1)(Encoders.STRING) + .agg(getPublicationAggregator().toColumn) + .map(p => p._2) + .write.mode(SaveMode.Overwrite).save(targetPath) +} def main(args: Array[String]): Unit = { - val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass) + val conf: SparkConf = new SparkConf() val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json"))) parser.parseArgument(args) @@ -26,19 +77,12 @@ object SparkConvertORCIDToOAF { .appName(getClass.getSimpleName) .master(parser.get("master")).getOrCreate() - implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] - implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs) - import spark.implicits._ + + val sourcePath = parser.get("sourcePath") val targetPath = parser.get("targetPath") - val dataset:Dataset[ORCIDElement] = spark.read.json(sourcePath).as[ORCIDElement] + run(spark, sourcePath, targetPath) - - logger.info("Converting ORCID to OAF") - val d:RDD[Publication] = dataset.map(o => ORCIDToOAF.convertTOOAF(o)).filter(p=>p!=null).map(p=>(p.getId,p)).rdd.reduceByKey(ConversionUtil.mergePublication) - .map(_._2) - - spark.createDataset(d).as[Publication].write.mode(SaveMode.Overwrite).save(targetPath) } } diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml index e35f88abd..dcde62c9d 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml @@ -39,14 +39,7 @@ Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - + diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml index 2277b79b0..9d19dddc7 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml @@ -8,6 +8,10 @@ targetPath the working dir base path + + workingPath + the working dir base path + sparkDriverMemory memory for driver process @@ -31,10 +35,10 @@ - - + + - + @@ -52,10 +56,10 @@ ${sparkExtraOPT} --sourcePath${sourcePath} - --targetPath${targetPath} + --targetPath${workingPath} --masteryarn-cluster - + @@ -65,7 +69,7 @@ yarn-cluster cluster - Convert Mag to Dataset + Convert Mag to OAF Dataset eu.dnetlib.doiboost.mag.SparkPreProcessMAG dhp-doiboost-${projectVersion}.jar @@ -75,7 +79,8 @@ --conf spark.sql.shuffle.partitions=3840 ${sparkExtraOPT} - --sourcePath${sourcePath} + --sourcePath${workingPath} + --workingPath${workingPath}/process --targetPath${targetPath} --masteryarn-cluster diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json index bf0b80f69..d45f7269f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json @@ -1,6 +1,7 @@ [ {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the base path of MAG input", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target dir path", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working dir path", "paramRequired": true}, {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala index 5b8240942..0222b393d 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -1,5 +1,8 @@ package eu.dnetlib.doiboost.orcid +import eu.dnetlib.dhp.schema.oaf.Publication +import eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF.getClass +import org.apache.spark.sql.{Encoder, Encoders, SparkSession} import org.codehaus.jackson.map.ObjectMapper import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.Test @@ -21,6 +24,30 @@ class MappingORCIDToOAFTest { }) } +// @Test +// def testOAFConvert():Unit ={ +// +// val spark: SparkSession = +// SparkSession +// .builder() +// .appName(getClass.getSimpleName) +// .master("local[*]").getOrCreate() +// +// +// SparkConvertORCIDToOAF.run( spark,"/Users/sandro/Downloads/orcid", "/Users/sandro/Downloads/orcid_oaf") +// implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] +// +// val df = spark.read.load("/Users/sandro/Downloads/orcid_oaf").as[Publication] +// println(df.first.getId) +// println(mapper.writeValueAsString(df.first())) +// +// +// +// +// } + + + From 197f286fa476f2670a268ca08b7db7ed4154734c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 7 Dec 2020 21:52:17 +0100 Subject: [PATCH 063/149] removed duplicated dependency (org.apache.httpcomponents:httpclent --- pom.xml | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/pom.xml b/pom.xml index d06bdbe20..a2e2587b3 100644 --- a/pom.xml +++ b/pom.xml @@ -278,12 +278,12 @@ org.apache.httpcomponents httpclient - 4.5.3 + ${org.apache.httpcomponents.version} org.apache.httpcomponents httpmime - 4.5.3 + ${org.apache.httpcomponents.version} org.noggit @@ -484,12 +484,6 @@ ${common.text.version} - - org.apache.httpcomponents - httpclient - ${org.apache.httpcomponents.version} - - @@ -719,7 +713,7 @@ 1.8 4.1.2 1.8 - 4.3.4 + 4.5.3 4.0.1 From 2fcc24b36e04b6ee52ab148d7ecaaa885ea25576 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 7 Dec 2020 21:52:32 +0100 Subject: [PATCH 064/149] code formatting --- .../eu/dnetlib/dhp/schema/orcid/OrcidDOI.java | 29 ++++++++++--------- 1 file changed, 15 insertions(+), 14 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java index 11bce26c8..cf372c12a 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java @@ -1,24 +1,25 @@ + package eu.dnetlib.dhp.schema.orcid; import java.util.List; public class OrcidDOI { - private String doi; - private List authors; + private String doi; + private List authors; - public String getDoi() { - return doi; - } + public String getDoi() { + return doi; + } - public void setDoi(String doi) { - this.doi = doi; - } + public void setDoi(String doi) { + this.doi = doi; + } - public List getAuthors() { - return authors; - } + public List getAuthors() { + return authors; + } - public void setAuthors(List authors) { - this.authors = authors; - } + public void setAuthors(List authors) { + this.authors = authors; + } } From fba11eef2ab857ab16810c4f522be2d7e9b06127 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 7 Dec 2020 21:53:13 +0100 Subject: [PATCH 065/149] cleanup --- .../broker/oa/PartitionEventsByDsIdJob.java | 31 ++++++++++++------- 1 file changed, 20 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index 65d5e6f94..e9644122f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -18,6 +18,8 @@ import org.apache.hadoop.fs.FileStatus; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.slf4j.Logger; @@ -40,8 +42,9 @@ public class PartitionEventsByDsIdJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(PartitionEventsByDsIdJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); + .toString( + PartitionEventsByDsIdJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -63,21 +66,27 @@ public class PartitionEventsByDsIdJob { final Set validOpendoarIds = new HashSet<>(); if (!opendoarIds.trim().equals("-")) { - validOpendoarIds.addAll(Arrays.stream(opendoarIds.split(",")) - .map(String::trim) - .filter(StringUtils::isNotBlank) - .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) - .collect(Collectors.toSet())); + validOpendoarIds + .addAll( + Arrays + .stream(opendoarIds.split(",")) + .map(String::trim) + .filter(StringUtils::isNotBlank) + .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) + .collect(Collectors.toSet())); } + log.info("validOpendoarIds: {}", validOpendoarIds); runWithSparkSession(conf, isSparkSessionManaged, spark -> { ClusterUtils .readPath(spark, eventsPath, Event.class) - .filter(e -> StringUtils.isNotBlank(e.getMap().getTargetDatasourceId())) - .filter(e -> e.getMap().getTargetDatasourceId().startsWith(OPENDOAR_NSPREFIX)) - .filter(e -> validOpendoarIds.contains(e.getMap().getTargetDatasourceId())) - .map(e -> messageFromNotification(e), Encoders.bean(ShortEventMessageWithGroupId.class)) + .filter((FilterFunction) e -> StringUtils.isNotBlank(e.getMap().getTargetDatasourceId())) + .filter((FilterFunction) e -> e.getMap().getTargetDatasourceId().startsWith(OPENDOAR_NSPREFIX)) + .filter((FilterFunction) e -> validOpendoarIds.contains(e.getMap().getTargetDatasourceId())) + .map( + (MapFunction) e -> messageFromNotification(e), + Encoders.bean(ShortEventMessageWithGroupId.class)) .coalesce(1) .write() .partitionBy("group") From 620e1307a39e54e3ee5d3da50a5675355f36d08e Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 9 Dec 2020 10:30:47 +0100 Subject: [PATCH 066/149] indentation --- .../broker/oa/PartitionEventsByDsIdJob.java | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index 65d5e6f94..efb7a035c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -40,8 +40,9 @@ public class PartitionEventsByDsIdJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(PartitionEventsByDsIdJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); + .toString( + PartitionEventsByDsIdJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -63,11 +64,14 @@ public class PartitionEventsByDsIdJob { final Set validOpendoarIds = new HashSet<>(); if (!opendoarIds.trim().equals("-")) { - validOpendoarIds.addAll(Arrays.stream(opendoarIds.split(",")) - .map(String::trim) - .filter(StringUtils::isNotBlank) - .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) - .collect(Collectors.toSet())); + validOpendoarIds + .addAll( + Arrays + .stream(opendoarIds.split(",")) + .map(String::trim) + .filter(StringUtils::isNotBlank) + .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) + .collect(Collectors.toSet())); } runWithSparkSession(conf, isSparkSessionManaged, spark -> { From 370a5e650b0c9bdfac969f4d952e8491cd805694 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 9 Dec 2020 11:18:26 +0100 Subject: [PATCH 067/149] validation attributes in resultProject relations --- .../raw/AbstractMdRecordToOafMapper.java | 168 ++++++++---------- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 9 +- .../dnetlib/dhp/oa/graph/raw/oaf_record.xml | 2 +- .../dnetlib/dhp/oa/graph/raw/odf_dataset.xml | 2 +- 4 files changed, 88 insertions(+), 93 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 95dd1e1ca..4e60e9fdd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -70,10 +70,8 @@ public abstract class AbstractMdRecordToOafMapper { protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; - protected static final Qualifier ORCID_PID_TYPE = qualifier( - "ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); - protected static final Qualifier MAG_PID_TYPE = qualifier( - "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); protected static final Map nsContext = new HashMap<>(); @@ -87,8 +85,7 @@ public abstract class AbstractMdRecordToOafMapper { nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); } - protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier( - "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible) { this.vocs = vocs; @@ -100,26 +97,20 @@ public abstract class AbstractMdRecordToOafMapper { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); final Document doc = DocumentHelper - .parseText( - xml - .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); + .parseText(xml + .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); - final KeyValue collectedFrom = getProvenanceDatasource( - doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); - if (collectedFrom == null) { - return null; - } + if (collectedFrom == null) { return null; } final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); - if (hostedBy == null) { - return null; - } + if (hostedBy == null) { return null; } final DataInfo info = prepareDataInfo(doc, invisible); final long lastUpdateTimestamp = new Date().getTime(); @@ -161,9 +152,7 @@ public abstract class AbstractMdRecordToOafMapper { final String dsId = doc.valueOf(xpathId); final String dsName = doc.valueOf(xpathName); - if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { - return null; - } + if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; } return keyValue(createOpenaireId(10, dsId, true), dsName); } @@ -179,47 +168,47 @@ public abstract class AbstractMdRecordToOafMapper { final List oafs = new ArrayList<>(); switch (type.toLowerCase()) { - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); - p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); - p.setJournal(prepareJournal(doc, info)); - oafs.add(p); - break; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); - d.setResulttype(DATASET_DEFAULT_RESULTTYPE); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - oafs.add(d); - break; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); - s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - oafs.add(s); - break; - case "": - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); - o.setResulttype(ORP_DEFAULT_RESULTTYPE); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - oafs.add(o); - break; + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); + p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); + p.setJournal(prepareJournal(doc, info)); + oafs.add(p); + break; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); + d.setResulttype(DATASET_DEFAULT_RESULTTYPE); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + oafs.add(d); + break; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); + s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + oafs.add(s); + break; + case "": + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); + o.setResulttype(ORP_DEFAULT_RESULTTYPE); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + oafs.add(o); + break; } if (!oafs.isEmpty()) { @@ -244,25 +233,37 @@ public abstract class AbstractMdRecordToOafMapper { final String originalId = ((Node) o).getText(); + final String validationdDate = ((Node) o).valueOf("@validationDate"); + if (StringUtils.isNotBlank(originalId)) { final String projectId = createOpenaireId(40, originalId, true); res - .add( - getRelation( - docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, - lastUpdateTimestamp)); + .add(getRelationWithValidationDate(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp, validationdDate)); res - .add( - getRelation( - projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, - lastUpdateTimestamp)); + .add(getRelationWithValidationDate(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp, validationdDate)); } } return res; } + protected Relation getRelationWithValidationDate(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp, + final String validationDate) { + + final Relation r = getRelation(source, target, relType, subRelType, relClass, collectedFrom, info, lastUpdateTimestamp); + r.setValidated(StringUtils.isNotBlank(validationDate)); + r.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); + return r; + } + protected Relation getRelation(final String source, final String target, final String relType, @@ -455,9 +456,7 @@ public abstract class AbstractMdRecordToOafMapper { final String sp = n.valueOf("@sp"); final String vol = n.valueOf("@vol"); final String edition = n.valueOf("@edition"); - if (StringUtils.isNotBlank(name)) { - return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); - } + if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } } return null; } @@ -466,9 +465,7 @@ public abstract class AbstractMdRecordToOafMapper { final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); if (n != null) { final String id = n.valueOf("./*[local-name()='identifier']"); - if (StringUtils.isNotBlank(id)) { - return id; - } + if (StringUtils.isNotBlank(id)) { return id; } } return doc.valueOf("//*[local-name()='header']/*[local-name()='identifier']"); @@ -537,10 +534,7 @@ public abstract class AbstractMdRecordToOafMapper { for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; res - .add( - structuredProperty( - n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), - n.valueOf("@schemename"), info)); + .add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info)); } return res; } @@ -548,9 +542,7 @@ public abstract class AbstractMdRecordToOafMapper { protected OAIProvenance prepareOAIprovenance(final Document doc) { final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - if (n == null) { - return null; - } + if (n == null) { return null; } final String identifier = n.valueOf("./*[local-name()='identifier']"); final String baseURL = n.valueOf("./*[local-name()='baseURL']"); @@ -565,9 +557,7 @@ public abstract class AbstractMdRecordToOafMapper { protected DataInfo prepareDataInfo(final Document doc, final boolean invisible) { final Node n = doc.selectSingleNode("//oaf:datainfo"); - if (n == null) { - return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); - } + if (n == null) { return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); @@ -579,9 +569,7 @@ public abstract class AbstractMdRecordToOafMapper { final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); final String trust = n.valueOf("./oaf:trust"); - return dataInfo( - deletedbyinference, inferenceprovenance, inferred, invisible, - qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); + return dataInfo(deletedbyinference, inferenceprovenance, inferred, invisible, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); } protected Field prepareField(final Node node, final String xpath, final DataInfo info) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 46cb1a535..a0348f8ec 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -141,7 +141,10 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(r2.getRelClass())); assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r2.getRelType())); - + assertTrue(r1.getValidated()); + assertTrue(r2.getValidated()); + assertEquals(r1.getValidationDate(), "2020-01-01"); + assertEquals(r2.getValidationDate(), "2020-01-01"); // System.out.println(new ObjectMapper().writeValueAsString(p)); // System.out.println(new ObjectMapper().writeValueAsString(r1)); // System.out.println(new ObjectMapper().writeValueAsString(r2)); @@ -246,6 +249,10 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(r2.getRelClass())); assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r2.getRelType())); + assertTrue(r1.getValidated()); + assertTrue(r2.getValidated()); + assertEquals(r1.getValidationDate(), "2020-01-01"); + assertEquals(r2.getValidationDate(), "2020-01-01"); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml index 2c6c98ebb..f4b0c477f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml @@ -51,7 +51,7 @@ 0001 2017-01-01 - corda_______::226852 + corda_______::226852 OPEN und - corda_______::226852 + corda_______::226852 0001s From 5f21a356fd61432713af2431ff36987d8d0b2e40 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 9 Dec 2020 11:24:30 +0100 Subject: [PATCH 068/149] reindent --- .../raw/AbstractMdRecordToOafMapper.java | 153 +++++++++++------- 1 file changed, 92 insertions(+), 61 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 4e60e9fdd..267c6026d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -70,8 +70,10 @@ public abstract class AbstractMdRecordToOafMapper { protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; - protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); - protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier ORCID_PID_TYPE = qualifier( + "ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier MAG_PID_TYPE = qualifier( + "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); protected static final Map nsContext = new HashMap<>(); @@ -85,7 +87,8 @@ public abstract class AbstractMdRecordToOafMapper { nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); } - protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier( + "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible) { this.vocs = vocs; @@ -97,20 +100,26 @@ public abstract class AbstractMdRecordToOafMapper { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); final Document doc = DocumentHelper - .parseText(xml - .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); + .parseText( + xml + .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); - final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + final KeyValue collectedFrom = getProvenanceDatasource( + doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); - if (collectedFrom == null) { return null; } + if (collectedFrom == null) { + return null; + } final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); - if (hostedBy == null) { return null; } + if (hostedBy == null) { + return null; + } final DataInfo info = prepareDataInfo(doc, invisible); final long lastUpdateTimestamp = new Date().getTime(); @@ -152,7 +161,9 @@ public abstract class AbstractMdRecordToOafMapper { final String dsId = doc.valueOf(xpathId); final String dsName = doc.valueOf(xpathName); - if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; } + if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { + return null; + } return keyValue(createOpenaireId(10, dsId, true), dsName); } @@ -168,47 +179,47 @@ public abstract class AbstractMdRecordToOafMapper { final List oafs = new ArrayList<>(); switch (type.toLowerCase()) { - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); - p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); - p.setJournal(prepareJournal(doc, info)); - oafs.add(p); - break; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); - d.setResulttype(DATASET_DEFAULT_RESULTTYPE); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - oafs.add(d); - break; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); - s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - oafs.add(s); - break; - case "": - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); - o.setResulttype(ORP_DEFAULT_RESULTTYPE); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - oafs.add(o); - break; + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); + p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); + p.setJournal(prepareJournal(doc, info)); + oafs.add(p); + break; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); + d.setResulttype(DATASET_DEFAULT_RESULTTYPE); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + oafs.add(d); + break; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); + s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + oafs.add(s); + break; + case "": + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); + o.setResulttype(ORP_DEFAULT_RESULTTYPE); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + oafs.add(o); + break; } if (!oafs.isEmpty()) { @@ -239,9 +250,15 @@ public abstract class AbstractMdRecordToOafMapper { final String projectId = createOpenaireId(40, originalId, true); res - .add(getRelationWithValidationDate(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp, validationdDate)); + .add( + getRelationWithValidationDate( + docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, + lastUpdateTimestamp, validationdDate)); res - .add(getRelationWithValidationDate(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp, validationdDate)); + .add( + getRelationWithValidationDate( + projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, + lastUpdateTimestamp, validationdDate)); } } @@ -258,7 +275,8 @@ public abstract class AbstractMdRecordToOafMapper { final long lastUpdateTimestamp, final String validationDate) { - final Relation r = getRelation(source, target, relType, subRelType, relClass, collectedFrom, info, lastUpdateTimestamp); + final Relation r = getRelation( + source, target, relType, subRelType, relClass, collectedFrom, info, lastUpdateTimestamp); r.setValidated(StringUtils.isNotBlank(validationDate)); r.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); return r; @@ -456,7 +474,9 @@ public abstract class AbstractMdRecordToOafMapper { final String sp = n.valueOf("@sp"); final String vol = n.valueOf("@vol"); final String edition = n.valueOf("@edition"); - if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } + if (StringUtils.isNotBlank(name)) { + return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); + } } return null; } @@ -465,7 +485,9 @@ public abstract class AbstractMdRecordToOafMapper { final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); if (n != null) { final String id = n.valueOf("./*[local-name()='identifier']"); - if (StringUtils.isNotBlank(id)) { return id; } + if (StringUtils.isNotBlank(id)) { + return id; + } } return doc.valueOf("//*[local-name()='header']/*[local-name()='identifier']"); @@ -534,7 +556,10 @@ public abstract class AbstractMdRecordToOafMapper { for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; res - .add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info)); + .add( + structuredProperty( + n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), + n.valueOf("@schemename"), info)); } return res; } @@ -542,7 +567,9 @@ public abstract class AbstractMdRecordToOafMapper { protected OAIProvenance prepareOAIprovenance(final Document doc) { final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - if (n == null) { return null; } + if (n == null) { + return null; + } final String identifier = n.valueOf("./*[local-name()='identifier']"); final String baseURL = n.valueOf("./*[local-name()='baseURL']"); @@ -557,7 +584,9 @@ public abstract class AbstractMdRecordToOafMapper { protected DataInfo prepareDataInfo(final Document doc, final boolean invisible) { final Node n = doc.selectSingleNode("//oaf:datainfo"); - if (n == null) { return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); } + if (n == null) { + return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); + } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); @@ -569,7 +598,9 @@ public abstract class AbstractMdRecordToOafMapper { final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); final String trust = n.valueOf("./oaf:trust"); - return dataInfo(deletedbyinference, inferenceprovenance, inferred, invisible, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); + return dataInfo( + deletedbyinference, inferenceprovenance, inferred, invisible, + qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); } protected Field prepareField(final Node node, final String xpath, final DataInfo info) { From 1bc9adc10d79455cd910249fcc431ef23b7a214f Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 9 Dec 2020 16:18:37 +0100 Subject: [PATCH 069/149] default trust for validated rels --- .../oa/graph/raw/AbstractMdRecordToOafMapper.java | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 267c6026d..cccf15398 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -75,6 +75,8 @@ public abstract class AbstractMdRecordToOafMapper { protected static final Qualifier MAG_PID_TYPE = qualifier( "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final String DEFAULT_TRUST_FOR_VALIDATED_RELS = "0.999"; + protected static final Map nsContext = new HashMap<>(); static { @@ -279,6 +281,16 @@ public abstract class AbstractMdRecordToOafMapper { source, target, relType, subRelType, relClass, collectedFrom, info, lastUpdateTimestamp); r.setValidated(StringUtils.isNotBlank(validationDate)); r.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); + + if (StringUtils.isNotBlank(validationDate)) { + r.setValidated(true); + r.setValidationDate(validationDate); + r.getDataInfo().setTrust(DEFAULT_TRUST_FOR_VALIDATED_RELS); + } else { + r.setValidated(false); + r.setValidationDate(null); + } + return r; } From 212b52614fefa9a08dc3fc08c8325a0c5a0dc5b5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 9 Dec 2020 16:59:02 +0100 Subject: [PATCH 070/149] added graph mapper versus community result without context and project in common to be used for the doiboost mapping --- .../java/eu/dnetlib/dhp/common/Constants.java | 44 ++ .../dnetlib/dhp/common/GraphResultMapper.java | 415 ++++++++++++++++++ 2 files changed, 459 insertions(+) create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java new file mode 100644 index 000000000..c9d15ff76 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java @@ -0,0 +1,44 @@ + +package eu.dnetlib.dhp.common; + +import com.google.common.collect.Maps; + +import java.util.Map; + +public class Constants { + + public static final Map accessRightsCoarMap = Maps.newHashMap(); + public static final Map coarCodeLabelMap = Maps.newHashMap(); + + public static final String INFERRED = "Inferred by OpenAIRE"; + + public static final String HARVESTED = "Harvested"; + public static final String DEFAULT_TRUST = "0.9"; + public static final String USER_CLAIM = "Linked by user";; + + public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; + + public static String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; + + public static String RESEARCH_COMMUNITY = "Research Community"; + + public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; + + public static String ORCID = "orcid"; + + static { + accessRightsCoarMap.put("OPEN", "c_abf2"); + accessRightsCoarMap.put("RESTRICTED", "c_16ec"); + accessRightsCoarMap.put("OPEN SOURCE", "c_abf2"); + accessRightsCoarMap.put("CLOSED", "c_14cb"); + accessRightsCoarMap.put("EMBARGO", "c_f1cf"); + } + + static { + coarCodeLabelMap.put("c_abf2", "OPEN"); + coarCodeLabelMap.put("c_16ec", "RESTRICTED"); + coarCodeLabelMap.put("c_14cb", "CLOSED"); + coarCodeLabelMap.put("c_f1cf", "EMBARGO"); + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java new file mode 100644 index 000000000..5e37f15db --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java @@ -0,0 +1,415 @@ + +package eu.dnetlib.dhp.common; + +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.*; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +public class GraphResultMapper implements Serializable { + + public static Result map( + E in) { + + CommunityResult out = new CommunityResult(); + + eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; + Optional ort = Optional.ofNullable(input.getResulttype()); + if (ort.isPresent()) { + switch (ort.get().getClassid()) { + case "publication": + Optional journal = Optional + .ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal()); + if (journal.isPresent()) { + Journal j = journal.get(); + Container c = new Container(); + c.setConferencedate(j.getConferencedate()); + c.setConferenceplace(j.getConferenceplace()); + c.setEdition(j.getEdition()); + c.setEp(j.getEp()); + c.setIss(j.getIss()); + c.setIssnLinking(j.getIssnLinking()); + c.setIssnOnline(j.getIssnOnline()); + c.setIssnPrinted(j.getIssnPrinted()); + c.setName(j.getName()); + c.setSp(j.getSp()); + c.setVol(j.getVol()); + out.setContainer(c); + out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); + } + break; + case "dataset": + eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; + Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); + Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); + + out + .setGeolocation( + Optional + .ofNullable(id.getGeolocation()) + .map( + igl -> igl + .stream() + .filter(Objects::nonNull) + .map(gli -> { + GeoLocation gl = new GeoLocation(); + gl.setBox(gli.getBox()); + gl.setPlace(gli.getPlace()); + gl.setPoint(gli.getPoint()); + return gl; + }) + .collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); + break; + case "software": + + eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input; + Optional + .ofNullable(is.getCodeRepositoryUrl()) + .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); + Optional + .ofNullable(is.getDocumentationUrl()) + .ifPresent( + value -> out + .setDocumentationUrl( + value + .stream() + .map(v -> v.getValue()) + .collect(Collectors.toList()))); + + Optional + .ofNullable(is.getProgrammingLanguage()) + .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); + + out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); + break; + case "other": + + eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input; + out + .setContactgroup( + Optional + .ofNullable(ir.getContactgroup()) + .map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList())) + .orElse(null)); + + out + .setContactperson( + Optional + .ofNullable(ir.getContactperson()) + .map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList())) + .orElse(null)); + out + .setTool( + Optional + .ofNullable(ir.getTool()) + .map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); + + break; + } + + Optional + .ofNullable(input.getAuthor()) + .ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList()))); + + // I do not map Access Right UNKNOWN or OTHER + + Optional oar = Optional.ofNullable(input.getBestaccessright()); + if (oar.isPresent()) { + if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); + out + .setBestaccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + } + } + + final List contributorList = new ArrayList<>(); + Optional + .ofNullable(input.getContributor()) + .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); + out.setContributor(contributorList); + + Optional + .ofNullable(input.getCountry()) + .ifPresent( + value -> out + .setCountry( + value + .stream() + .map( + c -> { + if (c.getClassid().equals((ModelConstants.UNKNOWN))) { + return null; + } + Country country = new Country(); + country.setCode(c.getClassid()); + country.setLabel(c.getClassname()); + Optional + .ofNullable(c.getDataInfo()) + .ifPresent( + provenance -> country + .setProvenance( + Provenance + .newInstance( + provenance + .getProvenanceaction() + .getClassname(), + c.getDataInfo().getTrust()))); + return country; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList()))); + + final List coverageList = new ArrayList<>(); + Optional + .ofNullable(input.getCoverage()) + .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); + out.setCoverage(coverageList); + + out.setDateofcollection(input.getDateofcollection()); + + final List descriptionList = new ArrayList<>(); + Optional + .ofNullable(input.getDescription()) + .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); + out.setDescription(descriptionList); + Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); + if (oStr.isPresent()) { + out.setEmbargoenddate(oStr.get().getValue()); + } + + final List formatList = new ArrayList<>(); + Optional + .ofNullable(input.getFormat()) + .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); + out.setFormat(formatList); + out.setId(input.getId()); + out.setOriginalId(input.getOriginalId()); + + Optional> oInst = Optional + .ofNullable(input.getInstance()); + + if (oInst.isPresent()) { + out + .setInstance( + oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList())); + + } + + Optional oL = Optional.ofNullable(input.getLanguage()); + if (oL.isPresent()) { + eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); + out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); + } + Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); + if (oLong.isPresent()) { + out.setLastupdatetimestamp(oLong.get()); + } + Optional> otitle = Optional.ofNullable(input.getTitle()); + if (otitle.isPresent()) { + List iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setMaintitle(iTitle.get(0).getValue()); + } + + iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setSubtitle(iTitle.get(0).getValue()); + } + + } + + List pids = new ArrayList<>(); + Optional + .ofNullable(input.getPid()) + .ifPresent( + value -> value + .stream() + .forEach( + p -> pids + .add( + ControlledField + .newInstance(p.getQualifier().getClassid(), p.getValue())))); + out.setPid(pids); + oStr = Optional.ofNullable(input.getDateofacceptance()); + if (oStr.isPresent()) { + out.setPublicationdate(oStr.get().getValue()); + } + oStr = Optional.ofNullable(input.getPublisher()); + if (oStr.isPresent()) { + out.setPublisher(oStr.get().getValue()); + } + + List sourceList = new ArrayList<>(); + Optional + .ofNullable(input.getSource()) + .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); + // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); + List subjectList = new ArrayList<>(); + Optional + .ofNullable(input.getSubject()) + .ifPresent( + value -> value + .forEach(s -> subjectList.add(getSubject(s)))); + + out.setSubjects(subjectList); + + out.setType(input.getResulttype().getClassid()); + } + + out + .setCollectedfrom( + input + .getCollectedfrom() + .stream() + .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) + .collect(Collectors.toList())); + + + return out; + + } + + + private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { + CommunityInstance instance = new CommunityInstance(); + + setCommonValue(i, instance); + + instance + .setCollectedfrom( + KeyValue + .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); + + instance + .setHostedby( + KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); + + return instance; + + } + + private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { + Optional opAr = Optional + .ofNullable(i.getAccessright()); + if (opAr.isPresent()) { + if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); + instance + .setAccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + } + } + + Optional + .ofNullable(i.getLicense()) + .ifPresent(value -> instance.setLicense(value.getValue())); + Optional + .ofNullable(i.getDateofacceptance()) + .ifPresent(value -> instance.setPublicationdate(value.getValue())); + Optional + .ofNullable(i.getRefereed()) + .ifPresent(value -> instance.setRefereed(value.getClassname())); + Optional + .ofNullable(i.getInstancetype()) + .ifPresent(value -> instance.setType(value.getClassname())); + Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); + + } + + + private static Subject getSubject(StructuredProperty s) { + Subject subject = new Subject(); + subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue())); + Optional di = Optional.ofNullable(s.getDataInfo()); + if (di.isPresent()) { + Provenance p = new Provenance(); + p.setProvenance(di.get().getProvenanceaction().getClassname()); + p.setTrust(di.get().getTrust()); + subject.setProvenance(p); + } + + return subject; + } + + private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { + Author a = new Author(); + a.setFullname(oa.getFullname()); + a.setName(oa.getName()); + a.setSurname(oa.getSurname()); + a.setRank(oa.getRank()); + + Optional> oPids = Optional + .ofNullable(oa.getPid()); + if (oPids.isPresent()) { + Pid pid = getOrcid(oPids.get()); + if (pid != null) { + a.setPid(pid); + } + } + + return a; + } + + private static Pid getOrcid(List p) { + for (StructuredProperty pid : p) { + if (pid.getQualifier().getClassid().equals(Constants.ORCID)) { + Optional di = Optional.ofNullable(pid.getDataInfo()); + if (di.isPresent()) { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()), + Provenance + .newInstance( + di.get().getProvenanceaction().getClassname(), + di.get().getTrust())); + } else { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()) + + ); + } + + } + } + return null; + } + +} From 6fbc67a9595564c5df9976e0751016c4843317c7 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 9 Dec 2020 17:10:20 +0100 Subject: [PATCH 071/149] using ModelConstant.ORCID and removing not used constants --- .../main/java/eu/dnetlib/dhp/common/Constants.java | 14 -------------- .../eu/dnetlib/dhp/common/GraphResultMapper.java | 2 +- 2 files changed, 1 insertion(+), 15 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java index c9d15ff76..6a986e145 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java @@ -10,22 +10,8 @@ public class Constants { public static final Map accessRightsCoarMap = Maps.newHashMap(); public static final Map coarCodeLabelMap = Maps.newHashMap(); - public static final String INFERRED = "Inferred by OpenAIRE"; - - public static final String HARVESTED = "Harvested"; - public static final String DEFAULT_TRUST = "0.9"; - public static final String USER_CLAIM = "Linked by user";; - public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; - public static String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; - - public static String RESEARCH_COMMUNITY = "Research Community"; - - public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; - - public static String ORCID = "orcid"; - static { accessRightsCoarMap.put("OPEN", "c_abf2"); accessRightsCoarMap.put("RESTRICTED", "c_16ec"); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java index 5e37f15db..3956410d5 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java @@ -383,7 +383,7 @@ public class GraphResultMapper implements Serializable { private static Pid getOrcid(List p) { for (StructuredProperty pid : p) { - if (pid.getQualifier().getClassid().equals(Constants.ORCID)) { + if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) { Optional di = Optional.ofNullable(pid.getDataInfo()); if (di.isPresent()) { return Pid From db4e400a0b77e29f3ccc9e48286024263465925b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 9 Dec 2020 18:01:45 +0100 Subject: [PATCH 072/149] introduced Oaf.mergeFrom method to allow merging of dataInfo(s), with prevalence based on datainfo.trust --- .../java/eu/dnetlib/dhp/schema/oaf/Oaf.java | 38 +++++++++++++++++-- .../eu/dnetlib/dhp/schema/oaf/OafEntity.java | 6 +-- .../eu/dnetlib/dhp/schema/oaf/Relation.java | 14 +------ 3 files changed, 36 insertions(+), 22 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index 3496492e8..fef32c0c6 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -2,8 +2,12 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Collection; import java.util.List; import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; +import java.util.stream.Stream; public abstract class Oaf implements Serializable { @@ -40,9 +44,35 @@ public abstract class Oaf implements Serializable { this.lastupdatetimestamp = lastupdatetimestamp; } - public void mergeOAFDataInfo(Oaf e) { - if (e.getDataInfo() != null && compareTrust(this, e) < 0) - dataInfo = e.getDataInfo(); + public void mergeFrom(Oaf o) { + if (Objects.isNull(o)) { + return; + } + setCollectedfrom( + Stream + .concat( + Optional + .ofNullable(getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty()), + Optional + .ofNullable(o.getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty())) + .distinct() // relies on KeyValue.equals + .collect(Collectors.toList())); + + mergeOAFDataInfo(o); + + setLastupdatetimestamp( + Math.max( + Optional.ofNullable(getLastupdatetimestamp()).orElse(0L), + Optional.ofNullable(o.getLastupdatetimestamp()).orElse(0L))); + } + + public void mergeOAFDataInfo(Oaf o) { + if (o.getDataInfo() != null && compareTrust(this, o) < 0) + dataInfo = o.getDataInfo(); } protected String extractTrust(Oaf e) { @@ -62,7 +92,7 @@ public abstract class Oaf implements Serializable { if (o == null || getClass() != o.getClass()) return false; Oaf oaf = (Oaf) o; - return Objects.equals(dataInfo, oaf.dataInfo) + return Objects.equals(getDataInfo(), oaf.getDataInfo()) && Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp); } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java index 2823ee49d..17c3e6bdd 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java @@ -78,14 +78,10 @@ public abstract class OafEntity extends Oaf implements Serializable { } public void mergeFrom(OafEntity e) { - - if (e == null) - return; + super.mergeFrom(e); originalId = mergeLists(originalId, e.getOriginalId()); - collectedfrom = mergeLists(collectedfrom, e.getCollectedfrom()); - pid = mergeLists(pid, e.getPid()); if (e.getDateofcollection() != null && compareTrust(this, e) < 0) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index 17a50d7ac..0de34dbec 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -130,19 +130,7 @@ public class Relation extends Oaf { Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal"); checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal"); - setCollectedfrom( - Stream - .concat( - Optional - .ofNullable(getCollectedfrom()) - .map(Collection::stream) - .orElse(Stream.empty()), - Optional - .ofNullable(r.getCollectedfrom()) - .map(Collection::stream) - .orElse(Stream.empty())) - .distinct() // relies on KeyValue.equals - .collect(Collectors.toList())); + super.mergeFrom(r); } @Override From 426b76ee8eb70265dd3103d7da48d6b774606b61 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 9 Dec 2020 19:46:11 +0100 Subject: [PATCH 073/149] more asserts for TextGrid record --- .../eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 46cb1a535..737a255e8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -355,7 +355,20 @@ public class MappersTest { assertValidId(p.getId()); assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); - System.out.println(p.getTitle().get(0).getValue()); + assertEquals(1, p.getAuthor().size()); + assertEquals("OPEN", p.getBestaccessright().getClassid()); + assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getValue())); + assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getQualifier().getClassid())); + assertEquals("dataset", p.getResulttype().getClassname()); + assertEquals(1, p.getInstance().size()); + assertEquals("OPEN", p.getInstance().get(0).getAccessright().getClassid()); + assertValidId(p.getInstance().get(0).getCollectedfrom().getKey()); + assertValidId(p.getInstance().get(0).getHostedby().getKey()); + assertEquals("http://creativecommons.org/licenses/by/3.0/de/legalcode", p.getInstance().get(0).getLicense().getValue()); + assertEquals(1, p.getInstance().get(0).getUrl().size()); +// System.out.println(p.getInstance().get(0).getUrl().get(0)); +// System.out.println(p.getInstance().get(0).getHostedby().getValue()); + System.out.println(p.getPid().get(0).getValue()); } @Test From 112da6d76a8c53777944d475f5115186b3b0e31c Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 9 Dec 2020 20:00:27 +0100 Subject: [PATCH 074/149] in theory, just auto-formatting after mvn compile --- .../java/eu/dnetlib/dhp/common/Constants.java | 4 +- .../dnetlib/dhp/common/GraphResultMapper.java | 695 +++++++++--------- .../java/eu/dnetlib/dhp/schema/oaf/Oaf.java | 27 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 3 +- 4 files changed, 364 insertions(+), 365 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java index 6a986e145..2b8ef4e30 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java @@ -1,10 +1,10 @@ package eu.dnetlib.dhp.common; -import com.google.common.collect.Maps; - import java.util.Map; +import com.google.common.collect.Maps; + public class Constants { public static final Map accessRightsCoarMap = Maps.newHashMap(); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java index 3956410d5..44599eb83 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java @@ -1,6 +1,10 @@ package eu.dnetlib.dhp.common; +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.*; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; @@ -10,406 +14,399 @@ import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.Journal; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; - public class GraphResultMapper implements Serializable { - public static Result map( - E in) { + public static Result map( + E in) { - CommunityResult out = new CommunityResult(); + CommunityResult out = new CommunityResult(); - eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; - Optional ort = Optional.ofNullable(input.getResulttype()); - if (ort.isPresent()) { - switch (ort.get().getClassid()) { - case "publication": - Optional journal = Optional - .ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal()); - if (journal.isPresent()) { - Journal j = journal.get(); - Container c = new Container(); - c.setConferencedate(j.getConferencedate()); - c.setConferenceplace(j.getConferenceplace()); - c.setEdition(j.getEdition()); - c.setEp(j.getEp()); - c.setIss(j.getIss()); - c.setIssnLinking(j.getIssnLinking()); - c.setIssnOnline(j.getIssnOnline()); - c.setIssnPrinted(j.getIssnPrinted()); - c.setName(j.getName()); - c.setSp(j.getSp()); - c.setVol(j.getVol()); - out.setContainer(c); - out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); - } - break; - case "dataset": - eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; - Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); - Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); + eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; + Optional ort = Optional.ofNullable(input.getResulttype()); + if (ort.isPresent()) { + switch (ort.get().getClassid()) { + case "publication": + Optional journal = Optional + .ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal()); + if (journal.isPresent()) { + Journal j = journal.get(); + Container c = new Container(); + c.setConferencedate(j.getConferencedate()); + c.setConferenceplace(j.getConferenceplace()); + c.setEdition(j.getEdition()); + c.setEp(j.getEp()); + c.setIss(j.getIss()); + c.setIssnLinking(j.getIssnLinking()); + c.setIssnOnline(j.getIssnOnline()); + c.setIssnPrinted(j.getIssnPrinted()); + c.setName(j.getName()); + c.setSp(j.getSp()); + c.setVol(j.getVol()); + out.setContainer(c); + out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); + } + break; + case "dataset": + eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; + Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); + Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); - out - .setGeolocation( - Optional - .ofNullable(id.getGeolocation()) - .map( - igl -> igl - .stream() - .filter(Objects::nonNull) - .map(gli -> { - GeoLocation gl = new GeoLocation(); - gl.setBox(gli.getBox()); - gl.setPlace(gli.getPlace()); - gl.setPoint(gli.getPoint()); - return gl; - }) - .collect(Collectors.toList())) - .orElse(null)); + out + .setGeolocation( + Optional + .ofNullable(id.getGeolocation()) + .map( + igl -> igl + .stream() + .filter(Objects::nonNull) + .map(gli -> { + GeoLocation gl = new GeoLocation(); + gl.setBox(gli.getBox()); + gl.setPlace(gli.getPlace()); + gl.setPoint(gli.getPoint()); + return gl; + }) + .collect(Collectors.toList())) + .orElse(null)); - out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); - break; - case "software": + out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); + break; + case "software": - eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input; - Optional - .ofNullable(is.getCodeRepositoryUrl()) - .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); - Optional - .ofNullable(is.getDocumentationUrl()) - .ifPresent( - value -> out - .setDocumentationUrl( - value - .stream() - .map(v -> v.getValue()) - .collect(Collectors.toList()))); + eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input; + Optional + .ofNullable(is.getCodeRepositoryUrl()) + .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); + Optional + .ofNullable(is.getDocumentationUrl()) + .ifPresent( + value -> out + .setDocumentationUrl( + value + .stream() + .map(v -> v.getValue()) + .collect(Collectors.toList()))); - Optional - .ofNullable(is.getProgrammingLanguage()) - .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); + Optional + .ofNullable(is.getProgrammingLanguage()) + .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); - out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); - break; - case "other": + out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); + break; + case "other": - eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input; - out - .setContactgroup( - Optional - .ofNullable(ir.getContactgroup()) - .map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList())) - .orElse(null)); + eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input; + out + .setContactgroup( + Optional + .ofNullable(ir.getContactgroup()) + .map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList())) + .orElse(null)); - out - .setContactperson( - Optional - .ofNullable(ir.getContactperson()) - .map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList())) - .orElse(null)); - out - .setTool( - Optional - .ofNullable(ir.getTool()) - .map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList())) - .orElse(null)); + out + .setContactperson( + Optional + .ofNullable(ir.getContactperson()) + .map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList())) + .orElse(null)); + out + .setTool( + Optional + .ofNullable(ir.getTool()) + .map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList())) + .orElse(null)); - out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); + out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); - break; - } + break; + } - Optional - .ofNullable(input.getAuthor()) - .ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList()))); + Optional + .ofNullable(input.getAuthor()) + .ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList()))); - // I do not map Access Right UNKNOWN or OTHER + // I do not map Access Right UNKNOWN or OTHER - Optional oar = Optional.ofNullable(input.getBestaccessright()); - if (oar.isPresent()) { - if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); - out - .setBestaccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - } - } + Optional oar = Optional.ofNullable(input.getBestaccessright()); + if (oar.isPresent()) { + if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); + out + .setBestaccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + } + } - final List contributorList = new ArrayList<>(); - Optional - .ofNullable(input.getContributor()) - .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); - out.setContributor(contributorList); + final List contributorList = new ArrayList<>(); + Optional + .ofNullable(input.getContributor()) + .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); + out.setContributor(contributorList); - Optional - .ofNullable(input.getCountry()) - .ifPresent( - value -> out - .setCountry( - value - .stream() - .map( - c -> { - if (c.getClassid().equals((ModelConstants.UNKNOWN))) { - return null; - } - Country country = new Country(); - country.setCode(c.getClassid()); - country.setLabel(c.getClassname()); - Optional - .ofNullable(c.getDataInfo()) - .ifPresent( - provenance -> country - .setProvenance( - Provenance - .newInstance( - provenance - .getProvenanceaction() - .getClassname(), - c.getDataInfo().getTrust()))); - return country; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList()))); + Optional + .ofNullable(input.getCountry()) + .ifPresent( + value -> out + .setCountry( + value + .stream() + .map( + c -> { + if (c.getClassid().equals((ModelConstants.UNKNOWN))) { + return null; + } + Country country = new Country(); + country.setCode(c.getClassid()); + country.setLabel(c.getClassname()); + Optional + .ofNullable(c.getDataInfo()) + .ifPresent( + provenance -> country + .setProvenance( + Provenance + .newInstance( + provenance + .getProvenanceaction() + .getClassname(), + c.getDataInfo().getTrust()))); + return country; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList()))); - final List coverageList = new ArrayList<>(); - Optional - .ofNullable(input.getCoverage()) - .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); - out.setCoverage(coverageList); + final List coverageList = new ArrayList<>(); + Optional + .ofNullable(input.getCoverage()) + .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); + out.setCoverage(coverageList); - out.setDateofcollection(input.getDateofcollection()); + out.setDateofcollection(input.getDateofcollection()); - final List descriptionList = new ArrayList<>(); - Optional - .ofNullable(input.getDescription()) - .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); - out.setDescription(descriptionList); - Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); - if (oStr.isPresent()) { - out.setEmbargoenddate(oStr.get().getValue()); - } + final List descriptionList = new ArrayList<>(); + Optional + .ofNullable(input.getDescription()) + .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); + out.setDescription(descriptionList); + Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); + if (oStr.isPresent()) { + out.setEmbargoenddate(oStr.get().getValue()); + } - final List formatList = new ArrayList<>(); - Optional - .ofNullable(input.getFormat()) - .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); - out.setFormat(formatList); - out.setId(input.getId()); - out.setOriginalId(input.getOriginalId()); + final List formatList = new ArrayList<>(); + Optional + .ofNullable(input.getFormat()) + .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); + out.setFormat(formatList); + out.setId(input.getId()); + out.setOriginalId(input.getOriginalId()); - Optional> oInst = Optional - .ofNullable(input.getInstance()); + Optional> oInst = Optional + .ofNullable(input.getInstance()); - if (oInst.isPresent()) { - out - .setInstance( - oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList())); + if (oInst.isPresent()) { + out + .setInstance( + oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList())); - } + } - Optional oL = Optional.ofNullable(input.getLanguage()); - if (oL.isPresent()) { - eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); - out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); - } - Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); - if (oLong.isPresent()) { - out.setLastupdatetimestamp(oLong.get()); - } - Optional> otitle = Optional.ofNullable(input.getTitle()); - if (otitle.isPresent()) { - List iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) - .collect(Collectors.toList()); - if (iTitle.size() > 0) { - out.setMaintitle(iTitle.get(0).getValue()); - } + Optional oL = Optional.ofNullable(input.getLanguage()); + if (oL.isPresent()) { + eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); + out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); + } + Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); + if (oLong.isPresent()) { + out.setLastupdatetimestamp(oLong.get()); + } + Optional> otitle = Optional.ofNullable(input.getTitle()); + if (otitle.isPresent()) { + List iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setMaintitle(iTitle.get(0).getValue()); + } - iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) - .collect(Collectors.toList()); - if (iTitle.size() > 0) { - out.setSubtitle(iTitle.get(0).getValue()); - } + iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setSubtitle(iTitle.get(0).getValue()); + } - } + } - List pids = new ArrayList<>(); - Optional - .ofNullable(input.getPid()) - .ifPresent( - value -> value - .stream() - .forEach( - p -> pids - .add( - ControlledField - .newInstance(p.getQualifier().getClassid(), p.getValue())))); - out.setPid(pids); - oStr = Optional.ofNullable(input.getDateofacceptance()); - if (oStr.isPresent()) { - out.setPublicationdate(oStr.get().getValue()); - } - oStr = Optional.ofNullable(input.getPublisher()); - if (oStr.isPresent()) { - out.setPublisher(oStr.get().getValue()); - } + List pids = new ArrayList<>(); + Optional + .ofNullable(input.getPid()) + .ifPresent( + value -> value + .stream() + .forEach( + p -> pids + .add( + ControlledField + .newInstance(p.getQualifier().getClassid(), p.getValue())))); + out.setPid(pids); + oStr = Optional.ofNullable(input.getDateofacceptance()); + if (oStr.isPresent()) { + out.setPublicationdate(oStr.get().getValue()); + } + oStr = Optional.ofNullable(input.getPublisher()); + if (oStr.isPresent()) { + out.setPublisher(oStr.get().getValue()); + } - List sourceList = new ArrayList<>(); - Optional - .ofNullable(input.getSource()) - .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); - // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); - List subjectList = new ArrayList<>(); - Optional - .ofNullable(input.getSubject()) - .ifPresent( - value -> value - .forEach(s -> subjectList.add(getSubject(s)))); + List sourceList = new ArrayList<>(); + Optional + .ofNullable(input.getSource()) + .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); + // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); + List subjectList = new ArrayList<>(); + Optional + .ofNullable(input.getSubject()) + .ifPresent( + value -> value + .forEach(s -> subjectList.add(getSubject(s)))); - out.setSubjects(subjectList); + out.setSubjects(subjectList); - out.setType(input.getResulttype().getClassid()); - } + out.setType(input.getResulttype().getClassid()); + } - out - .setCollectedfrom( - input - .getCollectedfrom() - .stream() - .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) - .collect(Collectors.toList())); + out + .setCollectedfrom( + input + .getCollectedfrom() + .stream() + .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) + .collect(Collectors.toList())); + return out; - return out; + } - } + private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { + CommunityInstance instance = new CommunityInstance(); + setCommonValue(i, instance); - private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { - CommunityInstance instance = new CommunityInstance(); + instance + .setCollectedfrom( + KeyValue + .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); - setCommonValue(i, instance); + instance + .setHostedby( + KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); - instance - .setCollectedfrom( - KeyValue - .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); + return instance; - instance - .setHostedby( - KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); + } - return instance; + private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { + Optional opAr = Optional + .ofNullable(i.getAccessright()); + if (opAr.isPresent()) { + if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); + instance + .setAccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + } + } - } + Optional + .ofNullable(i.getLicense()) + .ifPresent(value -> instance.setLicense(value.getValue())); + Optional + .ofNullable(i.getDateofacceptance()) + .ifPresent(value -> instance.setPublicationdate(value.getValue())); + Optional + .ofNullable(i.getRefereed()) + .ifPresent(value -> instance.setRefereed(value.getClassname())); + Optional + .ofNullable(i.getInstancetype()) + .ifPresent(value -> instance.setType(value.getClassname())); + Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); - private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { - Optional opAr = Optional - .ofNullable(i.getAccessright()); - if (opAr.isPresent()) { - if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); - instance - .setAccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - } - } + } - Optional - .ofNullable(i.getLicense()) - .ifPresent(value -> instance.setLicense(value.getValue())); - Optional - .ofNullable(i.getDateofacceptance()) - .ifPresent(value -> instance.setPublicationdate(value.getValue())); - Optional - .ofNullable(i.getRefereed()) - .ifPresent(value -> instance.setRefereed(value.getClassname())); - Optional - .ofNullable(i.getInstancetype()) - .ifPresent(value -> instance.setType(value.getClassname())); - Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); + private static Subject getSubject(StructuredProperty s) { + Subject subject = new Subject(); + subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue())); + Optional di = Optional.ofNullable(s.getDataInfo()); + if (di.isPresent()) { + Provenance p = new Provenance(); + p.setProvenance(di.get().getProvenanceaction().getClassname()); + p.setTrust(di.get().getTrust()); + subject.setProvenance(p); + } - } + return subject; + } + private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { + Author a = new Author(); + a.setFullname(oa.getFullname()); + a.setName(oa.getName()); + a.setSurname(oa.getSurname()); + a.setRank(oa.getRank()); - private static Subject getSubject(StructuredProperty s) { - Subject subject = new Subject(); - subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue())); - Optional di = Optional.ofNullable(s.getDataInfo()); - if (di.isPresent()) { - Provenance p = new Provenance(); - p.setProvenance(di.get().getProvenanceaction().getClassname()); - p.setTrust(di.get().getTrust()); - subject.setProvenance(p); - } + Optional> oPids = Optional + .ofNullable(oa.getPid()); + if (oPids.isPresent()) { + Pid pid = getOrcid(oPids.get()); + if (pid != null) { + a.setPid(pid); + } + } - return subject; - } + return a; + } - private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { - Author a = new Author(); - a.setFullname(oa.getFullname()); - a.setName(oa.getName()); - a.setSurname(oa.getSurname()); - a.setRank(oa.getRank()); + private static Pid getOrcid(List p) { + for (StructuredProperty pid : p) { + if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) { + Optional di = Optional.ofNullable(pid.getDataInfo()); + if (di.isPresent()) { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()), + Provenance + .newInstance( + di.get().getProvenanceaction().getClassname(), + di.get().getTrust())); + } else { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()) - Optional> oPids = Optional - .ofNullable(oa.getPid()); - if (oPids.isPresent()) { - Pid pid = getOrcid(oPids.get()); - if (pid != null) { - a.setPid(pid); - } - } + ); + } - return a; - } - - private static Pid getOrcid(List p) { - for (StructuredProperty pid : p) { - if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) { - Optional di = Optional.ofNullable(pid.getDataInfo()); - if (di.isPresent()) { - return Pid - .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()), - Provenance - .newInstance( - di.get().getProvenanceaction().getClassname(), - di.get().getTrust())); - } else { - return Pid - .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()) - - ); - } - - } - } - return null; - } + } + } + return null; + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index fef32c0c6..f4f5baa7b 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -49,23 +49,24 @@ public abstract class Oaf implements Serializable { return; } setCollectedfrom( - Stream - .concat( - Optional - .ofNullable(getCollectedfrom()) - .map(Collection::stream) - .orElse(Stream.empty()), - Optional - .ofNullable(o.getCollectedfrom()) - .map(Collection::stream) - .orElse(Stream.empty())) - .distinct() // relies on KeyValue.equals - .collect(Collectors.toList())); + Stream + .concat( + Optional + .ofNullable(getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty()), + Optional + .ofNullable(o.getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty())) + .distinct() // relies on KeyValue.equals + .collect(Collectors.toList())); mergeOAFDataInfo(o); setLastupdatetimestamp( - Math.max( + Math + .max( Optional.ofNullable(getLastupdatetimestamp()).orElse(0L), Optional.ofNullable(o.getLastupdatetimestamp()).orElse(0L))); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 3f80127f8..2a62e25b2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -371,7 +371,8 @@ public class MappersTest { assertEquals("OPEN", p.getInstance().get(0).getAccessright().getClassid()); assertValidId(p.getInstance().get(0).getCollectedfrom().getKey()); assertValidId(p.getInstance().get(0).getHostedby().getKey()); - assertEquals("http://creativecommons.org/licenses/by/3.0/de/legalcode", p.getInstance().get(0).getLicense().getValue()); + assertEquals( + "http://creativecommons.org/licenses/by/3.0/de/legalcode", p.getInstance().get(0).getLicense().getValue()); assertEquals(1, p.getInstance().get(0).getUrl().size()); // System.out.println(p.getInstance().get(0).getUrl().get(0)); // System.out.println(p.getInstance().get(0).getHostedby().getValue()); From 94bfed1c848fc003a60c6b6c922700bc1f3bae15 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 10 Dec 2020 11:59:28 +0100 Subject: [PATCH 075/149] gzipped output --- .../dhp/broker/oa/CheckDuplictedIdsJob.java | 9 ++++---- .../broker/oa/PartitionEventsByDsIdJob.java | 23 ++++++++----------- .../dhp/broker/oa/util/ClusterUtils.java | 1 + 3 files changed, 15 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java index 5ca865e8f..951afb6c5 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java @@ -30,9 +30,8 @@ public class CheckDuplictedIdsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - CheckDuplictedIdsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); + .toString(CheckDuplictedIdsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); @@ -59,8 +58,8 @@ public class CheckDuplictedIdsJob { .map(o -> ClusterUtils.incrementAccumulator(o, total), Encoders.tuple(Encoders.STRING(), Encoders.LONG())) .write() .mode(SaveMode.Overwrite) - .json(countPath); - ; + .option("compression", "gzip") + .json(countPath);; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index e9644122f..1e060d824 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -42,9 +42,8 @@ public class PartitionEventsByDsIdJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - PartitionEventsByDsIdJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); + .toString(PartitionEventsByDsIdJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -67,13 +66,12 @@ public class PartitionEventsByDsIdJob { final Set validOpendoarIds = new HashSet<>(); if (!opendoarIds.trim().equals("-")) { validOpendoarIds - .addAll( - Arrays - .stream(opendoarIds.split(",")) - .map(String::trim) - .filter(StringUtils::isNotBlank) - .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) - .collect(Collectors.toSet())); + .addAll(Arrays + .stream(opendoarIds.split(",")) + .map(String::trim) + .filter(StringUtils::isNotBlank) + .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) + .collect(Collectors.toSet())); } log.info("validOpendoarIds: {}", validOpendoarIds); @@ -84,13 +82,12 @@ public class PartitionEventsByDsIdJob { .filter((FilterFunction) e -> StringUtils.isNotBlank(e.getMap().getTargetDatasourceId())) .filter((FilterFunction) e -> e.getMap().getTargetDatasourceId().startsWith(OPENDOAR_NSPREFIX)) .filter((FilterFunction) e -> validOpendoarIds.contains(e.getMap().getTargetDatasourceId())) - .map( - (MapFunction) e -> messageFromNotification(e), - Encoders.bean(ShortEventMessageWithGroupId.class)) + .map((MapFunction) e -> messageFromNotification(e), Encoders.bean(ShortEventMessageWithGroupId.class)) .coalesce(1) .write() .partitionBy("group") .mode(SaveMode.Overwrite) + .option("compression", "gzip") .json(partitionPath); }); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java index d8b8dd807..04985a6ab 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java @@ -67,6 +67,7 @@ public class ClusterUtils { .map(o -> ClusterUtils.incrementAccumulator(o, acc), Encoders.bean(clazz)) .write() .mode(SaveMode.Overwrite) + .option("compression", "gzip") .json(path); } From 2e7df07328cf53083567d990ccba3421cde0a280 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 10 Dec 2020 14:47:22 +0100 Subject: [PATCH 076/149] workingDir and outputDir --- .../dhp/broker/oa/CheckDuplictedIdsJob.java | 6 +-- .../dhp/broker/oa/GenerateEventsJob.java | 19 ++++------ .../dhp/broker/oa/GenerateStatsJob.java | 7 ++-- .../dhp/broker/oa/IndexEventSubsetJob.java | 7 ++-- .../dhp/broker/oa/IndexNotificationsJob.java | 19 ++++------ .../dnetlib/dhp/broker/oa/IndexOnESJob.java | 7 ++-- .../dnetlib/dhp/broker/oa/JoinStep0Job.java | 10 ++--- .../dnetlib/dhp/broker/oa/JoinStep1Job.java | 10 ++--- .../dnetlib/dhp/broker/oa/JoinStep2Job.java | 10 ++--- .../dnetlib/dhp/broker/oa/JoinStep3Job.java | 10 ++--- .../dnetlib/dhp/broker/oa/JoinStep4Job.java | 10 ++--- .../broker/oa/PartitionEventsByDsIdJob.java | 4 +- .../dhp/broker/oa/PrepareGroupsJob.java | 8 ++-- .../broker/oa/PrepareRelatedDatasetsJob.java | 6 +-- .../oa/PrepareRelatedDatasourcesJob.java | 6 +-- .../broker/oa/PrepareRelatedProjectsJob.java | 6 +-- .../oa/PrepareRelatedPublicationsJob.java | 6 +-- .../broker/oa/PrepareRelatedSoftwaresJob.java | 6 +-- .../broker/oa/PrepareSimpleEntititiesJob.java | 6 +-- .../dhp/broker/oa/check_duplicates.json | 9 +++++ .../dnetlib/dhp/broker/oa/common_params.json | 2 +- .../oa/generate_all/oozie_app/workflow.xml | 37 ++++++++++--------- .../dhp/broker/oa/generate_events.json | 8 +++- .../eu/dnetlib/dhp/broker/oa/index_es.json | 4 +- .../dhp/broker/oa/index_event_subset.json | 4 +- .../dhp/broker/oa/index_notifications.json | 4 +- .../notifications_only/oozie_app/workflow.xml | 6 +-- .../dhp/broker/oa/od_partitions_params.json | 4 +- .../opendoarPartition/oozie_app/workflow.xml | 4 +- .../dnetlib/dhp/broker/oa/stats_params.json | 6 +-- 30 files changed, 128 insertions(+), 123 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java index 951afb6c5..416ee5024 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java @@ -31,15 +31,15 @@ public class CheckDuplictedIdsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString(CheckDuplictedIdsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); - final String countPath = parser.get("workingPath") + "/counts"; + final String countPath = parser.get("outputDir") + "/counts"; log.info("countPath: {}", countPath); final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java index cfee360c5..9e128d49e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java @@ -33,9 +33,8 @@ public class GenerateEventsJob { public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - GenerateEventsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_events.json"))); + .toString(GenerateEventsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_events.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -44,10 +43,10 @@ public class GenerateEventsJob { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String eventsPath = workingPath + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final Set dsIdWhitelist = ClusterUtils.parseParamAsList(parser, "datasourceIdWhitelist"); @@ -70,13 +69,11 @@ public class GenerateEventsJob { final LongAccumulator total = spark.sparkContext().longAccumulator("total_events"); final Dataset groups = ClusterUtils - .readPath(spark, workingPath + "/duplicates", ResultGroup.class); + .readPath(spark, workingDir + "/duplicates", ResultGroup.class); final Dataset dataset = groups - .map( - g -> EventFinder - .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), - Encoders + .map(g -> EventFinder + .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), Encoders .bean(EventGroup.class)) .flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java index d5c53ea36..c44aead5e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java @@ -33,9 +33,8 @@ public class GenerateStatsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - GenerateStatsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/stats_params.json"))); + .toString(GenerateStatsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/stats_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -46,7 +45,7 @@ public class GenerateStatsJob { final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String dbUrl = parser.get("dbUrl"); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java index d3cbe0034..929c31600 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java @@ -39,14 +39,13 @@ public class IndexEventSubsetJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - IndexEventSubsetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_event_subset.json"))); + .toString(IndexEventSubsetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_event_subset.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String index = parser.get("index"); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index 792a2354a..e1d2e7d24 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -47,14 +47,13 @@ public class IndexNotificationsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - IndexNotificationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); + .toString(IndexNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String index = parser.get("index"); @@ -117,8 +116,7 @@ public class IndexNotificationsJob { final long date) { final List list = subscriptions .stream() - .filter( - s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) + .filter(s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) .filter(s -> verifyConditions(e.getMap(), s.conditionsAsMap())) .map(s -> generateNotification(s, e, date)) .collect(Collectors.toList()); @@ -149,18 +147,15 @@ public class IndexNotificationsJob { if (conditions.containsKey("trust") && !SubscriptionUtils - .verifyFloatRange( - map.getTrust(), conditions.get("trust").get(0).getValue(), - conditions.get("trust").get(0).getOtherValue())) { + .verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) { return false; } if (conditions.containsKey("targetDateofacceptance") && !conditions .get("targetDateofacceptance") .stream() - .anyMatch( - c -> SubscriptionUtils - .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { + .anyMatch(c -> SubscriptionUtils + .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { return false; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java index 762bfbb90..106528666 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java @@ -29,14 +29,13 @@ public class IndexOnESJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - IndexOnESJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_es.json"))); + .toString(IndexOnESJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_es.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String index = parser.get("index"); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java index 39fa76e43..01778ad74 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java @@ -42,10 +42,10 @@ public class JoinStep0Job { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step0"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step0"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -57,10 +57,10 @@ public class JoinStep0Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/simpleEntities", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/simpleEntities", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedDatasources", RelatedDatasource.class); + .readPath(spark, workingDir + "/relatedDatasources", RelatedDatasource.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedDatasourceAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java index 8e502f736..82c3619e1 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java @@ -40,10 +40,10 @@ public class JoinStep1Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step1"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step1"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -55,10 +55,10 @@ public class JoinStep1Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step0", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step0", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedProjects", RelatedProject.class); + .readPath(spark, workingDir + "/relatedProjects", RelatedProject.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedProjectAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java index 55ab497f0..bd6135d41 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java @@ -39,10 +39,10 @@ public class JoinStep2Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step2"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step2"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -54,10 +54,10 @@ public class JoinStep2Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step1", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step1", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedSoftwares", RelatedSoftware.class); + .readPath(spark, workingDir + "/relatedSoftwares", RelatedSoftware.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedSoftwareAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java index 4d06f6f13..18e8c00b2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java @@ -40,10 +40,10 @@ public class JoinStep3Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step3"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step3"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -55,10 +55,10 @@ public class JoinStep3Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step2", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step2", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedDatasets", RelatedDataset.class); + .readPath(spark, workingDir + "/relatedDatasets", RelatedDataset.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedDatasetAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java index b53d7e39b..965530362 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java @@ -40,10 +40,10 @@ public class JoinStep4Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step4"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step4"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -55,10 +55,10 @@ public class JoinStep4Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step3", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step3", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedPublications", RelatedPublication.class); + .readPath(spark, workingDir + "/relatedPublications", RelatedPublication.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedPublicationAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index 1e060d824..ec694f5d3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -54,10 +54,10 @@ public class PartitionEventsByDsIdJob { final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); - final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId"; + final String partitionPath = parser.get("outputDir") + "/eventsByOpendoarId"; log.info("partitionPath: {}", partitionPath); final String opendoarIds = parser.get("opendoarIds"); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java index eb9add00d..a575328e8 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java @@ -45,10 +45,10 @@ public class PrepareGroupsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String groupsPath = workingPath + "/duplicates"; + final String groupsPath = workingDir + "/duplicates"; log.info("groupsPath: {}", groupsPath); final SparkConf conf = new SparkConf(); @@ -60,7 +60,7 @@ public class PrepareGroupsJob { final LongAccumulator total = spark.sparkContext().longAccumulator("total_groups"); final Dataset results = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step4", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step4", OaBrokerMainEntity.class); final Dataset mergedRels = ClusterUtils .readPath(spark, graphPath + "/relation", Relation.class) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java index 0cfc1adcb..8c2879b38 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java @@ -42,10 +42,10 @@ public class PrepareRelatedDatasetsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedDatasets"; + final String relsPath = workingDir + "/relatedDatasets"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java index 166372a7f..0c2318127 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java @@ -48,10 +48,10 @@ public class PrepareRelatedDatasourcesJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedDatasources"; + final String relsPath = workingDir + "/relatedDatasources"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java index e988366c8..1952b5d9c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java @@ -44,10 +44,10 @@ public class PrepareRelatedProjectsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedProjects"; + final String relsPath = workingDir + "/relatedProjects"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java index 724acc4dc..d6ac27fc5 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java @@ -43,10 +43,10 @@ public class PrepareRelatedPublicationsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedPublications"; + final String relsPath = workingDir + "/relatedPublications"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java index d15565d0d..c4ccf4af6 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java @@ -44,10 +44,10 @@ public class PrepareRelatedSoftwaresJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedSoftwares"; + final String relsPath = workingDir + "/relatedSoftwares"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java index d3c7113ec..cf4450603 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java @@ -44,10 +44,10 @@ public class PrepareSimpleEntititiesJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String simpleEntitiesPath = workingPath + "/simpleEntities"; + final String simpleEntitiesPath = workingDir + "/simpleEntities"; log.info("simpleEntitiesPath: {}", simpleEntitiesPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json new file mode 100644 index 000000000..2584b78fc --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json @@ -0,0 +1,9 @@ +[ + + { + "paramName": "o", + "paramLongName": "outputDir", + "paramDescription": "the path where the data are stored", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json index adee1888a..0d942cd59 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json @@ -7,7 +7,7 @@ }, { "paramName": "o", - "paramLongName": "workingPath", + "paramLongName": "workingDir", "paramDescription": "the path where the temporary data will be stored", "paramRequired": true } diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index 14e33b091..1a1df418b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the path where the graph is stored - workingPath + outputDir the path where the the generated data will be stored @@ -119,7 +119,7 @@ - + @@ -152,7 +152,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -176,7 +176,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -201,7 +201,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -225,7 +225,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -249,7 +249,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -273,7 +273,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -299,7 +299,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -323,7 +323,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -347,7 +347,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -371,7 +371,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -395,7 +395,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -419,7 +419,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -442,7 +442,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --workingDir${workingDir} + --outputDir${outputDir} --datasourceIdWhitelist${datasourceIdWhitelist} --datasourceTypeWhitelist${datasourceTypeWhitelist} --datasourceIdBlacklist${datasourceIdBlacklist} @@ -468,7 +469,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --index${esEventIndexName} --esHost${esIndexHost} --maxEventsForTopic${maxIndexedEventsForDsAndTopic} @@ -495,7 +496,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --index${esNotificationsIndexName} --esHost${esIndexHost} --brokerApiBaseUrl${brokerApiBaseUrl} @@ -521,7 +522,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --dbUrl${brokerDbUrl} --dbUser${brokerDbUser} --dbPassword${brokerDbPassword} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json index bab808193..a482ee2dc 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json @@ -1,7 +1,13 @@ [ + { + "paramName": "wp", + "paramLongName": "workingDir", + "paramDescription": "the path where the temporary data are stored", + "paramRequired": true + }, { "paramName": "o", - "paramLongName": "workingPath", + "paramLongName": "outputDir", "paramDescription": "the path where the generated events will be stored", "paramRequired": true }, diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json index ac1dbf786..079709ad8 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the workinh path", + "paramLongName": "outputDir", + "paramDescription": "the data path", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json index 4921bc03e..441249661 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the workinh path", + "paramLongName": "outputDir", + "paramDescription": "the path where the generated data are stored", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json index 5eea894c8..63e9b1263 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the workinh path", + "paramLongName": "outputDir", + "paramDescription": "the dir that contains the events folder", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml index 879c0d349..c73b3fb52 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml @@ -6,8 +6,8 @@ the path where the graph is stored - workingPath - the path where the the generated data will be stored + outputDir + the path where the the generated data are stored datasourceIdWhitelist @@ -122,7 +122,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --index${esNotificationsIndexName} --esHost${esIndexHost} --brokerApiBaseUrl${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json index 10ba926ab..12cd6a391 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the path where the temporary data will be stored", + "paramLongName": "outputDir", + "paramDescription": "the path where the data will be stored", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index dba3c9f73..83fe47c75 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the opendoar IDs whitelist (comma separated) - workingPath + outputDir the path where the the generated data will be stored @@ -87,7 +87,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --workingDir${workingDir} --opendoarIds${opendoarIds} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json index 15d7d251f..2388b1c1f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json @@ -1,8 +1,8 @@ [ { - "paramName": "wp", - "paramLongName": "workingPath", - "paramDescription": "the working path", + "paramName": "o", + "paramLongName": "outputDir", + "paramDescription": "the path where generated data are stored", "paramRequired": true }, { From 933b4c1ada5611572b38f9acb539382ce132f6cb Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 10 Dec 2020 14:47:51 +0100 Subject: [PATCH 077/149] workingDir and outputDir --- .../dhp/broker/oa/CheckDuplictedIdsJob.java | 8 ++++--- .../dhp/broker/oa/GenerateEventsJob.java | 11 ++++++---- .../dhp/broker/oa/GenerateStatsJob.java | 5 +++-- .../dhp/broker/oa/IndexEventSubsetJob.java | 5 +++-- .../dhp/broker/oa/IndexNotificationsJob.java | 17 +++++++++----- .../dnetlib/dhp/broker/oa/IndexOnESJob.java | 5 +++-- .../broker/oa/PartitionEventsByDsIdJob.java | 22 +++++++++++-------- 7 files changed, 45 insertions(+), 28 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java index 416ee5024..d42c692f7 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java @@ -30,8 +30,9 @@ public class CheckDuplictedIdsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(CheckDuplictedIdsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json"))); + .toString( + CheckDuplictedIdsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); @@ -59,7 +60,8 @@ public class CheckDuplictedIdsJob { .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(countPath);; + .json(countPath); + ; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java index 9e128d49e..457b82517 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java @@ -33,8 +33,9 @@ public class GenerateEventsJob { public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(GenerateEventsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_events.json"))); + .toString( + GenerateEventsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_events.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -72,8 +73,10 @@ public class GenerateEventsJob { .readPath(spark, workingDir + "/duplicates", ResultGroup.class); final Dataset dataset = groups - .map(g -> EventFinder - .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), Encoders + .map( + g -> EventFinder + .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), + Encoders .bean(EventGroup.class)) .flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java index c44aead5e..2772f8fd1 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java @@ -33,8 +33,9 @@ public class GenerateStatsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(GenerateStatsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/stats_params.json"))); + .toString( + GenerateStatsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/stats_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java index 929c31600..72efc9e6b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java @@ -39,8 +39,9 @@ public class IndexEventSubsetJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(IndexEventSubsetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_event_subset.json"))); + .toString( + IndexEventSubsetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_event_subset.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index e1d2e7d24..29fc72d04 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -47,8 +47,9 @@ public class IndexNotificationsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(IndexNotificationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); + .toString( + IndexNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); @@ -116,7 +117,8 @@ public class IndexNotificationsJob { final long date) { final List list = subscriptions .stream() - .filter(s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) + .filter( + s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) .filter(s -> verifyConditions(e.getMap(), s.conditionsAsMap())) .map(s -> generateNotification(s, e, date)) .collect(Collectors.toList()); @@ -147,15 +149,18 @@ public class IndexNotificationsJob { if (conditions.containsKey("trust") && !SubscriptionUtils - .verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) { + .verifyFloatRange( + map.getTrust(), conditions.get("trust").get(0).getValue(), + conditions.get("trust").get(0).getOtherValue())) { return false; } if (conditions.containsKey("targetDateofacceptance") && !conditions .get("targetDateofacceptance") .stream() - .anyMatch(c -> SubscriptionUtils - .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { + .anyMatch( + c -> SubscriptionUtils + .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { return false; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java index 106528666..006cde48c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java @@ -29,8 +29,9 @@ public class IndexOnESJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(IndexOnESJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_es.json"))); + .toString( + IndexOnESJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_es.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index ec694f5d3..08c74a291 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -42,8 +42,9 @@ public class PartitionEventsByDsIdJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(PartitionEventsByDsIdJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); + .toString( + PartitionEventsByDsIdJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -66,12 +67,13 @@ public class PartitionEventsByDsIdJob { final Set validOpendoarIds = new HashSet<>(); if (!opendoarIds.trim().equals("-")) { validOpendoarIds - .addAll(Arrays - .stream(opendoarIds.split(",")) - .map(String::trim) - .filter(StringUtils::isNotBlank) - .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) - .collect(Collectors.toSet())); + .addAll( + Arrays + .stream(opendoarIds.split(",")) + .map(String::trim) + .filter(StringUtils::isNotBlank) + .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) + .collect(Collectors.toSet())); } log.info("validOpendoarIds: {}", validOpendoarIds); @@ -82,7 +84,9 @@ public class PartitionEventsByDsIdJob { .filter((FilterFunction) e -> StringUtils.isNotBlank(e.getMap().getTargetDatasourceId())) .filter((FilterFunction) e -> e.getMap().getTargetDatasourceId().startsWith(OPENDOAR_NSPREFIX)) .filter((FilterFunction) e -> validOpendoarIds.contains(e.getMap().getTargetDatasourceId())) - .map((MapFunction) e -> messageFromNotification(e), Encoders.bean(ShortEventMessageWithGroupId.class)) + .map( + (MapFunction) e -> messageFromNotification(e), + Encoders.bean(ShortEventMessageWithGroupId.class)) .coalesce(1) .write() .partitionBy("group") From 7fe2433137854c0354782bb342fa4f7ad380003b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 11 Dec 2020 12:42:55 +0100 Subject: [PATCH 078/149] excluded transitive older junit dependencies, they can compromise the unit test executions --- dhp-workflows/dhp-graph-provision/pom.xml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index 1547056b9..c8fab5207 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -59,6 +59,10 @@ solr-test-framework test + + junit + junit + com.carrotsearch * @@ -140,6 +144,12 @@ org.apache.zookeeper zookeeper + + + junit + junit + + From ce7a319e01654d5893488d8542e945219a8816e8 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 11 Dec 2020 12:44:17 +0100 Subject: [PATCH 079/149] using the correct assertion import --- .../eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java index 33def91b3..f57b8dcaf 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java @@ -6,15 +6,13 @@ import org.apache.solr.client.solrj.response.UpdateResponse; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; -import junit.framework.Assert; - public class SolrAdminApplicationTest extends SolrTest { @Test public void testPing() throws Exception { SolrPingResponse pingResponse = miniCluster.getSolrClient().ping(); log.info("pingResponse: '{}'", pingResponse.getStatus()); - Assert.assertTrue(pingResponse.getStatus() == 0); + Assertions.assertTrue(pingResponse.getStatus() == 0); } @Test From 61cd129deda31bb47a6db856573dc502d9f8f3cb Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 11 Dec 2020 12:44:53 +0100 Subject: [PATCH 080/149] XML serialisation test --- .../oa/provision/XmlRecordFactoryTest.java | 18 +- .../dnetlib/dhp/oa/provision/publication.json | 827 ++++++++++++++++++ 2 files changed, 836 insertions(+), 9 deletions(-) create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 992ab26e8..0f1912cc3 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -19,9 +19,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; +import eu.dnetlib.dhp.schema.oaf.Publication; -//TODO to enable it we need to update the joined_entity.json test file -@Disabled public class XmlRecordFactoryTest { private static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource"; @@ -29,18 +28,15 @@ public class XmlRecordFactoryTest { @Test public void testXMLRecordFactory() throws IOException, DocumentException { - String json = IOUtils.toString(getClass().getResourceAsStream("joined_entity.json")); - - assertNotNull(json); - JoinedEntity je = new ObjectMapper().readValue(json, JoinedEntity.class); - assertNotNull(je); - ContextMapper contextMapper = new ContextMapper(); XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, otherDsTypeId); - String xml = xmlRecordFactory.build(je); + Publication p = new ObjectMapper() + .readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class); + + String xml = xmlRecordFactory.build(new JoinedEntity<>(p)); assertNotNull(xml); @@ -48,6 +44,10 @@ public class XmlRecordFactoryTest { assertNotNull(doc); + // System.out.println(doc.asXML()); + + Assertions.assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid")); + Assertions.assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending")); // TODO add assertions based of values extracted from the XML record } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json new file mode 100644 index 000000000..b6b183b15 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -0,0 +1,827 @@ +{ + "author": [ + { + "affiliation": [], + "fullname": "Lee, Jaehyun", + "name": "Jaehyun", + "pid": [ + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "orcid", + "classname": "Open Researcher and Contributor ID", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "0000-0001-9613-6639" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "trust": "" + }, + "qualifier": { + "classid": "orcid_pending", + "classname": "Open Researcher and Contributor ID", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "0000-0001-9613-6639" + } + ], + "rank": 1, + "surname": "Lee" + }, + { + "affiliation": [], + "fullname": "Berrada, Salim", + "name": "Salim", + "pid": [], + "rank": 2, + "surname": "Berrada" + }, + { + "affiliation": [], + "fullname": "Adamu-Lema, Fikru", + "name": "Fikru", + "pid": [], + "rank": 3, + "surname": "Adamu-Lema" + }, + { + "affiliation": [], + "fullname": "Nagy, Nicole", + "name": "Nicole", + "pid": [], + "rank": 4, + "surname": "Nagy" + }, + { + "affiliation": [], + "fullname": "Georgiev, Vihar P.", + "name": "Vihar P.", + "pid": [], + "rank": 5, + "surname": "Georgiev" + }, + { + "affiliation": [], + "fullname": "Sadi, Toufik", + "name": "Toufik", + "pid": [], + "rank": 6, + "surname": "Sadi" + }, + { + "affiliation": [], + "fullname": "Liang, Jie", + "name": "Jie", + "pid": [], + "rank": 7, + "surname": "Liang" + }, + { + "affiliation": [], + "fullname": "Ramos, Raphael", + "name": "Raphael", + "pid": [], + "rank": 8, + "surname": "Ramos" + }, + { + "affiliation": [], + "fullname": "Carrillo-Nunez, Hamilton", + "name": "Hamilton", + "pid": [], + "rank": 9, + "surname": "Carrillo-Nunez" + }, + { + "affiliation": [], + "fullname": "Kalita, Dipankar", + "name": "Dipankar", + "pid": [], + "rank": 10, + "surname": "Kalita" + }, + { + "affiliation": [], + "fullname": "Lilienthal, Katharina", + "name": "Katharina", + "pid": [], + "rank": 11, + "surname": "Lilienthal" + }, + { + "affiliation": [], + "fullname": "Wislicenus, Marcus", + "name": "Marcus", + "pid": [], + "rank": 12, + "surname": "Wislicenus" + }, + { + "affiliation": [], + "fullname": "Pandey, Reeturaj", + "name": "Reeturaj", + "pid": [], + "rank": 13, + "surname": "Pandey" + }, + { + "affiliation": [], + "fullname": "Chen, Bingan", + "name": "Bingan", + "pid": [], + "rank": 14, + "surname": "Chen" + }, + { + "affiliation": [], + "fullname": "Teo, Kenneth B.K.", + "name": "Kenneth B. 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.../DownloadReportsListFromDatacite.java | 199 ++-- .../export/ExecuteWorkflow.java | 25 +- .../export/ReadReportsListFromDatacite.java | 408 ++++++++ .../export/UsageStatsExporter.java | 275 ++---- .../dhp-usage-raw-data-update/pom.xml | 64 +- .../dhp-usage-raw-data-update/runworkflow.sh | 1 + .../graph/usagerawdata/export/ConnectDB.java | 2 +- .../usagerawdata/export/ExecuteWorkflow.java | 87 +- .../graph/usagerawdata/export/IrusStats.java | 619 ++++++------- .../export/LaReferenciaDownloadLogs.java | 336 +++---- .../export/LaReferenciaStats.java | 159 +--- .../export/PiwikDownloadLogs.java | 483 +++++----- .../usagerawdata/export/PiwikStatsDB.java | 672 +++++++------- .../graph/usagerawdata/export/SarcStats.java | 875 ++++++++---------- .../export/UsageStatsExporter.java | 96 +- .../export/usagerawdata_parameters.json | 12 - .../graph/usagerawdata/oozie_app/workflow.xml | 2 - dhp-workflows/dhp-usage-stats-build/pom.xml | 30 +- .../dhp-usage-stats-build/runworkflow.sh | 1 + .../usagestatsbuild/export/ConnectDB.java | 175 ++-- .../export/ExecuteWorkflow.java | 237 +++-- .../usagestatsbuild/export/IrusStats.java | 66 +- .../export/LaReferenciaStats.java | 8 +- .../usagestatsbuild/export/PiwikStatsDB.java | 546 +++++++---- .../usagestatsbuild/export/SarcStats.java | 119 +-- .../export/UsageStatsExporter.java | 143 +-- .../export/usagestatsbuild_parameters.json | 359 +++---- .../usagestatsbuild/oozie_app/workflow.xml | 20 +- 33 files changed, 3306 insertions(+), 3022 deletions(-) create mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/nb-configuration.xml create mode 100755 dhp-workflows/dhp-usage-datasets-stats-update/runworkflow.sh create mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DatasetsStatsDB.java create mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ReadReportsListFromDatacite.java create mode 100755 dhp-workflows/dhp-usage-raw-data-update/runworkflow.sh create mode 100755 dhp-workflows/dhp-usage-stats-build/runworkflow.sh diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/nb-configuration.xml b/dhp-workflows/dhp-usage-datasets-stats-update/nb-configuration.xml new file mode 100644 index 000000000..a65c4514a --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/nb-configuration.xml @@ -0,0 +1,18 @@ + + + + + + JDK_1.8 + + diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/pom.xml b/dhp-workflows/dhp-usage-datasets-stats-update/pom.xml index 14b543a57..5593d4d87 100644 --- a/dhp-workflows/dhp-usage-datasets-stats-update/pom.xml +++ b/dhp-workflows/dhp-usage-datasets-stats-update/pom.xml @@ -23,7 +23,35 @@ 4.0.0 dhp-usage-datasets-stats-update - + + + + pl.project13.maven + git-commit-id-plugin + 2.1.15 + + + + revision + + + + + ${project.basedir}/../.git + + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.6.1 + + 1.8 + 1.8 + + + + UTF-8 UTF-8 @@ -68,6 +96,11 @@ dhp-common ${project.version} + + com.mchange + c3p0 + 0.9.5.2 + c3p0 c3p0 diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/runworkflow.sh b/dhp-workflows/dhp-usage-datasets-stats-update/runworkflow.sh new file mode 100755 index 000000000..9b4325508 --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/runworkflow.sh @@ -0,0 +1 @@ +mvn clean package -Poozie-package,deploy,run -Dworkflow.source.dir=eu/dnetlib/dhp/oa/graph/datasetsusagestats \ No newline at end of file diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java index e6da7eff3..25b30e8ad 100644 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java @@ -32,8 +32,8 @@ public abstract class ConnectDB { private static String datasetUsageStatsDBSchema; private static String statsDBSchema; private final static Logger logger = Logger.getLogger(ConnectDB.class); - private Statement stmt = null; - + private Statement stmt = null; + static void init() throws ClassNotFoundException { dbHiveUrl = ExecuteWorkflow.dbHiveUrl; @@ -79,6 +79,7 @@ public abstract class ConnectDB { */ ComboPooledDataSource cpds = new ComboPooledDataSource(); cpds.setJdbcUrl(dbHiveUrl); + cpds.setUser("dimitris.pierrakos"); cpds.setAcquireIncrement(1); cpds.setMaxPoolSize(100); cpds.setMinPoolSize(1); @@ -93,10 +94,10 @@ public abstract class ConnectDB { cpds.setCheckoutTimeout(0); cpds.setPreferredTestQuery("SELECT 1"); cpds.setIdleConnectionTestPeriod(60); - - logger.info("Opened database successfully"); - return cpds.getConnection(); + logger.info("Opened database successfully"); + + return cpds.getConnection(); } @@ -107,6 +108,7 @@ public abstract class ConnectDB { */ ComboPooledDataSource cpds = new ComboPooledDataSource(); cpds.setJdbcUrl(dbImpalaUrl); + cpds.setUser("dimitris.pierrakos"); cpds.setAcquireIncrement(1); cpds.setMaxPoolSize(100); cpds.setMinPoolSize(1); @@ -122,81 +124,8 @@ public abstract class ConnectDB { cpds.setPreferredTestQuery("SELECT 1"); cpds.setIdleConnectionTestPeriod(60); - logger.info("Opened database successfully"); + logger.info("Opened database successfully"); return cpds.getConnection(); } - - private void createDatabase() throws Exception { - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - logger.info("Dropping logs DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); - String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema() + " CASCADE"; - stmt.executeUpdate(dropDatabase); - } catch (Exception e) { - logger.error("Failed to drop database: " + e); - throw new Exception("Failed to drop database: " + e.toString(), e); - } - - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - logger.info("Creating usagestats DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); - String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema(); - stmt.executeUpdate(createDatabase); - - } catch (Exception e) { - logger.error("Failed to create database: " + e); - throw new Exception("Failed to create database: " + e.toString(), e); - } - } - - private void createTables() throws Exception { - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - // Create Piwiklog table - This table should exist - String sqlCreateTablePiwikLog = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getDataSetUsageStatsDBSchema() - + ".piwiklog(source INT, id_visit STRING, country STRING, action STRING, url STRING, " - + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " - + "clustered by (source, id_visit, action, timestamp, entity_id) " - + "into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTablePiwikLog); - - ///////////////////////////////////////// - // Rule for duplicate inserts @ piwiklog - ///////////////////////////////////////// - - String sqlCreateTablePortalLog = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getDataSetUsageStatsDBSchema() - + ".process_portal_log(source INT, id_visit STRING, country STRING, action STRING, url STRING, " - + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " - + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTablePortalLog); - - ////////////////////////////////////////////////// - // Rule for duplicate inserts @ process_portal_log - ////////////////////////////////////////////////// - - stmt.close(); - ConnectDB.getHiveConnection().close(); - - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - } - } } -/* -CREATE TABLE IF NOT EXISTS dataciteReports (reportid STRING, - name STRING, - source STRING, - release STRING, - createdby STRING, - report_end_date STRING, - report_start_date STRING) - CLUSTERED BY (reportid) - into 100 buckets stored as orc tblproperties('transactional'='true'); -*/ \ No newline at end of file diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DatasetsStatsDB.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DatasetsStatsDB.java new file mode 100644 index 000000000..88db1f819 --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DatasetsStatsDB.java @@ -0,0 +1,168 @@ + +package eu.dnetlib.oa.graph.datasetsusagestats.export; + +import java.sql.Connection; +import java.sql.SQLException; +import java.sql.Statement; +import java.util.*; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author D. Pierrakos, S. Zoupanos + */ +public class DatasetsStatsDB { + + private String logPath; + private String logRepoPath; + private String logPortalPath; + + private Statement stmt = null; + + private static final Logger logger = LoggerFactory.getLogger(DatasetsStatsDB.class); + + private String CounterRobotsURL; + private ArrayList robotsList; + + public DatasetsStatsDB(String logRepoPath, String logPortalPath) throws Exception { + this.logRepoPath = logRepoPath; + this.logPortalPath = logPortalPath; + + } + + public void recreateDBAndTables() throws Exception { + this.createDatabase(); + this.createTables(); + } + +// public void reCreateLogDirs() throws IllegalArgumentException, IOException { +// FileSystem dfs = FileSystem.get(new Configuration()); +// +// logger.info("Deleting repoLog directory: " + ExecuteWorkflow.repoLogPath); +// dfs.delete(new Path(ExecuteWorkflow.repoLogPath), true); +// +// logger.info("Deleting portalLog directory: " + ExecuteWorkflow.portalLogPath); +// dfs.delete(new Path(ExecuteWorkflow.portalLogPath), true); +// +// logger.info("Creating repoLog directory: " + ExecuteWorkflow.repoLogPath); +// dfs.mkdirs(new Path(ExecuteWorkflow.repoLogPath)); +// +// logger.info("Creating portalLog directory: " + ExecuteWorkflow.portalLogPath); +// dfs.mkdirs(new Path(ExecuteWorkflow.portalLogPath)); +// } + public ArrayList getRobotsList() { + return robotsList; + } + + public void setRobotsList(ArrayList robotsList) { + this.robotsList = robotsList; + } + + public String getCounterRobotsURL() { + return CounterRobotsURL; + } + + public void setCounterRobotsURL(String CounterRobotsURL) { + this.CounterRobotsURL = CounterRobotsURL; + } + + private void createDatabase() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Dropping datasets DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); + String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema() + " CASCADE"; + stmt.executeUpdate(dropDatabase); + } catch (Exception e) { + logger.error("Failed to drop database: " + e); + throw new Exception("Failed to drop database: " + e.toString(), e); + } + + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating usagestats DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); + String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema(); + stmt.executeUpdate(createDatabase); + + } catch (Exception e) { + logger.error("Failed to create database: " + e); + throw new Exception("Failed to create database: " + e.toString(), e); + } + } + + private void createTables() throws Exception { + try { + stmt = ConnectDB.getHiveConnection().createStatement(); + + // Create Reports table - This table should exist + logger.info("Creating Reports Table"); + String sqlCreateTableDataciteReports = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getDataSetUsageStatsDBSchema() + + ".datacitereports(reportid STRING, \n" + + " name STRING, \n" + + " source STRING,\n" + + " release STRING,\n" + + " createdby STRING,\n" + + " report_start_date STRING,\n" + + " report_end_date STRING)\n" + + " CLUSTERED BY (reportid)\n" + + " into 100 buckets stored as orc tblproperties('transactional'='true')"; + + stmt.executeUpdate(sqlCreateTableDataciteReports); + logger.info("Reports Table Created"); + + // Create Datasets Table + logger.info("Creating DataSets Table"); + String sqlCreateTableDataSets = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getDataSetUsageStatsDBSchema() + + ".datasets(ds_type STRING,\n" + + " ds_title STRING,\n" + + " yop STRING,\n" + + " uri STRING,\n" + + " platform STRING,\n" + + " data_type STRING,\n" + + " publisher STRING,\n" + + " publisher_id_type STRING,\n" + + " publisher_id_value STRING,\n" + + " ds_dates_type STRING,\n" + + " ds_pub_date STRING,\n" + + " ds_contributors STRING,\n" + // + " ds_contributor_value array ,\n" + + " reportid STRING)\n" + + " CLUSTERED BY (ds_type)\n" + + " into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableDataSets); + logger.info("DataSets Table Created"); + + // Create Datasets Performance Table + logger.info("Creating DataSetsPerformance Table"); + String sqlCreateTableDataSetsPerformance = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getDataSetUsageStatsDBSchema() + + ".datasetsperformance(ds_type STRING,\n" + + " period_end STRING,\n" + + " period_from STRING,\n" + + " access_method STRING,\n" + + " metric_type STRING,\n" + + " count INT,\n" + + " country_counts STRING,\n" + + " reportid STRING)\n" + + " CLUSTERED BY (ds_type)\n" + + " into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableDataSetsPerformance); + logger.info("DataSetsPerformance Table Created"); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } + + private Connection getConnection() throws SQLException { + return ConnectDB.getHiveConnection(); + } +} diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java index 196238ea2..a73b299ec 100644 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java @@ -1,97 +1,102 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ -package eu.dnetlib.oa.graph.datasetsusagestats.export; - -import com.google.gson.Gson; -import com.google.gson.JsonArray; -import com.google.gson.JsonElement; -import java.io.BufferedInputStream; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; -import java.net.MalformedURLException; -import java.net.URL; -import com.google.gson.JsonObject; -import java.util.ArrayList; -import java.util.Iterator; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.json.simple.parser.ParseException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * - * @author dpie - */ -public class DownloadReportsListFromDatacite { - - private String dataciteBaseURL; - private String dataciteReportPath; - private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); - - public DownloadReportsListFromDatacite(String dataciteBaseURL, String dataciteReportPath) throws MalformedURLException, Exception { - - this.dataciteBaseURL = dataciteBaseURL; - this.dataciteReportPath = dataciteReportPath; - } - - public void downloadReportsList() throws ParseException { - StringBuilder responseStrBuilder = new StringBuilder(); - - Gson gson = new Gson(); - - try { - BufferedInputStream in = new BufferedInputStream(new URL(dataciteBaseURL).openStream()); - logger.info("Downloading from " + dataciteBaseURL); - - BufferedReader streamReader = new BufferedReader(new InputStreamReader(in, "UTF-8")); - String inputStr; - - while ((inputStr = streamReader.readLine()) != null) { - responseStrBuilder.append(inputStr); - } - } catch (IOException e) { - logger.info(e.getMessage()); - } - JsonObject jsonObject = gson.fromJson(responseStrBuilder.toString(), JsonObject.class); - JsonArray dataArray = jsonObject.getAsJsonArray("reports"); - ArrayList reportsList = new ArrayList(); - for (JsonElement element : dataArray) { - reportsList.add(element.getAsJsonObject().get("id").getAsString()); - } - - Iterator it = reportsList.iterator(); - while (it.hasNext()) { - String reportId = it.next().toString(); - String url = dataciteBaseURL + reportId; - - try { - BufferedInputStream in = new BufferedInputStream(new URL(url).openStream()); - BufferedReader streamReader = new BufferedReader(new InputStreamReader(in, "UTF-8")); - String inputStr; - StringBuilder responseStrBuilder2 = new StringBuilder(); - while ((inputStr = streamReader.readLine()) != null) { - responseStrBuilder2.append(inputStr); - } - FileSystem fs = FileSystem.get(new Configuration()); - FSDataOutputStream fin = fs.create(new Path(dataciteReportPath + "/" + reportId + ".json"), - true); - byte[] jsonObjectRawBytes = responseStrBuilder2.toString().getBytes(); - fin.write(jsonObjectRawBytes); - fin.writeChar('\n'); - - fin.close(); - - fin.close(); - } catch (IOException e) { - System.out.println(e); - } - } - } -} +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.datasetsusagestats.export; + +import java.io.BufferedInputStream; +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.Iterator; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.json.simple.parser.ParseException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.gson.Gson; +import com.google.gson.JsonArray; +import com.google.gson.JsonElement; +import com.google.gson.JsonObject; + +/** + * @author dpie + */ +public class DownloadReportsListFromDatacite { + + private String dataciteBaseURL; + private String dataciteReportPath; + private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); + + public DownloadReportsListFromDatacite(String dataciteBaseURL, String dataciteReportPath) + throws MalformedURLException, Exception { + + this.dataciteBaseURL = dataciteBaseURL; + this.dataciteReportPath = dataciteReportPath; + } + + public void downloadReportsList() throws ParseException { + StringBuilder responseStrBuilder = new StringBuilder(); + + Gson gson = new Gson(); + + try { + BufferedInputStream in = new BufferedInputStream(new URL(dataciteBaseURL).openStream()); + logger.info("Downloading from " + dataciteBaseURL); + + BufferedReader streamReader = new BufferedReader(new InputStreamReader(in, "UTF-8")); + String inputStr; + + while ((inputStr = streamReader.readLine()) != null) { + responseStrBuilder.append(inputStr); + } + } catch (IOException e) { + logger.info(e.getMessage()); + } + JsonObject jsonObject = gson.fromJson(responseStrBuilder.toString(), JsonObject.class); + JsonArray dataArray = jsonObject.getAsJsonArray("reports"); + ArrayList reportsList = new ArrayList(); + for (JsonElement element : dataArray) { + reportsList.add(element.getAsJsonObject().get("id").getAsString()); + } + + Iterator it = reportsList.iterator(); + while (it.hasNext()) { + String reportId = it.next().toString(); + String url = dataciteBaseURL + reportId; + + try { + BufferedInputStream in = new BufferedInputStream(new URL(url).openStream()); + BufferedReader streamReader = new BufferedReader(new InputStreamReader(in, "UTF-8")); + String inputStr; + StringBuilder responseStrBuilder2 = new StringBuilder(); + while ((inputStr = streamReader.readLine()) != null) { + responseStrBuilder2.append(inputStr); + } + FileSystem fs = FileSystem.get(new Configuration()); + FSDataOutputStream fin = fs + .create( + new Path(dataciteReportPath + "/" + reportId + ".json"), + true); + byte[] jsonObjectRawBytes = responseStrBuilder2.toString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); + + fin.close(); + + fin.close(); + } catch (IOException e) { + System.out.println(e); + } + } + } +} diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java index 7b3db3115..b28578e4b 100644 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java @@ -18,14 +18,13 @@ public class ExecuteWorkflow { static String dataciteBaseURL; static String dataciteReportPath; - static String dbHiveUrl; - static String dbImpalaUrl; - static String datasetUsageStatsDBSchema; - static String statsDBSchema; - static boolean recreateDbAndTables; - static boolean datasetsEmptyDirs; - static boolean finalTablesVisibleToImpala; - + static String dbHiveUrl; + static String dbImpalaUrl; + static String datasetUsageStatsDBSchema; + static String statsDBSchema; + static boolean recreateDbAndTables; + static boolean datasetsEmptyDirs; + static boolean finalTablesVisibleToImpala; public static void main(String args[]) throws Exception { @@ -58,11 +57,11 @@ public class ExecuteWorkflow { else datasetsEmptyDirs = false; - if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) - finalTablesVisibleToImpala = true; - else - finalTablesVisibleToImpala = false; - +// if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) +// finalTablesVisibleToImpala = true; +// else +// finalTablesVisibleToImpala = false; +// UsageStatsExporter usagestatsExport = new UsageStatsExporter(); usagestatsExport.export(); } diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ReadReportsListFromDatacite.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ReadReportsListFromDatacite.java new file mode 100644 index 000000000..ccb3eebd3 --- /dev/null +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ReadReportsListFromDatacite.java @@ -0,0 +1,408 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ + +package eu.dnetlib.oa.graph.datasetsusagestats.export; + +import java.io.*; +import java.io.ByteArrayInputStream; +import java.io.File; +import java.io.IOException; +import java.io.InputStreamReader; +import java.net.MalformedURLException; +import java.sql.Array; +import java.sql.PreparedStatement; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.sql.Statement; +import java.util.ArrayList; +import java.util.Base64; +import java.util.Iterator; +import java.util.Set; +import java.util.zip.GZIPInputStream; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocatedFileStatus; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.RemoteIterator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.gson.Gson; +import com.google.gson.JsonArray; +import com.google.gson.JsonElement; +import com.google.gson.JsonObject; + +/** + * @author dpie + */ +public class ReadReportsListFromDatacite { + + private String dataciteReportPath; + private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); + + public ReadReportsListFromDatacite(String dataciteReportPath) throws MalformedURLException, Exception { + + this.dataciteReportPath = dataciteReportPath; + } + + public void readReports() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + File folder = new File(dataciteReportPath); + ArrayList jsonFiles = listHdfsDir(dataciteReportPath); + for (String jsonFile : jsonFiles) { + logger.info("Reading report file " + jsonFile); + this.createTmpReportsTable(jsonFile); + + String sqlSelectReportID = "SELECT get_json_object(json, '$.report.id') FROM " + + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; + stmt.execute(sqlSelectReportID); + ResultSet rstmpReportID = stmt.getResultSet(); + + String reportID = null; + while (rstmpReportID.next()) { + reportID = rstmpReportID.getString(1); + } + + logger.info("Checking report with id " + reportID); + String sqlCheckIfReportExists = "SELECT source FROM " + ConnectDB.getDataSetUsageStatsDBSchema() + + ".datacitereports where reportid=?"; + PreparedStatement stGetReportID = ConnectDB.getHiveConnection().prepareStatement(sqlCheckIfReportExists); + stGetReportID.setString(1, reportID); + + ResultSet rsCheckIfReportExist = stGetReportID.executeQuery(); + + if (rsCheckIfReportExist.next()) { + logger.info("Report found with ID " + reportID); + dropTmpReportsTable(); + } else { + String sqlInsertReport = "INSERT INTO " + ConnectDB.getDataSetUsageStatsDBSchema() + + " .datacitereports " + + "SELECT\n" + + " get_json_object(json, '$.report.id') AS reportid,\n" + + " get_json_object(json, '$.report.report-header.report-name') AS name,\n" + + " get_json_object(json, '$.report.report-header.report-id') AS source,\n" + + " get_json_object(json, '$.report.report-header.release') AS release,\n" + + " get_json_object(json, '$.report.report-header.created-by\') AS createdby,\n" + + " get_json_object(json, '$.report.report-header.reporting-period.begin-date') AS fromdate,\n" + + " get_json_object(json, '$.report.report-header.reporting-period.end-date') AS todate \n" + + "FROM " + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; + stmt.execute(sqlInsertReport); + + logger.info("Report added"); + + logger.info("Adding datasets"); + String sqlSelecteDatasetsArray = "SELECT get_json_object(json, '$.report.report-datasets') FROM " + + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; + stmt.execute(sqlSelecteDatasetsArray); + ResultSet rstmpReportDatasets = stmt.getResultSet(); + + if (rstmpReportDatasets.next() && rstmpReportDatasets.getString(1).indexOf(',') > 0) { + String[] listDatasets = rstmpReportDatasets.getString(1).split(","); + logger.info("Datasets found " + listDatasets.length); + + for (int i = 0; i < listDatasets.length; i++) { + + String sqlInsertDataSets = "INSERT INTO " + ConnectDB.getDataSetUsageStatsDBSchema() + + " .datasets " + + "SELECT\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].dataset-id[0].value') AS ds_type,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].dataset-title') AS ds_title,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + "].yop') AS yop,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + "].uri') AS uri,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + "].platform') AS platform,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + "].data-type') AS data_type,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + "].publisher') AS publisher,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].publisher-id.type[0]') AS publisher_id_type,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].publisher-id.value[0]') AS publisher_id_value,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].dataset-dates.type[0]') AS ds_dates_type,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].dataset-dates.value[0]') AS ds_dates_value,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].dataset-contributors') AS ds_contributors,\n" + + " get_json_object(json, '$.report.id') AS reportid \n" + + "FROM " + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; + stmt.execute(sqlInsertDataSets); + + logger.info("Dataset added " + i); + + logger.info("Adding Dataset Performance"); + String sqlSelecteDatasetsPerformance = "SELECT get_json_object(json, '$.report.report-datasets[" + + i + "].performance') FROM " + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; + stmt.execute(sqlSelecteDatasetsPerformance); + ResultSet rstmpReportDatasetsPerformance = stmt.getResultSet(); + if (rstmpReportDatasetsPerformance.next() + && rstmpReportDatasetsPerformance.getString(1).indexOf(',') > 0) { + String[] listDatasetsPerformance = rstmpReportDatasetsPerformance.getString(1).split(","); + logger.info("Datasets Performance found " + listDatasetsPerformance.length); + for (int j = 0; j < listDatasetsPerformance.length; j++) { + String sqlSelecteDatasetsPerformanceInstance = "SELECT get_json_object(json, '$.report.report-datasets[" + + i + "].performance') FROM " + ConnectDB.getDataSetUsageStatsDBSchema() + + ".tmpjson"; + stmt.execute(sqlSelecteDatasetsPerformanceInstance); + ResultSet rstmpReportDatasetsPerformanceInstance = stmt.getResultSet(); + if (rstmpReportDatasetsPerformanceInstance.next() + && rstmpReportDatasetsPerformanceInstance.getString(1).indexOf(',') > 0) { + String[] listDatasetsPerformanceInstance = rstmpReportDatasetsPerformanceInstance + .getString(1) + .split(","); + logger.info("Datasets Performance found " + listDatasetsPerformanceInstance.length); + for (int k = 0; k < listDatasetsPerformanceInstance.length; k++) { + String sqlInsertDataSetsPerformance = "INSERT INTO " + + ConnectDB.getDataSetUsageStatsDBSchema() + " .datasetsperformance " + + "SELECT\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].dataset-id[0].value') AS ds_type,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].performance[" + j + "].period.end-date') AS period_end,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].performance[" + j + "].period.begin-date') AS period_from,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].performance[" + j + "].instance[" + k + + "].access-method') AS access_method,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].performance[" + j + "].instance[" + k + + "].metric-type') AS metric_type,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].performance[" + j + "].instance[" + k + "].count') AS count,\n" + + " get_json_object(json, '$.report.report-datasets[" + i + + "].performance[" + j + "].instance[" + k + + "].country-counts') AS country_counts,\n" + + " get_json_object(json, '$.report.id') AS reportid \n" + + "FROM " + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; + stmt.execute(sqlInsertDataSetsPerformance); + } + } + } + } + logger.info("DatasetPerformance added for dataset" + i); + } + } + logger.info("Adding gzip performance"); + String sqlSelecteReportSubsets = "SELECT get_json_object(json, '$.report.report-subsets.gzip[0]') FROM " + + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; + stmt.execute(sqlSelecteReportSubsets); + ResultSet rstmpReportSubsets = stmt.getResultSet(); + if (rstmpReportSubsets.next()) { + String unCompressedReport = uncompressString(rstmpReportSubsets.getString(1)); + this.readCompressedReport(unCompressedReport, reportID); + } + } + } + this.dropTmpReportsTable(); + } + + public void readCompressedReport(String report, String reportId) throws Exception { + Gson gson = new Gson(); + JsonObject jsonObject = gson.fromJson(report, JsonObject.class); + + JsonArray jsonReportDatasets; + if (jsonObject.getAsJsonArray("report_datasets") != null) { + jsonReportDatasets = jsonObject.getAsJsonArray("report_datasets"); + } else { + jsonReportDatasets = jsonObject.getAsJsonArray("report-datasets"); + } + + for (JsonElement datasetElement : jsonReportDatasets) { + // JsonElement dataset_title = datasetElement.getAsJsonObject().get("dataset-title"); + String dataset_title = datasetElement.getAsJsonObject().get("dataset-title").getAsString(); + String yop = datasetElement.getAsJsonObject().get("yop").getAsString(); + String uri = datasetElement.getAsJsonObject().get("uri").getAsString(); + String platform = datasetElement.getAsJsonObject().get("platform").getAsString(); + String data_type = datasetElement.getAsJsonObject().get("data-type").getAsString(); + String publisher = datasetElement.getAsJsonObject().get("publisher").getAsString(); + + JsonArray publisher_id = datasetElement.getAsJsonObject().getAsJsonArray("publisher-id"); + String publisher_id_type = ""; + String publisher_id_value = ""; + for (JsonElement publisher_id_Element : publisher_id) { + publisher_id_type = publisher_id_Element.getAsJsonObject().get("type").getAsString(); + publisher_id_value = publisher_id_Element.getAsJsonObject().get("value").getAsString(); + } + JsonArray dataset_days = datasetElement.getAsJsonObject().getAsJsonArray("dataset-dates"); + String ds_dates_type = ""; + String ds_dates_value = ""; + for (JsonElement datasetDaysElement : dataset_days) { + ds_dates_type = datasetDaysElement.getAsJsonObject().get("type").getAsString(); + ds_dates_value = datasetDaysElement.getAsJsonObject().get("value").getAsString(); + } + + JsonArray datasetContributors = null; + String ds_contributor_type = ""; + String[] ds_contributor_values = null; + Array ds_contributor_valuesArr = null; + + if (datasetElement.getAsJsonObject().getAsJsonArray("dataset-contributors") != null) { + datasetContributors = datasetElement.getAsJsonObject().getAsJsonArray("dataset-contributors"); + + JsonArray datasetid = datasetElement.getAsJsonObject().getAsJsonArray("dataset-id"); + String doi = ""; + for (JsonElement datasetIDElement : datasetid) +//System.out.println(datasetIDElement.getAsJsonObject().get("value").getAsString()); + { + doi = datasetIDElement.getAsJsonObject().get("value").getAsString(); + } + + String sqlInsertDataset = "INSERT INTO " + ConnectDB.getDataSetUsageStatsDBSchema() + + " .datasets(ds_type," + + "ds_title,yop,uri,platform,data_type,publisher,publisher_id_type,publisher_id_value," + + "ds_dates_type, ds_dates_value, ds_contributors,reportid) VALUES(?,?,?,?,?,?,?,?,?,?,?,?,?) "; + + PreparedStatement pstmtDataset = ConnectDB.DB_HIVE_CONNECTION.prepareStatement(sqlInsertDataset); + + pstmtDataset.setString(1, doi); + pstmtDataset.setString(2, dataset_title); + pstmtDataset.setString(3, yop); + pstmtDataset.setString(4, uri); + pstmtDataset.setString(5, platform); + pstmtDataset.setString(6, data_type); + pstmtDataset.setString(7, publisher); + pstmtDataset.setString(8, publisher_id_type); + pstmtDataset.setString(9, publisher_id_value); + pstmtDataset.setString(10, ds_dates_type); + pstmtDataset.setString(11, ds_dates_value); + pstmtDataset.setString(13, datasetContributors.getAsString()); + pstmtDataset.setString(14, reportId); + + pstmtDataset.execute(); + logger.info("Dataset from compressed report addded " + doi); + /* + * JsonArray performance = datasetElement.getAsJsonObject().getAsJsonArray("performance"); for + * (JsonElement performanceElement : performance) { JsonObject period = + * performanceElement.getAsJsonObject().getAsJsonObject("period"); String end_date = + * period.getAsJsonObject().get("end-date").getAsString(); String begin_date = + * period.getAsJsonObject().get("begin-date").getAsString(); JsonArray instance = + * performanceElement.getAsJsonObject().getAsJsonArray("instance"); for (JsonElement instanceElement : + * instance) { int count = instanceElement.getAsJsonObject().get("count").getAsInt(); JsonObject + * country_counts = instanceElement.getAsJsonObject().getAsJsonObject("country-counts"); Set + * keys = country_counts.keySet(); String[] country = new String[country_counts.size()]; String[] + * country_counts_val = new String[country_counts.size()]; Iterator it2 = keys.iterator(); int j = 0; + * while (it2.hasNext()) { country[j] = it2.next().toString(); country_counts_val[j] = + * country_counts.get(country[j]).getAsString(); } Array countryArr = conn.createArrayOf("text", + * country); Array countrycountsArr = conn.createArrayOf("text", country_counts_val); String metrictype + * = instanceElement.getAsJsonObject().get("metric-type").getAsString(); String accessMethod = + * instanceElement.getAsJsonObject().get("access-method").getAsString(); String + * sqlInsertDatasetPerformance = + * "INSERT INTO datasetperformance(ds_type,period_end,period_from,access_method,metric_type,count,country,country_count, reportid) VALUES(?,?,?,?,?,?,?,?,?)" + * ; PreparedStatement pstmtDatasetPerformance = conn.prepareStatement(sqlInsertDatasetPerformance); + * //System.out.println(begin_date + " " + end_date + " " + doi + " " + metrictype + " " + count); + * pstmtDatasetPerformance.setString(1, doi); pstmtDatasetPerformance.setString(2, end_date); + * pstmtDatasetPerformance.setString(3, begin_date); pstmtDatasetPerformance.setString(4, accessMethod); + * pstmtDatasetPerformance.setString(5, metrictype); pstmtDatasetPerformance.setInt(6, count); + * pstmtDatasetPerformance.setArray(7, countryArr); pstmtDatasetPerformance.setArray(8, + * countrycountsArr); pstmtDatasetPerformance.setString(9, reportId); pstmtDatasetPerformance.execute(); + * } } + */ + } + } + + } + + private ArrayList listHdfsDir(String dir) throws Exception { + + FileSystem hdfs = FileSystem.get(new Configuration()); + RemoteIterator Files; + ArrayList fileNames = new ArrayList<>(); + + try { + Path exportPath = new Path(hdfs.getUri() + dir); + Files = hdfs.listFiles(exportPath, false); + while (Files.hasNext()) { + String fileName = Files.next().getPath().toString(); + fileNames.add(fileName); + } + + hdfs.close(); + } catch (Exception e) { + logger.error("HDFS file path with exported data does not exist : " + new Path(hdfs.getUri() + dir)); + throw new Exception("HDFS file path with exported data does not exist : " + dir, e); + } + + return fileNames; + } + + private String readHDFSFile(String filename) throws Exception { + String result; + try { + + FileSystem fs = FileSystem.get(new Configuration()); + // log.info("reading file : " + filename); + + BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(new Path(filename)))); + + StringBuilder sb = new StringBuilder(); + String line = br.readLine(); + + while (line != null) { + sb.append(line); + // sb.append(line); + line = br.readLine(); + } + // result = sb.toString().replace("][{\"idSite\"", ",{\"idSite\""); + result = sb.toString().trim(); + // fs.close(); + } catch (Exception e) { + throw new Exception(e); + } + + return result; + } + + public static String uncompressString(String zippedBase64Str) + throws IOException { + String result = null; + + // In my solr project, I use org.apache.solr.common.util.Base64. + // byte[] bytes = + // org.apache.solr.common.util.Base64.base64ToByteArray(zippedBase64Str); + byte[] bytes = Base64.getDecoder().decode(zippedBase64Str); + GZIPInputStream zi = null; + try { + zi = new GZIPInputStream(new ByteArrayInputStream(bytes)); + result = IOUtils.toString(zi); + } finally { + IOUtils.closeQuietly(zi); + } + return result; + } + + private void createTmpReportsTable(String jsonFile) throws SQLException { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + dropTmpReportsTable(); + String createTmpTable = "CREATE TEMPORARY TABLE " + ConnectDB.getDataSetUsageStatsDBSchema() + + ".tmpjson (json STRING)"; + stmt.executeUpdate(createTmpTable); + logger.info("Tmp Table Created"); + + String insertJsonReport = "LOAD DATA INPATH '" + jsonFile + "' INTO TABLE " + + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; + stmt.execute(insertJsonReport); + logger.info("JSON Report File inserted to tmpjson Table"); + } + + private void dropTmpReportsTable() throws SQLException { + logger.info("Dropping tmpjson Table"); + String dropTmpTable = "DROP TABLE IF EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + stmt.executeUpdate(dropTmpTable); + logger.info("Dropped tmpjson Table"); + + } + +} + +/* + * PreparedStatement prepStatem = conn. + * prepareStatement("insert into usageStats (source, entityID,sourceItemType,entityType, counter,action,timestamp_month,referrer) values (?,?,?,?,?,?,?,?)" + * ); + */ diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java index 28c4f30a1..7b07fbc25 100644 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java +++ b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java @@ -1,3 +1,4 @@ + package eu.dnetlib.oa.graph.datasetsusagestats.export; import java.io.IOException; @@ -17,220 +18,94 @@ import org.slf4j.LoggerFactory; */ public class UsageStatsExporter { - private Statement stmt = null; + private Statement stmt = null; - public UsageStatsExporter() { + public UsageStatsExporter() { - } + } - private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); + private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); - private void reCreateLogDirs() throws IllegalArgumentException, IOException { - FileSystem dfs = FileSystem.get(new Configuration()); + private void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); - logger.info("Deleting Log directory: " + ExecuteWorkflow.dataciteReportPath); - dfs.delete(new Path(ExecuteWorkflow.dataciteReportPath), true); + logger.info("Deleting Log directory: " + ExecuteWorkflow.dataciteReportPath); + dfs.delete(new Path(ExecuteWorkflow.dataciteReportPath), true); - logger.info("Creating Log directory: " + ExecuteWorkflow.dataciteReportPath); - dfs.mkdirs(new Path(ExecuteWorkflow.dataciteReportPath)); + logger.info("Creating Log directory: " + ExecuteWorkflow.dataciteReportPath); + dfs.mkdirs(new Path(ExecuteWorkflow.dataciteReportPath)); - } + } - public void export() throws Exception { + public void export() throws Exception { - logger.info("Initialising DB properties"); - ConnectDB.init(); - ConnectDB.getHiveConnection(); + logger.info("Initialising DB properties"); + ConnectDB.init(); + ConnectDB.getHiveConnection(); - if (ExecuteWorkflow.recreateDbAndTables) { - createDatabase(); - createTables(); - reCreateLogDirs(); - } - logger.info("Initializing the download logs module"); - DownloadReportsListFromDatacite drfd = new DownloadReportsListFromDatacite(ExecuteWorkflow.dataciteBaseURL, ExecuteWorkflow.dataciteReportPath); + if (ExecuteWorkflow.recreateDbAndTables) { + DatasetsStatsDB datasetsDB = new DatasetsStatsDB("", ""); + datasetsDB.recreateDBAndTables(); + } + logger.info("Initializing the download logs module"); + DownloadReportsListFromDatacite drfd = new DownloadReportsListFromDatacite(ExecuteWorkflow.dataciteBaseURL, + ExecuteWorkflow.dataciteReportPath); - if (ExecuteWorkflow.datasetsEmptyDirs) { - logger.info("Downloading Reports List From Datacite"); - drfd.downloadReportsList(); - logger.info("Reports List has been downloaded"); - } - } + if (ExecuteWorkflow.datasetsEmptyDirs) { + logger.info("Downloading Reports List From Datacite"); + drfd.downloadReportsList(); + logger.info("Reports List has been downloaded"); + } - private void createDatabase() throws Exception { - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - logger.info("Dropping datasetUsageStats DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); - String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema() + " CASCADE"; - stmt.executeUpdate(dropDatabase); - } catch (Exception e) { - logger.error("Failed to drop database: " + e); - throw new Exception("Failed to drop database: " + e.toString(), e); - } - - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - logger.info("Creating datasetUsageStats DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); - String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema(); - stmt.executeUpdate(createDatabase); - - } catch (Exception e) { - logger.error("Failed to create database: " + e); - throw new Exception("Failed to create database: " + e.toString(), e); - } - } - - private void createTables() throws Exception { - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - // Create Reports table - This table should exist - String sqlCreateTableDataciteeReports = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getDataSetUsageStatsDBSchema() - + ".datacitereports(reportid STRING, \n" - + " name STRING, \n" - + " source STRING,\n" - + " release STRING,\n" - + " createdby STRING,\n" - + " report_end_date STRING,\n" - + " report_start_date STRING)\n" - + " CLUSTERED BY (reportid)\n" - + " into 100 buckets stored as orc tblproperties('transactional'='true')"; - - stmt.executeUpdate(sqlCreateTableDataciteeReports); - - stmt.close(); - ConnectDB.getHiveConnection().close(); - - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - } - } + ReadReportsListFromDatacite readReportsListFromDatacite = new ReadReportsListFromDatacite( + ExecuteWorkflow.dataciteReportPath); + logger.info("Store Reports To DB"); + readReportsListFromDatacite.readReports(); + logger.info("Reports Stored To DB"); + } // runImpalaQuery(); -/* - PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); - - logger.info("Re-creating database and tables"); - - logger.info("Initializing the download logs module"); - PiwikDownloadLogs piwd = new PiwikDownloadLogs(ExecuteWorkflow.matomoBaseURL, ExecuteWorkflow.matomoAuthToken); - - if (ExecuteWorkflow.piwikEmptyDirs) { - logger.info("Recreating Piwik log directories"); - piwikstatsdb.reCreateLogDirs(); - } - - // Downloading piwik logs (also managing directory creation) - if (ExecuteWorkflow.downloadPiwikLogs) { - logger.info("Downloading piwik logs"); - piwd - .GetOpenAIRELogs( - ExecuteWorkflow.repoLogPath, - ExecuteWorkflow.portalLogPath, ExecuteWorkflow.portalMatomoID); - } - logger.info("Downloaded piwik logs"); - - // Create DB tables, insert/update statistics - String cRobotsUrl = "https://raw.githubusercontent.com/atmire/COUNTER-Robots/master/COUNTER_Robots_list.json"; - piwikstatsdb.setCounterRobotsURL(cRobotsUrl); - - if (ExecuteWorkflow.processPiwikLogs) { - logger.info("Processing logs"); - piwikstatsdb.processLogs(); - } - - logger.info("Creating LaReferencia tables"); - LaReferenciaDownloadLogs lrf = new LaReferenciaDownloadLogs(ExecuteWorkflow.lareferenciaBaseURL, - ExecuteWorkflow.lareferenciaAuthToken); - - if (ExecuteWorkflow.laReferenciaEmptyDirs) { - logger.info("Recreating LaReferencia log directories"); - lrf.reCreateLogDirs(); - } - - if (ExecuteWorkflow.downloadLaReferenciaLogs) { - logger.info("Downloading LaReferencia logs"); - lrf.GetLaReferenciaRepos(ExecuteWorkflow.lareferenciaLogPath); - logger.info("Downloaded LaReferencia logs"); - } - LaReferenciaStats lastats = new LaReferenciaStats(ExecuteWorkflow.lareferenciaLogPath); - - if (ExecuteWorkflow.processLaReferenciaLogs) { - logger.info("Processing LaReferencia logs"); - lastats.processLogs(); - logger.info("LaReferencia logs done"); - } - - IrusStats irusstats = new IrusStats(ExecuteWorkflow.irusUKBaseURL); - if (ExecuteWorkflow.irusCreateTablesEmptyDirs) { - logger.info("Creating Irus Stats tables"); - irusstats.createTables(); - logger.info("Created Irus Stats tables"); - - logger.info("Re-create log dirs"); - irusstats.reCreateLogDirs(); - logger.info("Re-created log dirs"); - } - - if (ExecuteWorkflow.irusDownloadReports) { - irusstats.getIrusRRReport(ExecuteWorkflow.irusUKReportPath); - } - if (ExecuteWorkflow.irusProcessStats) { - irusstats.processIrusStats(); - logger.info("Irus done"); - } - - SarcStats sarcStats = new SarcStats(); - if (ExecuteWorkflow.sarcCreateTablesEmptyDirs) { - sarcStats.reCreateLogDirs(); - } - if (ExecuteWorkflow.sarcDownloadReports) { - sarcStats.getAndProcessSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); - } - if (ExecuteWorkflow.sarcProcessStats) { - sarcStats.processSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); - sarcStats.finalizeSarcStats(); - } - logger.info("Sarc done"); - - // finalize usagestats - if (ExecuteWorkflow.finalizeStats) { - piwikstatsdb.finalizeStats(); - logger.info("Finalized stats"); - } - - // Make the tables available to Impala - if (ExecuteWorkflow.finalTablesVisibleToImpala) { - logger.info("Making tables visible to Impala"); - invalidateMetadata(); - } - - logger.info("End"); - */ + /* + * PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); + * logger.info("Re-creating database and tables"); logger.info("Initializing the download logs module"); + * PiwikDownloadLogs piwd = new PiwikDownloadLogs(ExecuteWorkflow.matomoBaseURL, ExecuteWorkflow.matomoAuthToken); + * if (ExecuteWorkflow.piwikEmptyDirs) { logger.info("Recreating Piwik log directories"); + * piwikstatsdb.reCreateLogDirs(); } // Downloading piwik logs (also managing directory creation) if + * (ExecuteWorkflow.downloadPiwikLogs) { logger.info("Downloading piwik logs"); piwd .GetOpenAIRELogs( + * ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath, ExecuteWorkflow.portalMatomoID); } + * logger.info("Downloaded piwik logs"); // Create DB tables, insert/update statistics String cRobotsUrl = + * "https://raw.githubusercontent.com/atmire/COUNTER-Robots/master/COUNTER_Robots_list.json"; + * piwikstatsdb.setCounterRobotsURL(cRobotsUrl); if (ExecuteWorkflow.processPiwikLogs) { + * logger.info("Processing logs"); piwikstatsdb.processLogs(); } logger.info("Creating LaReferencia tables"); + * LaReferenciaDownloadLogs lrf = new LaReferenciaDownloadLogs(ExecuteWorkflow.lareferenciaBaseURL, + * ExecuteWorkflow.lareferenciaAuthToken); if (ExecuteWorkflow.laReferenciaEmptyDirs) { + * logger.info("Recreating LaReferencia log directories"); lrf.reCreateLogDirs(); } if + * (ExecuteWorkflow.downloadLaReferenciaLogs) { logger.info("Downloading LaReferencia logs"); + * lrf.GetLaReferenciaRepos(ExecuteWorkflow.lareferenciaLogPath); logger.info("Downloaded LaReferencia logs"); } + * LaReferenciaStats lastats = new LaReferenciaStats(ExecuteWorkflow.lareferenciaLogPath); if + * (ExecuteWorkflow.processLaReferenciaLogs) { logger.info("Processing LaReferencia logs"); lastats.processLogs(); + * logger.info("LaReferencia logs done"); } IrusStats irusstats = new IrusStats(ExecuteWorkflow.irusUKBaseURL); if + * (ExecuteWorkflow.irusCreateTablesEmptyDirs) { logger.info("Creating Irus Stats tables"); + * irusstats.createTables(); logger.info("Created Irus Stats tables"); logger.info("Re-create log dirs"); + * irusstats.reCreateLogDirs(); logger.info("Re-created log dirs"); } if (ExecuteWorkflow.irusDownloadReports) { + * irusstats.getIrusRRReport(ExecuteWorkflow.irusUKReportPath); } if (ExecuteWorkflow.irusProcessStats) { + * irusstats.processIrusStats(); logger.info("Irus done"); } SarcStats sarcStats = new SarcStats(); if + * (ExecuteWorkflow.sarcCreateTablesEmptyDirs) { sarcStats.reCreateLogDirs(); } if + * (ExecuteWorkflow.sarcDownloadReports) { sarcStats.getAndProcessSarc(ExecuteWorkflow.sarcsReportPathArray, + * ExecuteWorkflow.sarcsReportPathNonArray); } if (ExecuteWorkflow.sarcProcessStats) { + * sarcStats.processSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); + * sarcStats.finalizeSarcStats(); } logger.info("Sarc done"); // finalize usagestats if + * (ExecuteWorkflow.finalizeStats) { piwikstatsdb.finalizeStats(); logger.info("Finalized stats"); } // Make the + * tables available to Impala if (ExecuteWorkflow.finalTablesVisibleToImpala) { + * logger.info("Making tables visible to Impala"); invalidateMetadata(); } logger.info("End"); + */ } /* - private void invalidateMetadata() throws SQLException { - Statement stmt = null; - - stmt = ConnectDB.getImpalaConnection().createStatement(); - - String sql = "INVALIDATE METADATA " + ConnectDB.getDataSetUsageStatsDBSchema() + ".downloads_stats"; - stmt.executeUpdate(sql); - - sql = "INVALIDATE METADATA " + ConnectDB.getDataSetUsageStatsDBSchema() + ".views_stats"; - stmt.executeUpdate(sql); - - sql = "INVALIDATE METADATA " + ConnectDB.getDataSetUsageStatsDBSchema() + ".usage_stats"; - stmt.executeUpdate(sql); - - sql = "INVALIDATE METADATA " + ConnectDB.getDataSetUsageStatsDBSchema() + ".pageviews_stats"; - stmt.executeUpdate(sql); - - stmt.close(); - ConnectDB.getHiveConnection().close(); - } + * private void invalidateMetadata() throws SQLException { Statement stmt = null; stmt = + * ConnectDB.getImpalaConnection().createStatement(); String sql = "INVALIDATE METADATA " + + * ConnectDB.getDataSetUsageStatsDBSchema() + ".downloads_stats"; stmt.executeUpdate(sql); sql = "INVALIDATE METADATA " + * + ConnectDB.getDataSetUsageStatsDBSchema() + ".views_stats"; stmt.executeUpdate(sql); sql = "INVALIDATE METADATA " + + * ConnectDB.getDataSetUsageStatsDBSchema() + ".usage_stats"; stmt.executeUpdate(sql); sql = "INVALIDATE METADATA " + + * ConnectDB.getDataSetUsageStatsDBSchema() + ".pageviews_stats"; stmt.executeUpdate(sql); stmt.close(); + * ConnectDB.getHiveConnection().close(); } */ diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index 338b2a2c5..44f28ff56 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -2,13 +2,13 @@ - - + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.6.1 + + 1.8 + 1.8 + + + + + + UTF-8 + UTF-8 0.13.1-cdh5.2.1 2.5.0-cdh5.2.1 - - + + org.apache.spark @@ -53,16 +81,16 @@ 20180130 jar - - org.apache.hive - hive-jdbc - ${cdh.hive.version} - - - org.apache.hadoop - hadoop-common - ${cdh.hadoop.version} - + + org.apache.hive + hive-jdbc + ${cdh.hive.version} + + + org.apache.hadoop + hadoop-common + ${cdh.hadoop.version} + eu.dnetlib.dhp dhp-common diff --git a/dhp-workflows/dhp-usage-raw-data-update/runworkflow.sh b/dhp-workflows/dhp-usage-raw-data-update/runworkflow.sh new file mode 100755 index 000000000..4465dae21 --- /dev/null +++ b/dhp-workflows/dhp-usage-raw-data-update/runworkflow.sh @@ -0,0 +1 @@ +mvn clean package -Poozie-package,deploy,run -Dworkflow.source.dir=eu/dnetlib/dhp/oa/graph/usagerawdata \ No newline at end of file diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ConnectDB.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ConnectDB.java index f76644c83..5b2e6804b 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ConnectDB.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ConnectDB.java @@ -122,4 +122,4 @@ public abstract class ConnectDB { } -} +} diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java index 81e34b3e7..e0e0d3687 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/ExecuteWorkflow.java @@ -62,7 +62,6 @@ public class ExecuteWorkflow { static int sarcNumberOfIssnToDownload; static boolean finalizeStats; - static boolean finalTablesVisibleToImpala; static int numberOfDownloadThreads; @@ -98,98 +97,108 @@ public class ExecuteWorkflow { usageStatsDBSchema = parser.get("usageStatsDBSchema"); statsDBSchema = parser.get("statsDBSchema"); - if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) + if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) { recreateDbAndTables = true; - else + } else { recreateDbAndTables = false; + } - if (parser.get("piwikEmptyDirs").toLowerCase().equals("true")) + if (parser.get("piwikEmptyDirs").toLowerCase().equals("true")) { piwikEmptyDirs = true; - else + } else { piwikEmptyDirs = false; + } - if (parser.get("downloadPiwikLogs").toLowerCase().equals("true")) + if (parser.get("downloadPiwikLogs").toLowerCase().equals("true")) { downloadPiwikLogs = true; - else + } else { downloadPiwikLogs = false; + } - if (parser.get("processPiwikLogs").toLowerCase().equals("true")) + if (parser.get("processPiwikLogs").toLowerCase().equals("true")) { processPiwikLogs = true; - else + } else { processPiwikLogs = false; + } - String startingLogPeriodStr = parser.get("startingLogPeriod"); + String startingLogPeriodStr = parser.get("startingLogPeriod"); Date startingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(startingLogPeriodStr); startingLogPeriod = startingLogPeriodStr(startingLogPeriodDate); - String endingLogPeriodStr = parser.get("endingLogPeriod"); - Date endingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(endingLogPeriodStr); - endingLogPeriod = startingLogPeriodStr(endingLogPeriodDate); +// String endingLogPeriodStr = parser.get("endingLogPeriod"); +// Date endingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(endingLogPeriodStr); +// endingLogPeriod = startingLogPeriodStr(endingLogPeriodDate); numberOfPiwikIdsToDownload = Integer.parseInt(parser.get("numberOfPiwikIdsToDownload")); numberOfSiteIdsToDownload = Integer.parseInt(parser.get("numberOfSiteIdsToDownload")); - if (parser.get("laReferenciaEmptyDirs").toLowerCase().equals("true")) + if (parser.get("laReferenciaEmptyDirs").toLowerCase().equals("true")) { laReferenciaEmptyDirs = true; - else + } else { laReferenciaEmptyDirs = false; + } - if (parser.get("downloadLaReferenciaLogs").toLowerCase().equals("true")) + if (parser.get("downloadLaReferenciaLogs").toLowerCase().equals("true")) { downloadLaReferenciaLogs = true; - else + } else { downloadLaReferenciaLogs = false; + } - if (parser.get("processLaReferenciaLogs").toLowerCase().equals("true")) + if (parser.get("processLaReferenciaLogs").toLowerCase().equals("true")) { processLaReferenciaLogs = true; - else + } else { processLaReferenciaLogs = false; + } - if (parser.get("irusCreateTablesEmptyDirs").toLowerCase().equals("true")) + if (parser.get("irusCreateTablesEmptyDirs").toLowerCase().equals("true")) { irusCreateTablesEmptyDirs = true; - else + } else { irusCreateTablesEmptyDirs = false; + } - if (parser.get("irusDownloadReports").toLowerCase().equals("true")) + if (parser.get("irusDownloadReports").toLowerCase().equals("true")) { irusDownloadReports = true; - else + } else { irusDownloadReports = false; + } - if (parser.get("irusProcessStats").toLowerCase().equals("true")) + if (parser.get("irusProcessStats").toLowerCase().equals("true")) { irusProcessStats = true; - else + } else { irusProcessStats = false; + } irusNumberOfOpendoarsToDownload = Integer.parseInt(parser.get("irusNumberOfOpendoarsToDownload")); - if (parser.get("sarcCreateTablesEmptyDirs").toLowerCase().equals("true")) + if (parser.get("sarcCreateTablesEmptyDirs").toLowerCase().equals("true")) { sarcCreateTablesEmptyDirs = true; - else + } else { sarcCreateTablesEmptyDirs = false; + } - if (parser.get("sarcDownloadReports").toLowerCase().equals("true")) + if (parser.get("sarcDownloadReports").toLowerCase().equals("true")) { sarcDownloadReports = true; - else + } else { sarcDownloadReports = false; + } - if (parser.get("sarcProcessStats").toLowerCase().equals("true")) + if (parser.get("sarcProcessStats").toLowerCase().equals("true")) { sarcProcessStats = true; - else + } else { sarcProcessStats = false; + } sarcNumberOfIssnToDownload = Integer.parseInt(parser.get("sarcNumberOfIssnToDownload")); -/* - if (parser.get("finalizeStats").toLowerCase().equals("true")) + if (parser.get("finalizeStats").toLowerCase().equals("true")) { finalizeStats = true; - else + } else { finalizeStats = false; - if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) - finalTablesVisibleToImpala = true; - else - finalTablesVisibleToImpala = false; -*/ + } + numberOfDownloadThreads = Integer.parseInt(parser.get("numberOfDownloadThreads")); UsageStatsExporter usagestatsExport = new UsageStatsExporter(); usagestatsExport.export(); + // usagestatsExport.createdDBWithTablesOnly(); } private static Calendar startingLogPeriodStr(Date date) { diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java index bb8d8565e..7ec5b0fca 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/IrusStats.java @@ -1,3 +1,4 @@ + package eu.dnetlib.oa.graph.usagerawdata.export; import java.io.*; @@ -27,393 +28,331 @@ import org.slf4j.LoggerFactory; */ public class IrusStats { - private String irusUKURL; + private String irusUKURL; - private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); + private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); - public IrusStats(String irusUKURL) throws Exception { - this.irusUKURL = irusUKURL; - // The following may not be needed - It will be created when JSON tables are created + public IrusStats(String irusUKURL) throws Exception { + this.irusUKURL = irusUKURL; + // The following may not be needed - It will be created when JSON tables are created // createTmpTables(); - } + } - public void reCreateLogDirs() throws Exception { - FileSystem dfs = FileSystem.get(new Configuration()); + public void reCreateLogDirs() throws Exception { + FileSystem dfs = FileSystem.get(new Configuration()); - logger.info("Deleting irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); - dfs.delete(new Path(ExecuteWorkflow.irusUKReportPath), true); + logger.info("Deleting irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); + dfs.delete(new Path(ExecuteWorkflow.irusUKReportPath), true); - logger.info("Creating irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); - dfs.mkdirs(new Path(ExecuteWorkflow.irusUKReportPath)); - } + logger.info("Creating irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); + dfs.mkdirs(new Path(ExecuteWorkflow.irusUKReportPath)); + } - public void createTables() throws Exception { - try { - logger.info("Creating sushilog"); - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog(source STRING, " - + "repository STRING, rid STRING, date STRING, metric_type STRING, count INT) clustered by (source, " - + "repository, rid, date, metric_type) into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTableSushiLog); - logger.info("Created sushilog"); + public void createTables() throws Exception { + try { + logger.info("Creating sushilog"); + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog(source STRING, " + + "repository STRING, rid STRING, date STRING, metric_type STRING, count INT) clustered by (source, " + + "repository, rid, date, metric_type) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableSushiLog); + logger.info("Created sushilog"); - // To see how to apply to the ignore duplicate rules and indexes -// stmt.executeUpdate(sqlCreateTableSushiLog); -// String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " -// + " ON INSERT TO sushilog " -// + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," -// + "sushilog.rid, sushilog.date " -// + "FROM sushilog " -// + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; -// stmt.executeUpdate(sqlcreateRuleSushiLog); -// String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; -// stmt.executeUpdate(createSushiIndex); - stmt.close(); - ConnectDB.getHiveConnection().close(); - logger.info("Sushi Tables Created"); - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - } - } + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } -// // The following may not be needed - It will be created when JSON tables are created -// private void createTmpTables() throws Exception { -// try { -// -// Statement stmt = ConnectDB.getConnection().createStatement(); -// String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilogtmp(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; -// stmt.executeUpdate(sqlCreateTableSushiLog); -// -// // stmt.executeUpdate("CREATE TABLE IF NOT EXISTS public.sushilog AS TABLE sushilog;"); -// // String sqlCopyPublicSushiLog = "INSERT INTO sushilog SELECT * FROM public.sushilog;"; -// // stmt.executeUpdate(sqlCopyPublicSushiLog); -// String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " -// + " ON INSERT TO sushilogtmp " -// + " WHERE (EXISTS ( SELECT sushilogtmp.source, sushilogtmp.repository," -// + "sushilogtmp.rid, sushilogtmp.date " -// + "FROM sushilogtmp " -// + "WHERE sushilogtmp.source = new.source AND sushilogtmp.repository = new.repository AND sushilogtmp.rid = new.rid AND sushilogtmp.date = new.date AND sushilogtmp.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; -// stmt.executeUpdate(sqlcreateRuleSushiLog); -// -// stmt.close(); -// ConnectDB.getConnection().close(); -// log.info("Sushi Tmp Tables Created"); -// } catch (Exception e) { -// log.error("Failed to create tables: " + e); -// throw new Exception("Failed to create tables: " + e.toString(), e); -// } -// } - public void processIrusStats() throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); + public void processIrusStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); - logger.info("Adding JSON Serde jar"); - stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); - logger.info("Added JSON Serde jar"); + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); - logger.info("Dropping sushilogtmp_json table"); - String dropSushilogtmpJson = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".sushilogtmp_json"; - stmt.executeUpdate(dropSushilogtmpJson); - logger.info("Dropped sushilogtmp_json table"); + logger.info("Dropping sushilogtmp_json table"); + String dropSushilogtmpJson = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sushilogtmp_json"; + stmt.executeUpdate(dropSushilogtmpJson); + logger.info("Dropped sushilogtmp_json table"); - logger.info("Creating irus_sushilogtmp_json table"); - String createSushilogtmpJson = "CREATE EXTERNAL TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json(\n" - + " `ItemIdentifier` ARRAY<\n" - + " struct<\n" - + " Type: STRING,\n" - + " Value: STRING\n" - + " >\n" - + " >,\n" - + " `ItemPerformance` ARRAY<\n" - + " struct<\n" - + " `Period`: struct<\n" - + " `Begin`: STRING,\n" - + " `End`: STRING\n" - + " >,\n" - + " `Instance`: struct<\n" - + " `Count`: STRING,\n" - + " `MetricType`: STRING\n" - + " >\n" - + " >\n" - + " >\n" - + ")\n" - + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" - + "LOCATION '" + ExecuteWorkflow.irusUKReportPath + "'\n" - + "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(createSushilogtmpJson); - logger.info("Created irus_sushilogtmp_json table"); + logger.info("Creating irus_sushilogtmp_json table"); + String createSushilogtmpJson = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json(\n" + + " `ItemIdentifier` ARRAY<\n" + + " struct<\n" + + " Type: STRING,\n" + + " Value: STRING\n" + + " >\n" + + " >,\n" + + " `ItemPerformance` ARRAY<\n" + + " struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.irusUKReportPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(createSushilogtmpJson); + logger.info("Created irus_sushilogtmp_json table"); - logger.info("Dropping irus_sushilogtmp table"); - String dropSushilogtmp = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".irus_sushilogtmp"; - stmt.executeUpdate(dropSushilogtmp); - logger.info("Dropped irus_sushilogtmp table"); + logger.info("Dropping irus_sushilogtmp table"); + String dropSushilogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp"; + stmt.executeUpdate(dropSushilogtmp); + logger.info("Dropped irus_sushilogtmp table"); - logger.info("Creating irus_sushilogtmp table"); - String createSushilogtmp = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() - + ".irus_sushilogtmp(source STRING, repository STRING, " - + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " - + "tblproperties('transactional'='true')"; - stmt.executeUpdate(createSushilogtmp); - logger.info("Created irus_sushilogtmp table"); + logger.info("Creating irus_sushilogtmp table"); + String createSushilogtmp = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp(source STRING, repository STRING, " + + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " + + "tblproperties('transactional'='true')"; + stmt.executeUpdate(createSushilogtmp); + logger.info("Created irus_sushilogtmp table"); - logger.info("Inserting to irus_sushilogtmp table"); - String insertSushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp " - + "SELECT 'IRUS-UK', CONCAT('opendoar____::', split(split(INPUT__FILE__NAME,'IrusIRReport_')[1],'_')[0]), " - + "`ItemIdent`.`Value`, `ItemPerf`.`Period`.`Begin`, " - + "`ItemPerf`.`Instance`.`MetricType`, `ItemPerf`.`Instance`.`Count` " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json " - + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " - + "LATERAL VIEW posexplode(ItemPerformance) ItemPerformanceTable AS seqp, ItemPerf " - + "WHERE `ItemIdent`.`Type`= 'OAI'"; - stmt.executeUpdate(insertSushilogtmp); - logger.info("Inserted to irus_sushilogtmp table"); -/* - logger.info("Creating downloads_stats table"); - String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats " - + "(`source` string, " - + "`repository_id` string, " - + "`result_id` string, " - + "`date` string, " - + "`count` bigint, " - + "`openaire` bigint)"; - stmt.executeUpdate(createDownloadsStats); - logger.info("Created downloads_stats table"); + logger.info("Inserting to irus_sushilogtmp table"); + String insertSushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp " + + "SELECT 'IRUS-UK', CONCAT('opendoar____::', split(split(INPUT__FILE__NAME,'IrusIRReport_')[1],'_')[0]), " + + "`ItemIdent`.`Value`, `ItemPerf`.`Period`.`Begin`, " + + "`ItemPerf`.`Instance`.`MetricType`, `ItemPerf`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json " + + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + + "LATERAL VIEW posexplode(ItemPerformance) ItemPerformanceTable AS seqp, ItemPerf " + + "WHERE `ItemIdent`.`Type`= 'OAI'"; + stmt.executeUpdate(insertSushilogtmp); + logger.info("Inserted to irus_sushilogtmp table"); - logger.info("Inserting into downloads_stats"); - String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " - + "SELECT s.source, d.id AS repository_id, " - + "ro.id as result_id, CONCAT(YEAR(date), '/', LPAD(MONTH(date), 2, '0')) as date, s.count, '0' " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp s, " - + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " - + ConnectDB.getStatsDBSchema() + ".result_oids ro " - + "WHERE s.repository=d.oid AND s.rid=ro.oid AND metric_type='ft_total' AND s.source='IRUS-UK'"; - stmt.executeUpdate(insertDStats); - logger.info("Inserted into downloads_stats"); + logger.info("Inserting to sushilog table"); + String insertToShushilog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sushilog SELECT * FROM " + + ConnectDB.getUsageStatsDBSchema() + + ".irus_sushilogtmp"; + stmt.executeUpdate(insertToShushilog); + logger.info("Inserted to sushilog table"); - logger.info("Creating sushilog table"); - String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog " - + "(`source` string, " - + "`repository_id` string, " - + "`rid` string, " - + "`date` string, " - + "`metric_type` string, " - + "`count` int)"; - stmt.executeUpdate(createSushilog); - logger.info("Created sushilog table"); -*/ - logger.info("Inserting to sushilog table"); - String insertToShushilog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sushilog SELECT * FROM " - + ConnectDB.getUsageStatsDBSchema() - + ".irus_sushilogtmp"; - stmt.executeUpdate(insertToShushilog); - logger.info("Inserted to sushilog table"); + ConnectDB.getHiveConnection().close(); + } - ConnectDB.getHiveConnection().close(); - } + public void getIrusRRReport(String irusUKReportPath) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("YYYY-MM"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getIrusRRReport) Starting period for log download: " + sdf.format(start.getTime())); - public void getIrusRRReport(String irusUKReportPath) throws Exception { - SimpleDateFormat sdf = new SimpleDateFormat("YYYY-MM"); - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("(getIrusRRReport) Starting period for log download: " + sdf.format(start.getTime())); + // Setting the ending period (last day of the month) +// Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); +// end.add(Calendar.MONTH, +1); +// end.add(Calendar.DAY_OF_MONTH, -1); + Calendar end = Calendar.getInstance(); + end.add(Calendar.DAY_OF_MONTH, -1); - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("(getIrusRRReport) Ending period for log download: " + sdf.format(end.getTime())); + logger.info("(getIrusRRReport) Ending period for log download: " + sdf.format(end.getTime())); - String reportUrl = irusUKURL + "GetReport/?Report=RR1&Release=4&RequestorID=OpenAIRE&BeginDate=" - + sdf.format(start.getTime()) + "&EndDate=" + sdf.format(end.getTime()) - + "&RepositoryIdentifier=&ItemDataType=&NewJiscBand=&Granularity=Monthly&Callback="; + String reportUrl = irusUKURL + "GetReport/?Report=RR1&Release=4&RequestorID=OpenAIRE&BeginDate=" + + sdf.format(start.getTime()) + "&EndDate=" + sdf.format(end.getTime()) + + "&RepositoryIdentifier=&ItemDataType=&NewJiscBand=&Granularity=Monthly&Callback="; - logger.info("(getIrusRRReport) Getting report: " + reportUrl); + logger.info("(getIrusRRReport) Getting report: " + reportUrl); - String text = getJson(reportUrl, "", ""); + String text = getJson(reportUrl, "", ""); - List opendoarsToVisit = new ArrayList(); - JSONParser parser = new JSONParser(); - JSONObject jsonObject = (JSONObject) parser.parse(text); - jsonObject = (JSONObject) jsonObject.get("ReportResponse"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Customer"); - JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); - int i = 0; - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - JSONArray itemIdentifier = (JSONArray) jsonObjectRow.get("ItemIdentifier"); - for (Object identifier : itemIdentifier) { - JSONObject opendoar = (JSONObject) identifier; - if (opendoar.get("Type").toString().equals("OpenDOAR")) { - i++; - opendoarsToVisit.add(opendoar.get("Value").toString()); - break; - } - } - // break; - } + List opendoarsToVisit = new ArrayList(); + JSONParser parser = new JSONParser(); + JSONObject jsonObject = (JSONObject) parser.parse(text); + jsonObject = (JSONObject) jsonObject.get("ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Customer"); + JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); + if (jsonArray != null) { + int i = 0; + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + JSONArray itemIdentifier = (JSONArray) jsonObjectRow.get("ItemIdentifier"); + for (Object identifier : itemIdentifier) { + JSONObject opendoar = (JSONObject) identifier; + if (opendoar.get("Type").toString().equals("OpenDOAR")) { + i++; + opendoarsToVisit.add(opendoar.get("Value").toString()); + break; + } + } + // break; + } - logger.info("(getIrusRRReport) Found the following opendoars for download: " + opendoarsToVisit); + logger.info("(getIrusRRReport) Found the following opendoars for download: " + opendoarsToVisit); - if (ExecuteWorkflow.irusNumberOfOpendoarsToDownload > 0 - && ExecuteWorkflow.irusNumberOfOpendoarsToDownload <= opendoarsToVisit.size()) { - logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.irusNumberOfOpendoarsToDownload); - opendoarsToVisit = opendoarsToVisit.subList(0, ExecuteWorkflow.irusNumberOfOpendoarsToDownload); - } + if (ExecuteWorkflow.irusNumberOfOpendoarsToDownload > 0 + && ExecuteWorkflow.irusNumberOfOpendoarsToDownload <= opendoarsToVisit.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.irusNumberOfOpendoarsToDownload); + opendoarsToVisit = opendoarsToVisit.subList(0, ExecuteWorkflow.irusNumberOfOpendoarsToDownload); + } - logger.info("(getIrusRRReport) Downloading the followins opendoars: " + opendoarsToVisit); + logger.info("(getIrusRRReport) Downloading the followins opendoars: " + opendoarsToVisit); - for (String opendoar : opendoarsToVisit) { - logger.info("Now working on openDoar: " + opendoar); - this.getIrusIRReport(opendoar, irusUKReportPath); - } + for (String opendoar : opendoarsToVisit) { + logger.info("Now working on openDoar: " + opendoar); + this.getIrusIRReport(opendoar, irusUKReportPath); + } + logger.info("(getIrusRRReport) Finished with report: " + reportUrl); + } else { + logger.info("IRUS Reports not found for day"); + } - logger.info("(getIrusRRReport) Finished with report: " + reportUrl); - } + } - private void getIrusIRReport(String opendoar, String irusUKReportPath) throws Exception { + private void getIrusIRReport(String opendoar, String irusUKReportPath) throws Exception { - logger.info("(getIrusIRReport) Getting report(s) with opendoar: " + opendoar); + logger.info("(getIrusIRReport) Getting report(s) with opendoar: " + opendoar); - ConnectDB.getHiveConnection().setAutoCommit(false); + ConnectDB.getHiveConnection().setAutoCommit(false); - SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); + SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("(getIrusIRReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getIrusIRReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("(getIrusIRReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); + // Setting the ending period (last day of the month) + Calendar end = Calendar.getInstance(); + end.add(Calendar.DAY_OF_MONTH, -1); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - PreparedStatement st = ConnectDB - .getHiveConnection() - .prepareStatement( - "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); - st.setString(1, "opendoar____::" + opendoar); - ResultSet rs_date = st.executeQuery(); - Date dateMax = null; - while (rs_date.next()) { - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - dateMax = sdf.parse(rs_date.getString(1)); - } - } - rs_date.close(); - int batch_size = 0; +// Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); +// end.add(Calendar.MONTH, +1); +// end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("(getIrusIRReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); - if (dateMax != null && start.getTime().compareTo(dateMax) <= 0) { - logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + opendoar); - } else { - while (start.before(end)) { - logger.info("date: " + simpleDateFormat.format(start.getTime())); - String reportUrl = this.irusUKURL + "GetReport/?Report=IR1&Release=4&RequestorID=OpenAIRE&BeginDate=" - + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()) - + "&RepositoryIdentifier=opendoar%3A" + opendoar - + "&ItemIdentifier=&ItemDataType=&hasDOI=&Granularity=Monthly&Callback="; - start.add(Calendar.MONTH, 1); + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); + st.setString(1, "opendoar____::" + opendoar); + ResultSet rs_date = st.executeQuery(); + Date dateMax = null; + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); + int batch_size = 0; - logger.info("Downloading file: " + reportUrl); - String text = getJson(reportUrl, "", ""); - if (text == null) { - continue; - } + if (dateMax != null && end.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + opendoar); + } else { + start.add(Calendar.MONTH, 1); + while (start.before(end)) { + logger.info("Downloading for date: " + simpleDateFormat.format(start.getTime())); + String reportUrl = this.irusUKURL + "GetReport/?Report=IR1&Release=4&RequestorID=OpenAIRE&BeginDate=" + + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()) + + "&RepositoryIdentifier=opendoar%3A" + opendoar + + "&ItemIdentifier=&ItemDataType=&hasDOI=&Granularity=Monthly&Callback="; + start.add(Calendar.MONTH, 1); - FileSystem fs = FileSystem.get(new Configuration()); - String filePath = irusUKReportPath + "/" + "IrusIRReport_" - + opendoar + "_" + simpleDateFormat.format(start.getTime()) + ".json"; - logger.info("Storing to file: " + filePath); - FSDataOutputStream fin = fs.create(new Path(filePath), true); + logger.info("Downloading file: " + reportUrl); + String text = getJson(reportUrl, "", ""); + if (text == null) { + continue; + } - JSONParser parser = new JSONParser(); - JSONObject jsonObject = (JSONObject) parser.parse(text); - jsonObject = (JSONObject) jsonObject.get("ReportResponse"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Customer"); - JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); - if (jsonArray == null) { - continue; - } - String oai = ""; - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - fin.write(jsonObjectRow.toJSONString().getBytes()); - fin.writeChar('\n'); - } + FileSystem fs = FileSystem.get(new Configuration()); + String filePath = irusUKReportPath + "/" + "IrusIRReport_" + + opendoar + "_" + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePath); + FSDataOutputStream fin = fs.create(new Path(filePath), true); - fin.close(); - } + JSONParser parser = new JSONParser(); + JSONObject jsonObject = (JSONObject) parser.parse(text); + jsonObject = (JSONObject) jsonObject.get("ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Report"); + jsonObject = (JSONObject) jsonObject.get("Customer"); + JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); + if (jsonArray == null) { + continue; + } + String oai = ""; + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + fin.write(jsonObjectRow.toJSONString().getBytes()); + fin.writeChar('\n'); + } - } - //ConnectDB.getHiveConnection().close(); + fin.close(); + } - logger.info("(getIrusIRReport) Finished downloading report(s) with opendoar: " + opendoar); - } + } + // ConnectDB.getHiveConnection().close(); - private String getJson(String url) throws Exception { - try { - System.out.println("===> Connecting to: " + url); - URL website = new URL(url); - System.out.println("Connection url -----> " + url); - URLConnection connection = website.openConnection(); + logger.info("(getIrusIRReport) Finished downloading report(s) with opendoar: " + opendoar); + } - // connection.setRequestProperty ("Authorization", "Basic "+encoded); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); + private String getJson(String url) throws Exception { + try { + System.out.println("===> Connecting to: " + url); + URL website = new URL(url); + System.out.println("Connection url -----> " + url); + URLConnection connection = website.openConnection(); + + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); // response.append("\n"); - } - } + } + } - System.out.println("response ====> " + response.toString()); + System.out.println("response ====> " + response.toString()); - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL: " + e); - System.out.println("Failed to get URL: " + e); - throw new Exception("Failed to get URL: " + e.toString(), e); - } - } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + e); + System.out.println("Failed to get URL: " + e); + throw new Exception("Failed to get URL: " + e.toString(), e); + } + } - private String getJson(String url, String username, String password) throws Exception { - // String cred=username+":"+password; - // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); - try { - URL website = new URL(url); - URLConnection connection = website.openConnection(); - // connection.setRequestProperty ("Authorization", "Basic "+encoded); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); - response.append("\n"); - } - } - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL", e); - return null; - } - } + private String getJson(String url, String username, String password) throws Exception { + // String cred=username+":"+password; + // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + response.append("\n"); + } + } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL", e); + return null; + } + } } diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaDownloadLogs.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaDownloadLogs.java index 88550579b..904290af8 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaDownloadLogs.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaDownloadLogs.java @@ -1,3 +1,4 @@ + package eu.dnetlib.oa.graph.usagerawdata.export; import java.io.*; @@ -27,49 +28,49 @@ import org.slf4j.LoggerFactory; */ public class LaReferenciaDownloadLogs { - private final String piwikUrl; - private Date startDate; - private final String tokenAuth; + private final String piwikUrl; + private Date startDate; + private final String tokenAuth; - /* + /* * The Piwik's API method - */ - private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; - private final String format = "&format=json"; - private final String ApimethodGetAllSites = "?module=API&method=SitesManager.getSitesWithViewAccess"; + */ + private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; + private final String format = "&format=json"; + private final String ApimethodGetAllSites = "?module=API&method=SitesManager.getSitesWithViewAccess"; - private static final Logger logger = LoggerFactory.getLogger(LaReferenciaDownloadLogs.class); + private static final Logger logger = LoggerFactory.getLogger(LaReferenciaDownloadLogs.class); - public LaReferenciaDownloadLogs(String piwikUrl, String tokenAuth) throws Exception { - this.piwikUrl = piwikUrl; - this.tokenAuth = tokenAuth; - this.createTables(); + public LaReferenciaDownloadLogs(String piwikUrl, String tokenAuth) throws Exception { + this.piwikUrl = piwikUrl; + this.tokenAuth = tokenAuth; + this.createTables(); // this.createTmpTables(); - } + } - public void reCreateLogDirs() throws IllegalArgumentException, IOException { - FileSystem dfs = FileSystem.get(new Configuration()); + public void reCreateLogDirs() throws IllegalArgumentException, IOException { + FileSystem dfs = FileSystem.get(new Configuration()); - logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); - dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); + logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); - logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); - dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); - } + logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); + dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); + } - private void createTables() throws Exception { - try { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); + private void createTables() throws Exception { + try { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); - logger.info("Creating LaReferencia tables"); - String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " - + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " - + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " - + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " - + "stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTableLareferenciaLog); - logger.info("Created LaReferencia tables"); + logger.info("Creating LaReferencia tables"); + String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableLareferenciaLog); + logger.info("Created LaReferencia tables"); // String sqlcreateRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " // + " ON INSERT TO lareferencialog " // + " WHERE (EXISTS ( SELECT lareferencialog.matomoid, lareferencialog.source, lareferencialog.id_visit," @@ -80,16 +81,16 @@ public class LaReferenciaDownloadLogs { // stmt.executeUpdate(sqlcreateRuleLaReferenciaLog); // stmt.executeUpdate(sqlCreateRuleIndexLaReferenciaLog); - stmt.close(); - ConnectDB.getHiveConnection().close(); - logger.info("Lareferencia Tables Created"); + stmt.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Lareferencia Tables Created"); - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - // System.exit(0); - } - } + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + // System.exit(0); + } + } // private void createTmpTables() throws Exception { // @@ -114,152 +115,159 @@ public class LaReferenciaDownloadLogs { // // System.exit(0); // } // } - private String getPiwikLogUrl() { - return piwikUrl + "/"; - } + private String getPiwikLogUrl() { + return piwikUrl + "/"; + } - private String getJson(String url) throws Exception { - try { - URL website = new URL(url); - URLConnection connection = website.openConnection(); + private String getJson(String url) throws Exception { + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); // response.append("\n"); - } - } + } + } - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL: " + e); - throw new Exception("Failed to get URL: " + e.toString(), e); - } - } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + e); + throw new Exception("Failed to get URL: " + e.toString(), e); + } + } - public void GetLaReferenciaRepos(String repoLogsPath) throws Exception { + public void GetLaReferenciaRepos(String repoLogsPath) throws Exception { - String baseApiUrl = getPiwikLogUrl() + ApimethodGetAllSites + format + "&token_auth=" + this.tokenAuth; - String content = ""; + String baseApiUrl = getPiwikLogUrl() + ApimethodGetAllSites + format + "&token_auth=" + this.tokenAuth; + String content = ""; - List siteIdsToVisit = new ArrayList(); + List siteIdsToVisit = new ArrayList(); - // Getting all the siteIds in a list for logging reasons & limiting the list - // to the max number of siteIds - content = getJson(baseApiUrl); - JSONParser parser = new JSONParser(); - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - siteIdsToVisit.add(Integer.parseInt(jsonObjectRow.get("idsite").toString())); - } - logger.info("Found the following siteIds for download: " + siteIdsToVisit); + // Getting all the siteIds in a list for logging reasons & limiting the list + // to the max number of siteIds + content = getJson(baseApiUrl); + JSONParser parser = new JSONParser(); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + siteIdsToVisit.add(Integer.parseInt(jsonObjectRow.get("idsite").toString())); + } + logger.info("Found the following siteIds for download: " + siteIdsToVisit); - if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 - && ExecuteWorkflow.numberOfPiwikIdsToDownload <= siteIdsToVisit.size()) { - logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); - siteIdsToVisit = siteIdsToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); - } + if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 + && ExecuteWorkflow.numberOfPiwikIdsToDownload <= siteIdsToVisit.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); + siteIdsToVisit = siteIdsToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); + } - logger.info("Downloading from repos with the followins siteIds: " + siteIdsToVisit); + logger.info("Downloading from repos with the followins siteIds: " + siteIdsToVisit); - for (int siteId : siteIdsToVisit) { - logger.info("Now working on LaReferencia MatomoId: " + siteId); - this.GetLaReFerenciaLogs(repoLogsPath, siteId); - } - } + for (int siteId : siteIdsToVisit) { + logger.info("Now working on LaReferencia MatomoId: " + siteId); + this.GetLaReFerenciaLogs(repoLogsPath, siteId); + } + } - public void GetLaReFerenciaLogs(String repoLogsPath, - int laReferencialMatomoID) throws Exception { + public void GetLaReFerenciaLogs(String repoLogsPath, + int laReferencialMatomoID) throws Exception { - logger.info("Downloading logs for LaReferencia repoid " + laReferencialMatomoID); + logger.info("Downloading logs for LaReferencia repoid " + laReferencialMatomoID); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("Starting period for log download: " + sdf.format(start.getTime())); + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("Starting period for log download: " + sdf.format(start.getTime())); - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("Ending period for log download: " + sdf.format(end.getTime())); + // Setting the ending period (last day of the month) +// Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); +// end.add(Calendar.MONTH, +1); +// end.add(Calendar.DAY_OF_MONTH, -1); + Calendar end = Calendar.getInstance(); + end.add(Calendar.DAY_OF_MONTH, -1); - PreparedStatement st = ConnectDB - .getHiveConnection() - .prepareStatement( - "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() - + ".lareferencialog WHERE matomoid=?"); - st.setInt(1, laReferencialMatomoID); - Date dateMax = null; + logger.info("Ending period for log download: " + sdf.format(end.getTime())); - ResultSet rs_date = st.executeQuery(); - while (rs_date.next()) { - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - dateMax = sdf.parse(rs_date.getString(1)); - } - } - rs_date.close(); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialog WHERE matomoid=?"); + st.setInt(1, laReferencialMatomoID); + Date dateMax = null; - for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { - Date date = currDay.getTime(); - if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { - logger.info("Date found in logs " + dateMax + " and not downloanding Matomo logs for " + laReferencialMatomoID); - } else { - logger - .info( - "Downloading logs for LaReferencia repoid " + laReferencialMatomoID + " and for " - + sdf.format(date)); + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); - String period = "&period=day&date=" + sdf.format(date); - String outFolder = ""; - outFolder = repoLogsPath; + for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { + Date date = currDay.getTime(); + if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { + logger + .info( + "Date found in logs " + dateMax + " and not downloanding Matomo logs for " + + laReferencialMatomoID); + } else { + logger + .info( + "Downloading logs for LaReferencia repoid " + laReferencialMatomoID + " and for " + + sdf.format(date)); - FileSystem fs = FileSystem.get(new Configuration()); - FSDataOutputStream fin = fs - .create( - new Path(outFolder + "/" + laReferencialMatomoID + "_LaRefPiwiklog" + sdf.format((date)) + ".json"), - true); + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + outFolder = repoLogsPath; - String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + laReferencialMatomoID + period + format - + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; - String content = ""; - int i = 0; + FileSystem fs = FileSystem.get(new Configuration()); + FSDataOutputStream fin = fs + .create( + new Path( + outFolder + "/" + laReferencialMatomoID + "_LaRefPiwiklog" + sdf.format((date)) + ".json"), + true); - JSONParser parser = new JSONParser(); - do { - String apiUrl = baseApiUrl; + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + laReferencialMatomoID + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; + int i = 0; - if (i > 0) { - apiUrl += "&filter_offset=" + (i * 1000); - } + JSONParser parser = new JSONParser(); + do { + String apiUrl = baseApiUrl; - content = getJson(apiUrl); - if (content.length() == 0 || content.equals("[]")) { - break; - } + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRaw = (JSONObject) aJsonArray; - fin.write(jsonObjectRaw.toJSONString().getBytes()); - fin.writeChar('\n'); - } + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } - logger - .info( - "Downloaded part " + i + " of logs for LaReferencia repoid " + laReferencialMatomoID - + " and for " - + sdf.format(date)); - i++; - } while (true); - fin.close(); - } - } - } + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + fin.write(jsonObjectRaw.toJSONString().getBytes()); + fin.writeChar('\n'); + } + + logger + .info( + "Downloaded part " + i + " of logs for LaReferencia repoid " + laReferencialMatomoID + + " and for " + + sdf.format(date)); + i++; + } while (true); + fin.close(); + } + } + } } diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java index c20781767..bcf1711cb 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/LaReferenciaStats.java @@ -61,15 +61,6 @@ public class LaReferenciaStats { "stored as orc tblproperties('transactional'='true')"; stmt.executeUpdate(sqlCreateTableLareferenciaLog); logger.info("Created LaReferencia tables"); -// String sqlcreateRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " -// + " ON INSERT TO lareferencialog " -// + " WHERE (EXISTS ( SELECT lareferencialog.matomoid, lareferencialog.source, lareferencialog.id_visit," -// + "lareferencialog.action, lareferencialog.\"timestamp\", lareferencialog.entity_id " -// + "FROM lareferencialog " -// + "WHERE lareferencialog.matomoid=new.matomoid AND lareferencialog.source = new.source AND lareferencialog.id_visit = new.id_visit AND lareferencialog.action = new.action AND lareferencialog.entity_id = new.entity_id AND lareferencialog.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; -// String sqlCreateRuleIndexLaReferenciaLog = "create index if not exists lareferencialog_rule on lareferencialog(matomoid, source, id_visit, action, entity_id, \"timestamp\");"; -// stmt.executeUpdate(sqlcreateRuleLaReferenciaLog); -// stmt.executeUpdate(sqlCreateRuleIndexLaReferenciaLog); stmt.close(); ConnectDB.getHiveConnection().close(); @@ -82,30 +73,6 @@ public class LaReferenciaStats { } } -// private void createTmpTables() throws Exception { -// -// try { -// Statement stmt = ConnectDB.getConnection().createStatement(); -// String sqlCreateTmpTableLaReferenciaLog = "CREATE TABLE IF NOT EXISTS lareferencialogtmp(matomoid INTEGER, source TEXT, id_visit TEXT, country TEXT, action TEXT, url TEXT, entity_id TEXT, source_item_type TEXT, timestamp TEXT, referrer_name TEXT, agent TEXT, PRIMARY KEY(source, id_visit, action, timestamp, entity_id));"; -// String sqlcreateTmpRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " -// + " ON INSERT TO lareferencialogtmp " -// + " WHERE (EXISTS ( SELECT lareferencialogtmp.matomoid, lareferencialogtmp.source, lareferencialogtmp.id_visit," -// + "lareferencialogtmp.action, lareferencialogtmp.\"timestamp\", lareferencialogtmp.entity_id " -// + "FROM lareferencialogtmp " -// + "WHERE lareferencialogtmp.matomoid=new.matomoid AND lareferencialogtmp.source = new.source AND lareferencialogtmp.id_visit = new.id_visit AND lareferencialogtmp.action = new.action AND lareferencialogtmp.entity_id = new.entity_id AND lareferencialogtmp.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; -// stmt.executeUpdate(sqlCreateTmpTableLaReferenciaLog); -// stmt.executeUpdate(sqlcreateTmpRuleLaReferenciaLog); -// -// stmt.close(); -// log.info("Lareferencia Tmp Tables Created"); -// -// } catch (Exception e) { -// log.error("Failed to create tmptables: " + e); -// throw new Exception("Failed to create tmp tables: " + e.toString(), e); -// // System.exit(0); -// } -// } - public void processLogs() throws Exception { try { logger.info("Processing LaReferencia repository logs"); @@ -116,16 +83,7 @@ public class LaReferenciaStats { removeDoubleClicks(); logger.info("LaReferencia removed double clicks"); -/******** - logger.info("LaReferencia creating viewsStats"); - viewsStats(); - logger.info("LaReferencia created viewsStats"); - logger.info("LaReferencia creating downloadsStats"); - downloadsStats(); - logger.info("LaReferencia created downloadsStats"); - -************/ - logger.info("LaReferencia updating Production Tables"); + logger.info("LaReferencia updating Production Tables"); updateProdTables(); logger.info("LaReferencia updated Production Tables"); @@ -255,88 +213,6 @@ public class LaReferenciaStats { // conn.close(); } - public void viewsStats() throws Exception { - - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Creating la_result_views_monthly_tmp view"); - String sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + ".la_result_views_monthly_tmp AS " - + - "SELECT entity_id AS id, COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' " + - "THEN 1 ELSE 0 END) AS openaire_referrer, " + - "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp where action='action' and " + - "(source_item_type='oaItem' or source_item_type='repItem') " + - "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), " + - "source ORDER BY source, entity_id"; - stmt.executeUpdate(sql); - logger.info("Created la_result_views_monthly_tmp view"); - - logger.info("Dropping la_views_stats_tmp table"); - sql = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".la_views_stats_tmp"; - stmt.executeUpdate(sql); - logger.info("Dropped la_views_stats_tmp table"); - - logger.info("Creating la_views_stats_tmp table"); - sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".la_views_stats_tmp " + - "AS SELECT 'LaReferencia' as source, d.id as repository_id, ro.id as result_id, month as date, " + - "max(views) AS count, max(openaire_referrer) AS openaire " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_result_views_monthly_tmp p, " + - ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + - "WHERE p.source=d.oid AND p.id=ro.oid " + - "GROUP BY d.id, ro.id, month " + - "ORDER BY d.id, ro.id, month"; - stmt.executeUpdate(sql); - logger.info("Created la_views_stats_tmp table"); - - stmt.close(); - ConnectDB.getHiveConnection().close(); - } - - private void downloadsStats() throws Exception { - - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Creating la_result_downloads_monthly_tmp view"); - String sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() - + ".la_result_downloads_monthly_tmp AS " + - "SELECT entity_id AS id, COUNT(entity_id) as downloads, SUM(CASE WHEN referrer_name LIKE '%openaire%' " + - "THEN 1 ELSE 0 END) AS openaire_referrer, " + - "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp where action='download' and " + - "(source_item_type='oaItem' or source_item_type='repItem') " + - "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), " + - "source ORDER BY source, entity_id"; - stmt.executeUpdate(sql); - logger.info("Created la_result_downloads_monthly_tmp view"); - - logger.info("Dropping la_downloads_stats_tmp table"); - sql = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".la_downloads_stats_tmp"; - stmt.executeUpdate(sql); - logger.info("Dropped la_downloads_stats_tmp table"); - - logger.info("Creating la_downloads_stats_tmp table"); - sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".la_downloads_stats_tmp " + - "AS SELECT 'LaReferencia' as source, d.id as repository_id, ro.id as result_id, month as date, " + - "max(downloads) AS count, max(openaire_referrer) AS openaire " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_result_downloads_monthly_tmp p, " + - ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + - "WHERE p.source=d.oid AND p.id=ro.oid " + - "GROUP BY d.id, ro.id, month " + - "ORDER BY d.id, ro.id, month"; - stmt.executeUpdate(sql); - logger.info("Created la_downloads_stats_tmp table"); - - stmt.close(); - ConnectDB.getHiveConnection().close(); - } - private void updateProdTables() throws SQLException, Exception { Statement stmt = ConnectDB.getHiveConnection().createStatement(); @@ -346,40 +222,11 @@ public class LaReferenciaStats { String sql = "insert into " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog " + "select * from " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp"; stmt.executeUpdate(sql); -/***** - logger.info("Updating views_stats"); - sql = "insert into " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + - "select * from " + ConnectDB.getUsageStatsDBSchema() + ".la_views_stats_tmp"; - stmt.executeUpdate(sql); -// sql = "insert into public.views_stats select * from la_views_stats_tmp;"; -// stmt.executeUpdate(sql); - - logger.info("Updating downloads_stats"); - sql = "insert into " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + - "select * from " + ConnectDB.getUsageStatsDBSchema() + ".la_downloads_stats_tmp"; - stmt.executeUpdate(sql); - - logger.info("Inserting data to usage_stats from lareferencia"); - sql = "INSERT INTO "+ConnectDB.getUsageStatsDBSchema() + ".usage_stats " + - "SELECT coalesce(ds.source, vs.source) as source, " + - "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + - "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + - "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + - "coalesce(ds.openaire, 0) as openaire_downloads, " + - "coalesce(vs.openaire, 0) as openaire_views " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_downloads_stats_tmp AS ds FULL OUTER JOIN " + - ConnectDB.getUsageStatsDBSchema() + ".la_views_stats_tmp AS vs ON ds.source=vs.source " + - "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; - stmt.executeUpdate(sql); - logger.info("Inserted data to usage_stats from lareferencia"); -// sql = "insert into public.downloads_stats select * from la_downloads_stats_tmp;"; -// stmt.executeUpdate(sql); -****/ logger.info("Dropping lareferencialogtmp"); sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp"; - logger.info("Dropped lareferencialogtmp"); - stmt.executeUpdate(sql); + logger.info("Dropped lareferencialogtmp"); + stmt.executeUpdate(sql); stmt.close(); ConnectDB.getHiveConnection().close(); diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java index 5cc9ec563..a84d6743f 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikDownloadLogs.java @@ -1,9 +1,12 @@ + package eu.dnetlib.oa.graph.usagerawdata.export; import java.io.*; import java.net.Authenticator; import java.net.URL; import java.net.URLConnection; +import java.nio.file.Files; +import java.nio.file.Paths; import java.sql.PreparedStatement; import java.sql.ResultSet; import java.sql.Statement; @@ -30,299 +33,299 @@ import org.slf4j.LoggerFactory; */ public class PiwikDownloadLogs { - private final String piwikUrl; - private Date startDate; - private final String tokenAuth; + private final String piwikUrl; + private Date startDate; + private final String tokenAuth; - /* + /* * The Piwik's API method - */ - private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; - private final String format = "&format=json"; + */ + private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; + private final String format = "&format=json"; - private static final Logger logger = LoggerFactory.getLogger(PiwikDownloadLogs.class); + private static final Logger logger = LoggerFactory.getLogger(PiwikDownloadLogs.class); - public PiwikDownloadLogs(String piwikUrl, String tokenAuth) { - this.piwikUrl = piwikUrl; - this.tokenAuth = tokenAuth; + public PiwikDownloadLogs(String piwikUrl, String tokenAuth) { + this.piwikUrl = piwikUrl; + this.tokenAuth = tokenAuth; - } + } - private String getPiwikLogUrl() { - return "https://" + piwikUrl + "/"; - } + private String getPiwikLogUrl() { + return "https://" + piwikUrl + "/"; + } - private String getJson(String url) throws Exception { - try { - logger.debug("Connecting to download the JSON: " + url); - URL website = new URL(url); - URLConnection connection = website.openConnection(); + private String getJson(String url) throws Exception { + try { + logger.debug("Connecting to download the JSON: " + url); + URL website = new URL(url); + URLConnection connection = website.openConnection(); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); - } - } - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL: " + url + " Exception: " + e); - throw new Exception("Failed to get URL: " + url + " Exception: " + e.toString(), e); - } - } + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + } + } + return response.toString(); + } catch (Exception e) { + logger.error("Failed to get URL: " + url + " Exception: " + e); + throw new Exception("Failed to get URL: " + url + " Exception: " + e.toString(), e); + } + } - class WorkerThread implements Runnable { + class WorkerThread implements Runnable { - private Calendar currDay; - private int siteId; - private String repoLogsPath; - private String portalLogPath; - private String portalMatomoID; + private Calendar currDay; + private int siteId; + private String repoLogsPath; + private String portalLogPath; + private String portalMatomoID; - public WorkerThread(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, - String portalMatomoID) throws IOException { - this.currDay = (Calendar) currDay.clone(); - this.siteId = new Integer(siteId); - this.repoLogsPath = new String(repoLogsPath); - this.portalLogPath = new String(portalLogPath); - this.portalMatomoID = new String(portalMatomoID); - } + public WorkerThread(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws IOException { + this.currDay = (Calendar) currDay.clone(); + this.siteId = new Integer(siteId); + this.repoLogsPath = new String(repoLogsPath); + this.portalLogPath = new String(portalLogPath); + this.portalMatomoID = new String(portalMatomoID); + } - public void run() { - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - System.out - .println( - Thread.currentThread().getName() + " (Start) Thread for " - + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId - + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath - + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); - try { - GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + public void run() { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + System.out + .println( + Thread.currentThread().getName() + " (Start) Thread for " + + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); + try { + GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); - } catch (Exception e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - System.out - .println( - Thread.currentThread().getName() + " (End) Thread for " - + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId - + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath - + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); - } + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + System.out + .println( + Thread.currentThread().getName() + " (End) Thread for " + + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId + + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath + + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); + } - public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, - String portalMatomoID) throws Exception { - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - Date date = currDay.getTime(); - logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + Date date = currDay.getTime(); + logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); - String period = "&period=day&date=" + sdf.format(date); - String outFolder = ""; - if (siteId == Integer.parseInt(portalMatomoID)) { - outFolder = portalLogPath; - } else { - outFolder = repoLogsPath; - } + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + if (siteId == Integer.parseInt(portalMatomoID)) { + outFolder = portalLogPath; + } else { + outFolder = repoLogsPath; + } - String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format - + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; - String content = ""; + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; - int i = 0; + int i = 0; - JSONParser parser = new JSONParser(); - StringBuffer totalContent = new StringBuffer(); - FileSystem fs = FileSystem.get(new Configuration()); + JSONParser parser = new JSONParser(); + StringBuffer totalContent = new StringBuffer(); + FileSystem fs = FileSystem.get(new Configuration()); - do { - int writtenBytes = 0; - String apiUrl = baseApiUrl; + do { + int writtenBytes = 0; + String apiUrl = baseApiUrl; - if (i > 0) { - apiUrl += "&filter_offset=" + (i * 1000); - } + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } - content = getJson(apiUrl); - if (content.length() == 0 || content.equals("[]")) { - break; - } + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } - FSDataOutputStream fin = fs - .create( - new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"), - true); - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRaw = (JSONObject) aJsonArray; - byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); - fin.write(jsonObjectRawBytes); - fin.writeChar('\n'); + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"), + true); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); - writtenBytes += jsonObjectRawBytes.length + 1; - } + writtenBytes += jsonObjectRawBytes.length + 1; + } - fin.close(); - System.out - .println( - Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes - + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"); + fin.close(); + System.out + .println( + Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes + + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"); - i++; - } while (true); + i++; + } while (true); - fs.close(); - } - } + fs.close(); + } + } - public void GetOpenAIRELogs(String repoLogsPath, String portalLogPath, String portalMatomoID) throws Exception { + public void GetOpenAIRELogs(String repoLogsPath, String portalLogPath, String portalMatomoID) throws Exception { - Statement statement = ConnectDB.getHiveConnection().createStatement(); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + Statement statement = ConnectDB.getHiveConnection().createStatement(); + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - ResultSet rs = statement - .executeQuery( - "SELECT distinct piwik_id from " + ConnectDB.getStatsDBSchema() - + ".datasource where piwik_id is not null and piwik_id <> 0 order by piwik_id"); + ResultSet rs = statement + .executeQuery( + "SELECT distinct piwik_id from " + ConnectDB.getStatsDBSchema() + + ".datasource where piwik_id is not null and piwik_id <> 0 order by piwik_id"); - // Getting all the piwikids in a list for logging reasons & limitting the list - // to the max number of piwikids - List piwikIdToVisit = new ArrayList(); - //while (rs.next()) - //piwikIdToVisit.add(rs.getInt(1)); - piwikIdToVisit.add(13); - piwikIdToVisit.add(109); - - logger.info("Found the following piwikIds for download: " + piwikIdToVisit); + // Getting all the piwikids in a list for logging reasons & limitting the list + // to the max number of piwikids + List piwikIdToVisit = new ArrayList(); + while (rs.next()) { + piwikIdToVisit.add(rs.getInt(1)); + } + logger.info("Found the following piwikIds for download: " + piwikIdToVisit); - if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 - && ExecuteWorkflow.numberOfPiwikIdsToDownload <= piwikIdToVisit.size()) { - logger.info("Trimming piwikIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); - piwikIdToVisit = piwikIdToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); - } + if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 + && ExecuteWorkflow.numberOfPiwikIdsToDownload <= piwikIdToVisit.size()) { + logger.info("Trimming piwikIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); + piwikIdToVisit = piwikIdToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); + } - logger.info("Downloading from repos with the followins piwikIds: " + piwikIdToVisit); + logger.info("Downloading from repos with the followins piwikIds: " + piwikIdToVisit); - // ExecutorService executor = Executors.newFixedThreadPool(ExecuteWorkflow.numberOfDownloadThreads); - for (int siteId : piwikIdToVisit) { - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("Starting period for log download: " + sdf.format(start.getTime())); + // ExecutorService executor = Executors.newFixedThreadPool(ExecuteWorkflow.numberOfDownloadThreads); + for (int siteId : piwikIdToVisit) { + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("Starting period for log download: " + sdf.format(start.getTime())); - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("Ending period for log download: " + sdf.format(end.getTime())); + // Setting the ending period (last day of the month) + // Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); + Calendar end = Calendar.getInstance(); + end.add(Calendar.DAY_OF_MONTH, -1); + // end.add(Calendar.MONTH, +1); +// end.add(Calendar.DAY_OF_MONTH, -1); + logger.info("Ending period for log download: " + sdf.format(end.getTime())); - logger.info("Now working on piwikId: " + siteId); + logger.info("Now working on piwikId: " + siteId); - PreparedStatement st = ConnectDB.DB_HIVE_CONNECTION - .prepareStatement( - "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() - + ".piwiklog WHERE source=?"); - st.setInt(1, siteId); - Date dateMax = null; - ResultSet rs_date = st.executeQuery(); - while (rs_date.next()) { - logger.info("Found max date: " + rs_date.getString(1) + " for repository " + siteId); + PreparedStatement st = ConnectDB.DB_HIVE_CONNECTION + .prepareStatement( + "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() + + ".piwiklog WHERE source=?"); + st.setInt(1, siteId); + Date dateMax = null; + ResultSet rs_date = st.executeQuery(); + while (rs_date.next()) { + logger.info("Found max date: " + rs_date.getString(1) + " for repository " + siteId); - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - dateMax = sdf.parse(rs_date.getString(1)); - } - } - rs_date.close(); + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); - for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { - // logger.info("Date used " + currDay.toString()); - // Runnable worker = new WorkerThread(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); - // executor.execute(worker);// calling execute method of ExecutorService - logger.info("Date used " + currDay.getTime().toString()); + for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { + // logger.info("Date used " + currDay.toString()); + // Runnable worker = new WorkerThread(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + // executor.execute(worker);// calling execute method of ExecutorService + logger.info("Date used " + currDay.getTime().toString()); - if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { - logger.info("Date found in logs " + dateMax + " and not downloanding Matomo logs for " + siteId); - } else { - GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); - } + if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding Matomo logs for " + siteId); + } else { + GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); + } - } - } - // executor.shutdown(); - // while (!executor.isTerminated()) { - // } - // System.out.println("Finished all threads"); - } + } + } + // executor.shutdown(); + // while (!executor.isTerminated()) { + // } + // System.out.println("Finished all threads"); + } - public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, - String portalMatomoID) throws Exception { - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, + String portalMatomoID) throws Exception { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - Date date = currDay.getTime(); - logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); + Date date = currDay.getTime(); + logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); - String period = "&period=day&date=" + sdf.format(date); - String outFolder = ""; - if (siteId == Integer.parseInt(portalMatomoID)) { - outFolder = portalLogPath; - } else { - outFolder = repoLogsPath; - } + String period = "&period=day&date=" + sdf.format(date); + String outFolder = ""; + if (siteId == Integer.parseInt(portalMatomoID)) { + outFolder = portalLogPath; + } else { + outFolder = repoLogsPath; + } - String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format - + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; - String content = ""; + String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format + + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; + String content = ""; - int i = 0; + int i = 0; - JSONParser parser = new JSONParser(); - StringBuffer totalContent = new StringBuffer(); - FileSystem fs = FileSystem.get(new Configuration()); + JSONParser parser = new JSONParser(); + StringBuffer totalContent = new StringBuffer(); + FileSystem fs = FileSystem.get(new Configuration()); - do { - int writtenBytes = 0; - String apiUrl = baseApiUrl; + do { + int writtenBytes = 0; + String apiUrl = baseApiUrl; - if (i > 0) { - apiUrl += "&filter_offset=" + (i * 1000); - } + if (i > 0) { + apiUrl += "&filter_offset=" + (i * 1000); + } - content = getJson(apiUrl); - if (content.length() == 0 || content.equals("[]")) { - break; - } + content = getJson(apiUrl); + if (content.length() == 0 || content.equals("[]")) { + break; + } - FSDataOutputStream fin = fs - .create( - new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"), - true); - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRaw = (JSONObject) aJsonArray; - byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); - fin.write(jsonObjectRawBytes); - fin.writeChar('\n'); + FSDataOutputStream fin = fs + .create( + new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"), + true); + JSONArray jsonArray = (JSONArray) parser.parse(content); + for (Object aJsonArray : jsonArray) { + JSONObject jsonObjectRaw = (JSONObject) aJsonArray; + byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); + fin.write(jsonObjectRawBytes); + fin.writeChar('\n'); - writtenBytes += jsonObjectRawBytes.length + 1; - } + writtenBytes += jsonObjectRawBytes.length + 1; + } - fin.close(); - System.out - .println( - Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes - + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"); + fin.close(); + System.out + .println( + Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes + + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i + + ".json"); - i++; - } while (true); + i++; + } while (true); - fs.close(); - } + fs.close(); + } } diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java index 4903d9599..9144620b7 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/PiwikStatsDB.java @@ -60,7 +60,7 @@ public class PiwikStatsDB { this.createTables(); // The piwiklog table is not needed since it is built // on top of JSON files - ////////////this.createTmpTables(); + //////////// this.createTmpTables(); } public ArrayList getRobotsList() { @@ -86,6 +86,7 @@ public class PiwikStatsDB { logger.info("Dropping usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + " CASCADE"; stmt.executeUpdate(dropDatabase); + } catch (Exception e) { logger.error("Failed to drop database: " + e); throw new Exception("Failed to drop database: " + e.toString(), e); @@ -117,10 +118,15 @@ public class PiwikStatsDB { + "into 100 buckets stored as orc tblproperties('transactional'='true')"; stmt.executeUpdate(sqlCreateTablePiwikLog); +// String dropT = "TRUNCATE TABLE " +// + ConnectDB.getUsageStatsDBSchema() +// + ".piwiklog "; +// stmt.executeUpdate(dropT); +// logger.info("truncated piwiklog"); + ///////////////////////////////////////// // Rule for duplicate inserts @ piwiklog ///////////////////////////////////////// - String sqlCreateTablePortalLog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log(source INT, id_visit STRING, country STRING, action STRING, url STRING, " @@ -131,7 +137,6 @@ public class PiwikStatsDB { ////////////////////////////////////////////////// // Rule for duplicate inserts @ process_portal_log ////////////////////////////////////////////////// - stmt.close(); ConnectDB.getHiveConnection().close(); @@ -141,47 +146,6 @@ public class PiwikStatsDB { } } -/***** public void createTmpTables() throws Exception { - try { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - String sqlCreateTmpTablePiwikLog = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".piwiklogtmp(source INT, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " - + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " - + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " - + "stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTmpTablePiwikLog); - - ////////////////////////////////////////////////// - // Rule for duplicate inserts @ piwiklogtmp - ////////////////////////////////////////////////// - - ////////////////////////////////////////////////// - // Copy from public.piwiklog to piwiklog - ////////////////////////////////////////////////// - // String sqlCopyPublicPiwiklog="insert into piwiklog select * from public.piwiklog;"; - // stmt.executeUpdate(sqlCopyPublicPiwiklog); - - String sqlCreateTmpTablePortalLog = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".process_portal_log_tmp(source INT, id_visit STRING, country STRING, action STRING, url STRING, " - + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " - + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTmpTablePortalLog); - - ////////////////////////////////////////////////// - // Rule for duplicate inserts @ process_portal_log_tmp - ////////////////////////////////////////////////// - - stmt.close(); - - } catch (Exception e) { - logger.error("Failed to create tmptables: " + e); - throw new Exception("Failed to create tmp tables: " + e.toString(), e); - // System.exit(0); - } - } -******/ public void processLogs() throws Exception { try { ReadCounterRobotsList counterRobots = new ReadCounterRobotsList(this.getCounterRobotsURL()); @@ -203,23 +167,17 @@ public class PiwikStatsDB { processPortalLog(); logger.info("Portal logs process done"); - logger.info("Processing portal usagestats"); - portalStats(); + logger.info("Processing portal usagestats"); + portalLogs(); logger.info("Portal usagestats process done"); -/***** - logger.info("ViewsStats processing starts"); - viewsStats(); - logger.info("ViewsStats processing ends"); - - logger.info("DownloadsStats processing starts"); - downloadsStats(); - logger.info("DownloadsStats processing starts"); -*****/ logger.info("Updating Production Tables"); updateProdTables(); logger.info("Updated Production Tables"); + logger.info("Create Pedocs Tables"); + createPedocsOldUsageData(); + logger.info("Pedocs Tables Created"); } catch (Exception e) { logger.error("Failed to process logs: " + e); @@ -237,65 +195,65 @@ public class PiwikStatsDB { logger.info("Added JSON Serde jar"); logger.info("Dropping piwiklogtmp_json table"); - String drop_piwiklogtmp_json = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".piwiklogtmp_json"; + String drop_piwiklogtmp_json = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp_json"; stmt.executeUpdate(drop_piwiklogtmp_json); logger.info("Dropped piwiklogtmp_json table"); logger.info("Creating piwiklogtmp_json"); - String create_piwiklogtmp_json = "CREATE EXTERNAL TABLE IF NOT EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".piwiklogtmp_json(\n" + - " `idSite` STRING,\n" + - " `idVisit` STRING,\n" + - " `country` STRING,\n" + - " `referrerName` STRING,\n" + - " `browser` STRING,\n" + - " `actionDetails` ARRAY<\n" + - " struct<\n" + - " type: STRING,\n" + - " url: STRING,\n" + - " `customVariables`: struct<\n" + - " `1`: struct<\n" + - " `customVariablePageValue1`: STRING\n" + - " >\n" + - " >,\n" + - " timestamp: String\n" + - " >\n" + - " >\n" + - ")\n" + - "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + - "LOCATION '" + ExecuteWorkflow.repoLogPath + "'\n" + - "TBLPROPERTIES (\"transactional\"=\"false\")"; + String create_piwiklogtmp_json = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp_json(\n" + + " `idSite` STRING,\n" + + " `idVisit` STRING,\n" + + " `country` STRING,\n" + + " `referrerName` STRING,\n" + + " `browser` STRING,\n" + + " `actionDetails` ARRAY<\n" + + " struct<\n" + + " type: STRING,\n" + + " url: STRING,\n" + + " `customVariables`: struct<\n" + + " `1`: struct<\n" + + " `customVariablePageValue1`: STRING\n" + + " >\n" + + " >,\n" + + " timestamp: String\n" + + " >\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.repoLogPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; stmt.executeUpdate(create_piwiklogtmp_json); logger.info("Created piwiklogtmp_json"); logger.info("Dropping piwiklogtmp table"); - String drop_piwiklogtmp = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".piwiklogtmp"; + String drop_piwiklogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp"; stmt.executeUpdate(drop_piwiklogtmp); logger.info("Dropped piwiklogtmp"); logger.info("Creating piwiklogtmp"); - String create_piwiklogtmp = "CREATE TABLE " + - ConnectDB.getUsageStatsDBSchema() + - ".piwiklogtmp (source BIGINT, id_Visit STRING, country STRING, action STRING, url STRING, " + - "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + - "clustered by (source) into 100 buckets stored as orc tblproperties('transactional'='true')"; + String create_piwiklogtmp = "CREATE TABLE " + + ConnectDB.getUsageStatsDBSchema() + + ".piwiklogtmp (source BIGINT, id_Visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source) into 100 buckets stored as orc tblproperties('transactional'='true')"; stmt.executeUpdate(create_piwiklogtmp); logger.info("Created piwiklogtmp"); logger.info("Inserting into piwiklogtmp"); - String insert_piwiklogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, " + - "actiondetail.type as action, actiondetail.url as url, " + - "actiondetail.customVariables.`1`.`customVariablePageValue1` as entity_id, " + - "'repItem' as source_item_type, from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, " + - "referrerName as referrer_name, browser as agent\n" + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp_json\n" + - "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; + String insert_piwiklogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, " + + "actiondetail.type as action, actiondetail.url as url, " + + "actiondetail.customVariables.`1`.`customVariablePageValue1` as entity_id, " + + "'repItem' as source_item_type, from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, " + + "referrerName as referrer_name, browser as agent\n" + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp_json\n" + + "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; stmt.executeUpdate(insert_piwiklogtmp); logger.info("Inserted into piwiklogtmp"); @@ -308,33 +266,31 @@ public class PiwikStatsDB { logger.info("Cleaning download double clicks"); // clean download double clicks - String sql = "DELETE from " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "WHERE EXISTS (\n" + - "SELECT DISTINCT p1.source, p1.id_visit, p1.action, p1.entity_id, p1.timestamp \n" + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p1, " + - ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p2\n" + - "WHERE p1.source=p2.source AND p1.id_visit=p2.id_visit AND p1.entity_id=p2.entity_id \n" - + - "AND p1.action=p2.action AND p1.action='download' AND p1.timestamp!=p2.timestamp \n" + - "AND p1.timestamp\n" + - " >\n" + - ")\n" + - "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + - "LOCATION '" + ExecuteWorkflow.portalLogPath + "'\n" + - "TBLPROPERTIES (\"transactional\"=\"false\")"; + String create_process_portal_log_tmp_json = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp_json(" + + " `idSite` STRING,\n" + + " `idVisit` STRING,\n" + + " `country` STRING,\n" + + " `referrerName` STRING,\n" + + " `browser` STRING,\n" + + " `actionDetails` ARRAY<\n" + + " struct<\n" + + " type: STRING,\n" + + " url: STRING,\n" + + " timestamp: String\n" + + " >\n" + + " >\n" + + ")\n" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + ExecuteWorkflow.portalLogPath + "'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; stmt.executeUpdate(create_process_portal_log_tmp_json); logger.info("Created process_portal_log_tmp_json"); logger.info("Droping process_portal_log_tmp table"); - String drop_process_portal_log_tmp = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".process_portal_log_tmp"; + String drop_process_portal_log_tmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp"; stmt.executeUpdate(drop_process_portal_log_tmp); logger.info("Dropped process_portal_log_tmp"); logger.info("Creating process_portal_log_tmp"); - String create_process_portal_log_tmp = "CREATE TABLE " + - ConnectDB.getUsageStatsDBSchema() + - ".process_portal_log_tmp (source BIGINT, id_visit STRING, country STRING, action STRING, url STRING, " + - "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + - "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; + String create_process_portal_log_tmp = "CREATE TABLE " + + ConnectDB.getUsageStatsDBSchema() + + ".process_portal_log_tmp (source BIGINT, id_visit STRING, country STRING, action STRING, url STRING, " + + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; stmt.executeUpdate(create_process_portal_log_tmp); logger.info("Created process_portal_log_tmp"); logger.info("Inserting into process_portal_log_tmp"); String insert_process_portal_log_tmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() - + ".process_portal_log_tmp " + - "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, actiondetail.type as action, " - + - "actiondetail.url as url, " + - "CASE\n" + - " WHEN (actiondetail.url like '%datasourceId=%') THEN split(actiondetail.url,'datasourceId=')[1] " + - " WHEN (actiondetail.url like '%datasource=%') THEN split(actiondetail.url,'datasource=')[1] " + - " WHEN (actiondetail.url like '%datasourceFilter=%') THEN split(actiondetail.url,'datasourceFilter=')[1] " - + - " WHEN (actiondetail.url like '%articleId=%') THEN split(actiondetail.url,'articleId=')[1] " + - " WHEN (actiondetail.url like '%datasetId=%') THEN split(actiondetail.url,'datasetId=')[1] " + - " WHEN (actiondetail.url like '%projectId=%') THEN split(actiondetail.url,'projectId=')[1] " + - " WHEN (actiondetail.url like '%organizationId=%') THEN split(actiondetail.url,'organizationId=')[1] " + - " ELSE '' " + - "END AS entity_id, " + - "CASE " + - " WHEN (actiondetail.url like '%datasourceId=%') THEN 'datasource' " + - " WHEN (actiondetail.url like '%datasource=%') THEN 'datasource' " + - " WHEN (actiondetail.url like '%datasourceFilter=%') THEN 'datasource' " + - " WHEN (actiondetail.url like '%articleId=%') THEN 'result' " + - " WHEN (actiondetail.url like '%datasetId=%') THEN 'result' " + - " WHEN (actiondetail.url like '%projectId=%') THEN 'project' " + - " WHEN (actiondetail.url like '%organizationId=%') THEN 'organization' " + - " ELSE '' " + - "END AS source_item_type, " + - "from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, referrerName as referrer_name, " + - "browser as agent " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp_json " + - "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; + + ".process_portal_log_tmp " + + "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, actiondetail.type as action, " + + "actiondetail.url as url, " + + "CASE\n" + + " WHEN (actiondetail.url like '%datasourceId=%') THEN split(actiondetail.url,'datasourceId=')[1] " + + " WHEN (actiondetail.url like '%datasource=%') THEN split(actiondetail.url,'datasource=')[1] " + + " WHEN (actiondetail.url like '%datasourceFilter=%') THEN split(actiondetail.url,'datasourceFilter=')[1] " + + " WHEN (actiondetail.url like '%articleId=%') THEN split(actiondetail.url,'articleId=')[1] " + + " WHEN (actiondetail.url like '%datasetId=%') THEN split(actiondetail.url,'datasetId=')[1] " + + " WHEN (actiondetail.url like '%projectId=%') THEN split(actiondetail.url,'projectId=')[1] " + + " WHEN (actiondetail.url like '%organizationId=%') THEN split(actiondetail.url,'organizationId=')[1] " + + " ELSE '' " + + "END AS entity_id, " + + "CASE " + + " WHEN (actiondetail.url like '%datasourceId=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%datasource=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%datasourceFilter=%') THEN 'datasource' " + + " WHEN (actiondetail.url like '%articleId=%') THEN 'result' " + + " WHEN (actiondetail.url like '%datasetId=%') THEN 'result' " + + " WHEN (actiondetail.url like '%projectId=%') THEN 'project' " + + " WHEN (actiondetail.url like '%organizationId=%') THEN 'organization' " + + " ELSE '' " + + "END AS source_item_type, " + + "from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, referrerName as referrer_name, " + + "browser as agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp_json " + + "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; stmt.executeUpdate(insert_process_portal_log_tmp); logger.info("Inserted into process_portal_log_tmp"); stmt.close(); } - public void portalStats() throws SQLException { + public void portalLogs() throws SQLException { Connection con = ConnectDB.getHiveConnection(); Statement stmt = con.createStatement(); con.setAutoCommit(false); -// Original queries where of the style -// -// SELECT DISTINCT source, id_visit, country, action, url, roid.oid, 'oaItem', `timestamp`, referrer_name, agent -// FROM usagestats_20200907.process_portal_log_tmp2, -// openaire_prod_stats_20200821.result_oids roid -// WHERE entity_id IS NOT null AND entity_id=roid.oid AND roid.oid IS NOT null -// -// The following query is an example of how queries should be -// -// -// INSERT INTO usagestats_20200907.piwiklogtmp -// SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent -// FROM usagestats_20200907.process_portal_log_tmp -// WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id -// IN (SELECT roid.oid FROM openaire_prod_stats_20200821.result_oids roid WHERE roid.oid IS NOT NULL); -// -// We should consider if we would like the queries to be as the following -// -// INSERT INTO usagestats_20200907.piwiklogtmp -// SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent -// FROM usagestats_20200907.process_portal_log_tmp -// WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id != '' AND process_portal_log_tmp.entity_id -// IN (SELECT roid.oid FROM openaire_prod_stats_20200821.result_oids roid WHERE roid.oid IS NOT NULL AND -// roid.oid != ''); - logger.info("PortalStats - Step 1"); - String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent " - + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + - "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + - "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + ".result_oids roid WHERE roid.id IS NOT NULL)"; stmt.executeUpdate(sql); stmt.close(); logger.info("PortalStats - Step 2"); stmt = con.createStatement(); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'datasource', `timestamp`, referrer_name, agent " - + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + - "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + - "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'datasource', `timestamp`, referrer_name, agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + ".datasource_oids roid WHERE roid.id IS NOT NULL)"; stmt.executeUpdate(sql); stmt.close(); @@ -494,12 +421,11 @@ public class PiwikStatsDB { */ logger.info("PortalStats - Step 3"); stmt = con.createStatement(); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'project', `timestamp`, referrer_name, agent " - + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + - "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + - "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'project', `timestamp`, referrer_name, agent " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + + "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + + "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + ".project_oids roid WHERE roid.id IS NOT NULL)"; stmt.executeUpdate(sql); stmt.close(); @@ -512,233 +438,233 @@ public class PiwikStatsDB { logger.info("Cleaning oai - Step 1"); stmt = ConnectDB.getHiveConnection().createStatement(); - String sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chlc.min-saude.pt/'," + - "'oai:repositorio.chlc.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.chlc.min-saude.pt/%'"; + String sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chlc.min-saude.pt/'," + + "'oai:repositorio.chlc.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.chlc.min-saude.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 2"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hospitaldebraga.pt/'," + - "'oai:repositorio.hospitaldebraga.pt:') WHERE entity_id LIKE 'oai:repositorio.hospitaldebraga.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hospitaldebraga.pt/'," + + "'oai:repositorio.hospitaldebraga.pt:') WHERE entity_id LIKE 'oai:repositorio.hospitaldebraga.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 3"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipl.pt/'," + - "'oai:repositorio.ipl.pt:') WHERE entity_id LIKE 'oai:repositorio.ipl.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipl.pt/'," + + "'oai:repositorio.ipl.pt:') WHERE entity_id LIKE 'oai:repositorio.ipl.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 4"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:bibliotecadigital.ipb.pt/'," + - "'oai:bibliotecadigital.ipb.pt:') WHERE entity_id LIKE 'oai:bibliotecadigital.ipb.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:bibliotecadigital.ipb.pt/'," + + "'oai:bibliotecadigital.ipb.pt:') WHERE entity_id LIKE 'oai:bibliotecadigital.ipb.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 5"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ismai.pt/'," + - "'oai:repositorio.ismai.pt:') WHERE entity_id LIKE 'oai:repositorio.ismai.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ismai.pt/'," + + "'oai:repositorio.ismai.pt:') WHERE entity_id LIKE 'oai:repositorio.ismai.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 6"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorioaberto.uab.pt/'," + - "'oai:repositorioaberto.uab.pt:') WHERE entity_id LIKE 'oai:repositorioaberto.uab.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorioaberto.uab.pt/'," + + "'oai:repositorioaberto.uab.pt:') WHERE entity_id LIKE 'oai:repositorioaberto.uab.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 7"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.uac.pt/'," + - "'oai:repositorio.uac.pt:') WHERE entity_id LIKE 'oai:repositorio.uac.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.uac.pt/'," + + "'oai:repositorio.uac.pt:') WHERE entity_id LIKE 'oai:repositorio.uac.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 8"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.insa.pt/'," + - "'oai:repositorio.insa.pt:') WHERE entity_id LIKE 'oai:repositorio.insa.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.insa.pt/'," + + "'oai:repositorio.insa.pt:') WHERE entity_id LIKE 'oai:repositorio.insa.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 9"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipcb.pt/'," + - "'oai:repositorio.ipcb.pt:') WHERE entity_id LIKE 'oai:repositorio.ipcb.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipcb.pt/'," + + "'oai:repositorio.ipcb.pt:') WHERE entity_id LIKE 'oai:repositorio.ipcb.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 10"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ispa.pt/'," + - "'oai:repositorio.ispa.pt:') WHERE entity_id LIKE 'oai:repositorio.ispa.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ispa.pt/'," + + "'oai:repositorio.ispa.pt:') WHERE entity_id LIKE 'oai:repositorio.ispa.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 11"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chporto.pt/'," + - "'oai:repositorio.chporto.pt:') WHERE entity_id LIKE 'oai:repositorio.chporto.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chporto.pt/'," + + "'oai:repositorio.chporto.pt:') WHERE entity_id LIKE 'oai:repositorio.chporto.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 12"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ucp.pt/'," + - "'oai:repositorio.ucp.pt:') WHERE entity_id LIKE 'oai:repositorio.ucp.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ucp.pt/'," + + "'oai:repositorio.ucp.pt:') WHERE entity_id LIKE 'oai:repositorio.ucp.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 13"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:rihuc.huc.min-saude.pt/'," + - "'oai:rihuc.huc.min-saude.pt:') WHERE entity_id LIKE 'oai:rihuc.huc.min-saude.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:rihuc.huc.min-saude.pt/'," + + "'oai:rihuc.huc.min-saude.pt:') WHERE entity_id LIKE 'oai:rihuc.huc.min-saude.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 14"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipv.pt/'," + - "'oai:repositorio.ipv.pt:') WHERE entity_id LIKE 'oai:repositorio.ipv.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipv.pt/'," + + "'oai:repositorio.ipv.pt:') WHERE entity_id LIKE 'oai:repositorio.ipv.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 15"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:www.repository.utl.pt/'," + - "'oai:www.repository.utl.pt:') WHERE entity_id LIKE 'oai:www.repository.utl.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:www.repository.utl.pt/'," + + "'oai:www.repository.utl.pt:') WHERE entity_id LIKE 'oai:www.repository.utl.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 16"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:run.unl.pt/'," + - "'oai:run.unl.pt:') WHERE entity_id LIKE 'oai:run.unl.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:run.unl.pt/'," + + "'oai:run.unl.pt:') WHERE entity_id LIKE 'oai:run.unl.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 17"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:sapientia.ualg.pt/'," + - "'oai:sapientia.ualg.pt:') WHERE entity_id LIKE 'oai:sapientia.ualg.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:sapientia.ualg.pt/'," + + "'oai:sapientia.ualg.pt:') WHERE entity_id LIKE 'oai:sapientia.ualg.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 18"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipsantarem.pt/'," + - "'oai:repositorio.ipsantarem.pt:') WHERE entity_id LIKE 'oai:repositorio.ipsantarem.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipsantarem.pt/'," + + "'oai:repositorio.ipsantarem.pt:') WHERE entity_id LIKE 'oai:repositorio.ipsantarem.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 19"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:arca.igc.gulbenkian.pt/'," + - "'oai:arca.igc.gulbenkian.pt:') WHERE entity_id LIKE 'oai:arca.igc.gulbenkian.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:arca.igc.gulbenkian.pt/'," + + "'oai:arca.igc.gulbenkian.pt:') WHERE entity_id LIKE 'oai:arca.igc.gulbenkian.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 20"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:ubibliorum.ubi.pt/'," + - "'oai:ubibliorum.ubi.pt:') WHERE entity_id LIKE 'oai:ubibliorum.ubi.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:ubibliorum.ubi.pt/'," + + "'oai:ubibliorum.ubi.pt:') WHERE entity_id LIKE 'oai:ubibliorum.ubi.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 21"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:digituma.uma.pt/'," + - "'oai:digituma.uma.pt:') WHERE entity_id LIKE 'oai:digituma.uma.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:digituma.uma.pt/'," + + "'oai:digituma.uma.pt:') WHERE entity_id LIKE 'oai:digituma.uma.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 22"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ul.pt/'," + - "'oai:repositorio.ul.pt:') WHERE entity_id LIKE 'oai:repositorio.ul.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ul.pt/'," + + "'oai:repositorio.ul.pt:') WHERE entity_id LIKE 'oai:repositorio.ul.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 23"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hff.min-saude.pt/'," + - "'oai:repositorio.hff.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.hff.min-saude.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hff.min-saude.pt/'," + + "'oai:repositorio.hff.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.hff.min-saude.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 24"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorium.sdum.uminho.pt/'," + - "'oai:repositorium.sdum.uminho.pt:') WHERE entity_id LIKE 'oai:repositorium.sdum.uminho.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorium.sdum.uminho.pt/'," + + "'oai:repositorium.sdum.uminho.pt:') WHERE entity_id LIKE 'oai:repositorium.sdum.uminho.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 25"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:recipp.ipp.pt/'," + - "'oai:recipp.ipp.pt:') WHERE entity_id LIKE 'oai:recipp.ipp.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:recipp.ipp.pt/'," + + "'oai:recipp.ipp.pt:') WHERE entity_id LIKE 'oai:recipp.ipp.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 26"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:bdigital.ufp.pt/'," + - "'oai:bdigital.ufp.pt:') WHERE entity_id LIKE 'oai:bdigital.ufp.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:bdigital.ufp.pt/'," + + "'oai:bdigital.ufp.pt:') WHERE entity_id LIKE 'oai:bdigital.ufp.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 27"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.lneg.pt/'," + - "'oai:repositorio.lneg.pt:') WHERE entity_id LIKE 'oai:repositorio.lneg.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.lneg.pt/'," + + "'oai:repositorio.lneg.pt:') WHERE entity_id LIKE 'oai:repositorio.lneg.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 28"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:iconline.ipleiria.pt/'," + - "'oai:iconline.ipleiria.pt:') WHERE entity_id LIKE 'oai:iconline.ipleiria.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:iconline.ipleiria.pt/'," + + "'oai:iconline.ipleiria.pt:') WHERE entity_id LIKE 'oai:iconline.ipleiria.pt/%'"; stmt.executeUpdate(sql); stmt.close(); logger.info("Cleaning oai - Step 29"); stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:comum.rcaap.pt/'," + - "'oai:comum.rcaap.pt:') WHERE entity_id LIKE 'oai:comum.rcaap.pt/%'"; + sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + + "SET entity_id = regexp_replace(entity_id, '^oai:comum.rcaap.pt/'," + + "'oai:comum.rcaap.pt:') WHERE entity_id LIKE 'oai:comum.rcaap.pt/%'"; stmt.executeUpdate(sql); stmt.close(); @@ -746,63 +672,83 @@ public class PiwikStatsDB { ConnectDB.getHiveConnection().close(); } - private String processPortalURL(String url) { - - if (url.indexOf("explore.openaire.eu") > 0) { - try { - url = URLDecoder.decode(url, "UTF-8"); - } catch (Exception e) { - logger.info("Error when decoding the following URL: " + url); - } - if (url.indexOf("datasourceId=") > 0 && url.substring(url.indexOf("datasourceId=") + 13).length() >= 46) { - url = "datasource|" - + url.substring(url.indexOf("datasourceId=") + 13, url.indexOf("datasourceId=") + 59); - } else if (url.indexOf("datasource=") > 0 - && url.substring(url.indexOf("datasource=") + 11).length() >= 46) { - url = "datasource|" + url.substring(url.indexOf("datasource=") + 11, url.indexOf("datasource=") + 57); - } else if (url.indexOf("datasourceFilter=") > 0 - && url.substring(url.indexOf("datasourceFilter=") + 17).length() >= 46) { - url = "datasource|" - + url.substring(url.indexOf("datasourceFilter=") + 17, url.indexOf("datasourceFilter=") + 63); - } else if (url.indexOf("articleId=") > 0 && url.substring(url.indexOf("articleId=") + 10).length() >= 46) { - url = "result|" + url.substring(url.indexOf("articleId=") + 10, url.indexOf("articleId=") + 56); - } else if (url.indexOf("datasetId=") > 0 && url.substring(url.indexOf("datasetId=") + 10).length() >= 46) { - url = "result|" + url.substring(url.indexOf("datasetId=") + 10, url.indexOf("datasetId=") + 56); - } else if (url.indexOf("projectId=") > 0 && url.substring(url.indexOf("projectId=") + 10).length() >= 46 - && !url.contains("oai:dnet:corda")) { - url = "project|" + url.substring(url.indexOf("projectId=") + 10, url.indexOf("projectId=") + 56); - } else if (url.indexOf("organizationId=") > 0 - && url.substring(url.indexOf("organizationId=") + 15).length() >= 46) { - url = "organization|" - + url.substring(url.indexOf("organizationId=") + 15, url.indexOf("organizationId=") + 61); - } else { - url = ""; - } - } else { - url = ""; - } - - return url; - } - private void updateProdTables() throws SQLException { Statement stmt = ConnectDB.getHiveConnection().createStatement(); ConnectDB.getHiveConnection().setAutoCommit(false); logger.info("Inserting data to piwiklog"); - String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklog " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; + String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklog " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; stmt.executeUpdate(sql); - + logger.info("Dropping piwiklogtmp"); sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; stmt.executeUpdate(sql); - logger.info("Dropped piwiklogtmp"); - + logger.info("Dropped piwiklogtmp"); + logger.info("Dropping process_portal_log_tmp"); sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp"; stmt.executeUpdate(sql); - logger.info("Dropped process_portal_log_tmp"); + logger.info("Dropped process_portal_log_tmp"); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + + } + + public void finalizeStats() throws SQLException { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Dropping piwiklogtmp"); + String sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; + stmt.executeUpdate(sql); + logger.info("Dropped piwiklogtmp"); + + logger.info("Dropping process_portal_log_tmp"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp"; + stmt.executeUpdate(sql); + logger.info("Dropped process_portal_log_tmp"); + + logger.info("Dropping irus_sushilogtmp"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp"; + stmt.executeUpdate(sql); + logger.info("Dropped irus_sushilogtmp"); + + logger.info("Dropping irus_sushilogtmp_json"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json"; + stmt.executeUpdate(sql); + logger.info("Dropped irus_sushilogtmp_json"); + + logger.info("Dropping lareferencialogtmp_json"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp_json"; + stmt.executeUpdate(sql); + logger.info("Dropped lareferencialogtmp_json"); + + logger.info("Dropping piwiklogtmp_json"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp_json"; + stmt.executeUpdate(sql); + logger.info("Dropped piwiklogtmp_json"); + + logger.info("Dropping process_portal_log_tmp_json"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp_json"; + stmt.executeUpdate(sql); + logger.info("Dropped process_portal_log_tmp_json"); + + logger.info("Dropping sarc_sushilogtmp"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; + stmt.executeUpdate(sql); + logger.info("Dropped sarc_sushilogtmp"); + + logger.info("Dropping sarc_sushilogtmp_json_array"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array"; + stmt.executeUpdate(sql); + logger.info("Dropped sarc_sushilogtmp_json_array"); + + logger.info("Dropping sarc_sushilogtmp_json_non_array"); + sql = "DROP TABLE " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(sql); + logger.info("Dropped sarc_sushilogtmp_json_non_array"); stmt.close(); ConnectDB.getHiveConnection().close(); @@ -868,4 +814,22 @@ public class PiwikStatsDB { private Connection getConnection() throws SQLException { return ConnectDB.getHiveConnection(); } + + public void createPedocsOldUsageData() throws SQLException { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + logger.info("Creating PeDocs Old Views Table"); + String sql = "Create TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".pedocsoldviews as select * from default.pedocsviews"; + stmt.executeUpdate(sql); + logger.info("PeDocs Old Views Table created"); + + logger.info("Creating PeDocs Old Downloads Table"); + sql = "Create TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".pedocsolddownloads as select * from default.pedocsdownloads"; + stmt.executeUpdate(sql); + logger.info("PeDocs Old Downloads Table created"); + + } } diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java index 4ca20c52e..e85c972f5 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/SarcStats.java @@ -1,3 +1,4 @@ + package eu.dnetlib.oa.graph.usagerawdata.export; import java.io.*; @@ -33,543 +34,467 @@ import org.slf4j.LoggerFactory; */ public class SarcStats { - private Statement stmtHive = null; - private Statement stmtImpala = null; + private Statement stmtHive = null; + private Statement stmtImpala = null; - private static final Logger logger = LoggerFactory.getLogger(SarcStats.class); + private static final Logger logger = LoggerFactory.getLogger(SarcStats.class); - public SarcStats() throws Exception { + public SarcStats() throws Exception { // createTables(); - } + } - private void createTables() throws Exception { - try { + private void createTables() throws Exception { + try { - stmtHive = ConnectDB.getHiveConnection().createStatement(); - String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilog(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; - stmtHive.executeUpdate(sqlCreateTableSushiLog); + stmtHive = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilog(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; + stmtHive.executeUpdate(sqlCreateTableSushiLog); - // String sqlCopyPublicSushiLog="INSERT INTO sushilog SELECT * FROM public.sushilog;"; - // stmt.executeUpdate(sqlCopyPublicSushiLog); - String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " - + " ON INSERT TO sushilog " - + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," - + "sushilog.rid, sushilog.date " - + "FROM sushilog " - + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; - stmtHive.executeUpdate(sqlcreateRuleSushiLog); - String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; - stmtHive.executeUpdate(createSushiIndex); + // String sqlCopyPublicSushiLog="INSERT INTO sushilog SELECT * FROM public.sushilog;"; + // stmt.executeUpdate(sqlCopyPublicSushiLog); + String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " + + " ON INSERT TO sushilog " + + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," + + "sushilog.rid, sushilog.date " + + "FROM sushilog " + + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; + stmtHive.executeUpdate(sqlcreateRuleSushiLog); + String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; + stmtHive.executeUpdate(createSushiIndex); - stmtHive.close(); - ConnectDB.getHiveConnection().close(); - logger.info("Sushi Tables Created"); - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - } - } + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } - public void reCreateLogDirs() throws IOException { - FileSystem dfs = FileSystem.get(new Configuration()); + public void reCreateLogDirs() throws IOException { + FileSystem dfs = FileSystem.get(new Configuration()); - logger.info("Deleting sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); - dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathArray), true); + logger.info("Deleting sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); + dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathArray), true); - logger.info("Deleting sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); - dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathNonArray), true); + logger.info("Deleting sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); + dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathNonArray), true); - logger.info("Creating sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); - dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathArray)); + logger.info("Creating sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); + dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathArray)); - logger.info("Creating sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); - dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathNonArray)); - } + logger.info("Creating sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); + dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathNonArray)); + } - public void processSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); + public void processSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); - logger.info("Adding JSON Serde jar"); - stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); - logger.info("Added JSON Serde jar"); + logger.info("Adding JSON Serde jar"); + stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); + logger.info("Added JSON Serde jar"); - logger.info("Dropping sarc_sushilogtmp_json_array table"); - String drop_sarc_sushilogtmp_json_array = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array"; - stmt.executeUpdate(drop_sarc_sushilogtmp_json_array); - logger.info("Dropped sarc_sushilogtmp_json_array table"); + logger.info("Dropping sarc_sushilogtmp_json_array table"); + String drop_sarc_sushilogtmp_json_array = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array"; + stmt.executeUpdate(drop_sarc_sushilogtmp_json_array); + logger.info("Dropped sarc_sushilogtmp_json_array table"); - logger.info("Creating sarc_sushilogtmp_json_array table"); - String create_sarc_sushilogtmp_json_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array(\n" - + " `ItemIdentifier` ARRAY<\n" - + " struct<\n" - + " `Type`: STRING,\n" - + " `Value`: STRING\n" - + " >\n" - + " >,\n" - + " `ItemPerformance` struct<\n" - + " `Period`: struct<\n" - + " `Begin`: STRING,\n" - + " `End`: STRING\n" - + " >,\n" - + " `Instance`: struct<\n" - + " `Count`: STRING,\n" - + " `MetricType`: STRING\n" - + " >\n" - + " >\n" - + ")" - + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" - + "LOCATION '" + sarcsReportPathArray + "/'\n" - + "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(create_sarc_sushilogtmp_json_array); - logger.info("Created sarc_sushilogtmp_json_array table"); + logger.info("Creating sarc_sushilogtmp_json_array table"); + String create_sarc_sushilogtmp_json_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array(\n" + + " `ItemIdentifier` ARRAY<\n" + + " struct<\n" + + " `Type`: STRING,\n" + + " `Value`: STRING\n" + + " >\n" + + " >,\n" + + " `ItemPerformance` struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >\n" + + ")" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + sarcsReportPathArray + "/'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_sarc_sushilogtmp_json_array); + logger.info("Created sarc_sushilogtmp_json_array table"); - logger.info("Dropping sarc_sushilogtmp_json_non_array table"); - String drop_sarc_sushilogtmp_json_non_array = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp_json_non_array"; - stmt.executeUpdate(drop_sarc_sushilogtmp_json_non_array); - logger.info("Dropped sarc_sushilogtmp_json_non_array table"); + logger.info("Dropping sarc_sushilogtmp_json_non_array table"); + String drop_sarc_sushilogtmp_json_non_array = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(drop_sarc_sushilogtmp_json_non_array); + logger.info("Dropped sarc_sushilogtmp_json_non_array table"); - logger.info("Creating sarc_sushilogtmp_json_non_array table"); - String create_sarc_sushilogtmp_json_non_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array (\n" - + " `ItemIdentifier` struct<\n" - + " `Type`: STRING,\n" - + " `Value`: STRING\n" - + " >,\n" - + " `ItemPerformance` struct<\n" - + " `Period`: struct<\n" - + " `Begin`: STRING,\n" - + " `End`: STRING\n" - + " >,\n" - + " `Instance`: struct<\n" - + " `Count`: STRING,\n" - + " `MetricType`: STRING\n" - + " >\n" - + " >" - + ")" - + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" - + "LOCATION '" + sarcsReportPathNonArray + "/'\n" - + "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(create_sarc_sushilogtmp_json_non_array); - logger.info("Created sarc_sushilogtmp_json_non_array table"); + logger.info("Creating sarc_sushilogtmp_json_non_array table"); + String create_sarc_sushilogtmp_json_non_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array (\n" + + " `ItemIdentifier` struct<\n" + + " `Type`: STRING,\n" + + " `Value`: STRING\n" + + " >,\n" + + " `ItemPerformance` struct<\n" + + " `Period`: struct<\n" + + " `Begin`: STRING,\n" + + " `End`: STRING\n" + + " >,\n" + + " `Instance`: struct<\n" + + " `Count`: STRING,\n" + + " `MetricType`: STRING\n" + + " >\n" + + " >" + + ")" + + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + + "LOCATION '" + sarcsReportPathNonArray + "/'\n" + + "TBLPROPERTIES (\"transactional\"=\"false\")"; + stmt.executeUpdate(create_sarc_sushilogtmp_json_non_array); + logger.info("Created sarc_sushilogtmp_json_non_array table"); - logger.info("Creating sarc_sushilogtmp table"); - String create_sarc_sushilogtmp = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp(source STRING, repository STRING, " - + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " - + "tblproperties('transactional'='true')"; - stmt.executeUpdate(create_sarc_sushilogtmp); - logger.info("Created sarc_sushilogtmp table"); + logger.info("Creating sarc_sushilogtmp table"); + String create_sarc_sushilogtmp = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp(source STRING, repository STRING, " + + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " + + "tblproperties('transactional'='true')"; + stmt.executeUpdate(create_sarc_sushilogtmp); + logger.info("Created sarc_sushilogtmp table"); - logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); - String insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " - + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " - + " `ItemIdent`.`Value`, `ItemPerformance`.`Period`.`Begin`, " - + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array " - + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " - + "WHERE `ItemIdent`.`Type`='DOI'"; - stmt.executeUpdate(insert_sarc_sushilogtmp); - logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); + logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); + String insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + + " `ItemIdent`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array " + + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " + + "WHERE `ItemIdent`.`Type`='DOI'"; + stmt.executeUpdate(insert_sarc_sushilogtmp); + logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); - logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); - insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " - + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " - + "`ItemIdentifier`.`Value`, `ItemPerformance`.`Period`.`Begin`, " - + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array"; - stmt.executeUpdate(insert_sarc_sushilogtmp); - logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); + logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); + insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " + + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " + + "`ItemIdentifier`.`Value`, `ItemPerformance`.`Period`.`Begin`, " + + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array"; + stmt.executeUpdate(insert_sarc_sushilogtmp); + logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); - ConnectDB.getHiveConnection().close(); - } + ConnectDB.getHiveConnection().close(); + } - public void getAndProcessSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { + public void getAndProcessSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); - logger.info("Creating sushilog table"); - String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog " - + "(`source` string, " - + "`repository` string, " - + "`rid` string, " - + "`date` string, " - + "`metric_type` string, " - + "`count` int)"; - stmt.executeUpdate(createSushilog); - logger.info("Created sushilog table"); + logger.info("Creating sushilog table"); + String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog " + + "(`source` string, " + + "`repository` string, " + + "`rid` string, " + + "`date` string, " + + "`metric_type` string, " + + "`count` int)"; + stmt.executeUpdate(createSushilog); + logger.info("Created sushilog table"); - logger.info("Dropping sarc_sushilogtmp table"); - String drop_sarc_sushilogtmp = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp"; - stmt.executeUpdate(drop_sarc_sushilogtmp); - logger.info("Dropped sarc_sushilogtmp table"); - ConnectDB.getHiveConnection().close(); + logger.info("Dropping sarc_sushilogtmp table"); + String drop_sarc_sushilogtmp = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".sarc_sushilogtmp"; + stmt.executeUpdate(drop_sarc_sushilogtmp); + logger.info("Dropped sarc_sushilogtmp table"); + ConnectDB.getHiveConnection().close(); - List issnAndUrls = new ArrayList(); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/motricidade/sushiLite/v1_7/", "1646-107X" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/antropologicas/sushiLite/v1_7/", "0873-819X" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/interaccoes/sushiLite/v1_7/", "1646-2335" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/cct/sushiLite/v1_7/", "2182-3030" - }); - issnAndUrls.add(new String[]{ - "https://actapediatrica.spp.pt/sushiLite/v1_7/", "0873-9781" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/sociologiapp/sushiLite/v1_7/", "0873-6529" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/finisterra/sushiLite/v1_7/", "0430-5027" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/sisyphus/sushiLite/v1_7/", "2182-8474" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/anestesiologia/sushiLite/v1_7/", "0871-6099" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/rpe/sushiLite/v1_7/", "0871-9187" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/psilogos/sushiLite/v1_7/", "1646-091X" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/juridica/sushiLite/v1_7/", "2183-5799" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/ecr/sushiLite/v1_7/", "1647-2098" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/nascercrescer/sushiLite/v1_7/", "0872-0754" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/cea/sushiLite/v1_7/", "1645-3794" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/proelium/sushiLite/v1_7/", "1645-8826" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/millenium/sushiLite/v1_7/", "0873-3015" - }); + List issnAndUrls = new ArrayList(); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/motricidade/sushiLite/v1_7/", "1646-107X" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/antropologicas/sushiLite/v1_7/", "0873-819X" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/interaccoes/sushiLite/v1_7/", "1646-2335" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/cct/sushiLite/v1_7/", "2182-3030" + }); + issnAndUrls.add(new String[] { + "https://actapediatrica.spp.pt/sushiLite/v1_7/", "0873-9781" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/sociologiapp/sushiLite/v1_7/", "0873-6529" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/finisterra/sushiLite/v1_7/", "0430-5027" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/sisyphus/sushiLite/v1_7/", "2182-8474" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/anestesiologia/sushiLite/v1_7/", "0871-6099" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/rpe/sushiLite/v1_7/", "0871-9187" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/psilogos/sushiLite/v1_7/", "1646-091X" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/juridica/sushiLite/v1_7/", "2183-5799" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/ecr/sushiLite/v1_7/", "1647-2098" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/nascercrescer/sushiLite/v1_7/", "0872-0754" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/cea/sushiLite/v1_7/", "1645-3794" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/proelium/sushiLite/v1_7/", "1645-8826" + }); + issnAndUrls.add(new String[] { + "https://revistas.rcaap.pt/millenium/sushiLite/v1_7/", "0873-3015" + }); - if (ExecuteWorkflow.sarcNumberOfIssnToDownload > 0 - && ExecuteWorkflow.sarcNumberOfIssnToDownload <= issnAndUrls.size()) { - logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.sarcNumberOfIssnToDownload); - issnAndUrls = issnAndUrls.subList(0, ExecuteWorkflow.sarcNumberOfIssnToDownload); - } + if (ExecuteWorkflow.sarcNumberOfIssnToDownload > 0 + && ExecuteWorkflow.sarcNumberOfIssnToDownload <= issnAndUrls.size()) { + logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.sarcNumberOfIssnToDownload); + issnAndUrls = issnAndUrls.subList(0, ExecuteWorkflow.sarcNumberOfIssnToDownload); + } - logger.info("(getAndProcessSarc) Downloading the followins opendoars: " + issnAndUrls); + logger.info("(getAndProcessSarc) Downloading the followins opendoars: " + issnAndUrls); - for (String[] issnAndUrl : issnAndUrls) { - logger.info("Now working on ISSN: " + issnAndUrl[1]); - getARReport(sarcsReportPathArray, sarcsReportPathNonArray, issnAndUrl[0], issnAndUrl[1]); - } + for (String[] issnAndUrl : issnAndUrls) { + logger.info("Now working on ISSN: " + issnAndUrl[1]); + getARReport(sarcsReportPathArray, sarcsReportPathNonArray, issnAndUrl[0], issnAndUrl[1]); + } - } + } - public void finalizeSarcStats() throws Exception { - stmtHive = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - stmtImpala = ConnectDB.getImpalaConnection().createStatement(); -/* - logger.info("Creating downloads_stats table_tmp"); - String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_tmp " - + "(`source` string, " - + "`repository_id` string, " - + "`result_id` string, " - + "`date` string, " - + "`count` bigint, " - + "`openaire` bigint)"; - stmtHive.executeUpdate(createDownloadsStats); - logger.info("Created downloads_stats_tmp table"); + public void updateSarcLogs() throws Exception { + stmtHive = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + stmtImpala = ConnectDB.getImpalaConnection().createStatement(); - logger.info("Dropping sarc_sushilogtmp_impala table"); - String drop_sarc_sushilogtmp_impala = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp_impala"; - stmtHive.executeUpdate(drop_sarc_sushilogtmp_impala); - logger.info("Dropped sarc_sushilogtmp_impala table"); + // Insert into sushilog + logger.info("Inserting into sushilog"); + String insertSushiLog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog SELECT * " + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; + stmtHive.executeUpdate(insertSushiLog); + logger.info("Inserted into sushilog"); - logger.info("Creating sarc_sushilogtmp_impala, a table readable by impala"); - String createSarcSushilogtmpImpala = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp_impala " - + "STORED AS PARQUET AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; - stmtHive.executeUpdate(createSarcSushilogtmpImpala); - logger.info("Created sarc_sushilogtmp_impala"); + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + } - logger.info("Making sarc_sushilogtmp visible to impala"); - String invalidateMetadata = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp_impala;"; - stmtImpala.executeUpdate(invalidateMetadata); + public void getARReport(String sarcsReportPathArray, String sarcsReportPathNonArray, + String url, String issn) throws Exception { + logger.info("Processing SARC! issn: " + issn + " with url: " + url); + ConnectDB.getHiveConnection().setAutoCommit(false); - logger.info("Dropping downloads_stats_impala table"); - String drop_downloads_stats_impala = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_impala"; - stmtHive.executeUpdate(drop_downloads_stats_impala); - logger.info("Dropped downloads_stats_impala table"); + SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); + // Setting the starting period + Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); + logger.info("(getARReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); - logger.info("Making downloads_stats_impala deletion visible to impala"); - try { - String invalidateMetadataDownloadsStatsImpala = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_impala;"; - stmtImpala.executeUpdate(invalidateMetadataDownloadsStatsImpala); - } catch (SQLException sqle) { - } + // Setting the ending period (last day of the month) +// Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); +// end.add(Calendar.MONTH, +1); +// end.add(Calendar.DAY_OF_MONTH, -1); + Calendar end = Calendar.getInstance(); + end.add(Calendar.DAY_OF_MONTH, -1); - // We run the following query in Impala because it is faster - logger.info("Creating downloads_stats_impala"); - String createDownloadsStatsImpala = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_impala AS " - + "SELECT s.source, d.id AS repository_id, " - + "ro.id as result_id, CONCAT(CAST(YEAR(`date`) AS STRING), '/', " - + "LPAD(CAST(MONTH(`date`) AS STRING), 2, '0')) AS `date`, s.count, '0' " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_impala s, " - + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " - + ConnectDB.getStatsDBSchema() + ".result_pids ro " - + "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND d.id like CONCAT('%', 'sarcservicod', '%') " - + "AND s.rid=ro.pid AND ro.type='Digital Object Identifier' AND s.metric_type='ft_total' AND s.source='SARC-OJS'"; - stmtImpala.executeUpdate(createDownloadsStatsImpala); - logger.info("Creating downloads_stats_impala"); + logger.info("(getARReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); - // Insert into downloads_stats - logger.info("Inserting data from downloads_stats_impala into downloads_stats_tmp"); - String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_tmp SELECT * " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_impala"; - stmtHive.executeUpdate(insertDStats); - logger.info("Inserted into downloads_stats_tmp"); + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + PreparedStatement st = ConnectDB + .getHiveConnection() + .prepareStatement( + "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); + st.setString(1, issn); + ResultSet rs_date = st.executeQuery(); + Date dateMax = null; + while (rs_date.next()) { + if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") + && !rs_date.getString(1).equals("")) { + start.setTime(sdf.parse(rs_date.getString(1))); + dateMax = sdf.parse(rs_date.getString(1)); + } + } + rs_date.close(); - logger.info("Creating sushilog table"); - String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog " - + "(`source` string, " - + "`repository_id` string, " - + "`rid` string, " - + "`date` string, " - + "`metric_type` string, " - + "`count` int)"; - stmtHive.executeUpdate(createSushilog); - logger.info("Created sushilog table"); -*/ - // Insert into sushilog - logger.info("Inserting into sushilog"); - String insertSushiLog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog SELECT * " + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; - stmtHive.executeUpdate(insertSushiLog); - logger.info("Inserted into sushilog"); + // Creating the needed configuration for the correct storing of data + Configuration config = new Configuration(); + config.addResource(new Path("/etc/hadoop/conf/core-site.xml")); + config.addResource(new Path("/etc/hadoop/conf/hdfs-site.xml")); + config + .set( + "fs.hdfs.impl", + org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + config + .set( + "fs.file.impl", + org.apache.hadoop.fs.LocalFileSystem.class.getName()); + FileSystem dfs = FileSystem.get(config); - stmtHive.close(); - ConnectDB.getHiveConnection().close(); - } + if (dateMax != null && end.getTime().compareTo(dateMax) <= 0) { + logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + issn); + } else { + start.add(Calendar.MONTH, 1); + while (start.before(end)) { + String reportUrl = url + "GetReport/?Report=AR1&Format=json&BeginDate=" + + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()); + start.add(Calendar.MONTH, 1); - public void getARReport(String sarcsReportPathArray, String sarcsReportPathNonArray, - String url, String issn) throws Exception { - logger.info("Processing SARC! issn: " + issn + " with url: " + url); - ConnectDB.getHiveConnection().setAutoCommit(false); + logger.info("(getARReport) Getting report: " + reportUrl); + String text = getJson(reportUrl); + if (text == null) { + continue; + } - SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("(getARReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); + JSONParser parser = new JSONParser(); + JSONObject jsonObject = null; + try { + jsonObject = (JSONObject) parser.parse(text); + } // if there is a parsing error continue with the next url + catch (ParseException pe) { + continue; + } - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("(getARReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); + jsonObject = (JSONObject) jsonObject.get("sc:ReportResponse"); + jsonObject = (JSONObject) jsonObject.get("sc:Report"); + if (jsonObject == null) { + continue; + } + jsonObject = (JSONObject) jsonObject.get("c:Report"); + jsonObject = (JSONObject) jsonObject.get("c:Customer"); + Object obj = jsonObject.get("c:ReportItems"); + JSONArray jsonArray = new JSONArray(); + if (obj instanceof JSONObject) { + jsonArray.add(obj); + } else { + jsonArray = (JSONArray) obj; + // jsonArray = (JSONArray) jsonObject.get("c:ReportItems"); + } + if (jsonArray == null) { + continue; + } - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - PreparedStatement st = ConnectDB - .getHiveConnection() - .prepareStatement( - "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); - st.setString(1, issn); - ResultSet rs_date = st.executeQuery(); - Date dateMax = null; - while (rs_date.next()) { - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - dateMax = sdf.parse(rs_date.getString(1)); - } - } - rs_date.close(); + // Creating the file in the filesystem for the ItemIdentifier as array object + String filePathArray = sarcsReportPathArray + "/SarcsARReport_" + issn + "_" + + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePathArray); + FSDataOutputStream finArray = dfs.create(new Path(filePathArray), true); - // Creating the needed configuration for the correct storing of data - Configuration config = new Configuration(); - config.addResource(new Path("/etc/hadoop/conf/core-site.xml")); - config.addResource(new Path("/etc/hadoop/conf/hdfs-site.xml")); - config - .set( - "fs.hdfs.impl", - org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); - config - .set( - "fs.file.impl", - org.apache.hadoop.fs.LocalFileSystem.class.getName()); - FileSystem dfs = FileSystem.get(config); + // Creating the file in the filesystem for the ItemIdentifier as array object + String filePathNonArray = sarcsReportPathNonArray + "/SarcsARReport_" + issn + "_" + + simpleDateFormat.format(start.getTime()) + ".json"; + logger.info("Storing to file: " + filePathNonArray); + FSDataOutputStream finNonArray = dfs.create(new Path(filePathNonArray), true); - if (dateMax != null && start.getTime().compareTo(dateMax) <= 0) { - logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + issn); - } else { - - while (start.before(end)) { - String reportUrl = url + "GetReport/?Report=AR1&Format=json&BeginDate=" - + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()); - start.add(Calendar.MONTH, 1); + for (Object aJsonArray : jsonArray) { - logger.info("(getARReport) Getting report: " + reportUrl); - String text = getJson(reportUrl); - if (text == null) { - continue; - } + JSONObject jsonObjectRow = (JSONObject) aJsonArray; + renameKeysRecursively(":", jsonObjectRow); - JSONParser parser = new JSONParser(); - JSONObject jsonObject = null; - try { - jsonObject = (JSONObject) parser.parse(text); - } // if there is a parsing error continue with the next url - catch (ParseException pe) { - continue; - } + if (jsonObjectRow.get("ItemIdentifier") instanceof JSONObject) { + finNonArray.write(jsonObjectRow.toJSONString().getBytes()); + finNonArray.writeChar('\n'); + } else { + finArray.write(jsonObjectRow.toJSONString().getBytes()); + finArray.writeChar('\n'); + } + } - jsonObject = (JSONObject) jsonObject.get("sc:ReportResponse"); - jsonObject = (JSONObject) jsonObject.get("sc:Report"); - if (jsonObject == null) { - continue; - } - jsonObject = (JSONObject) jsonObject.get("c:Report"); - jsonObject = (JSONObject) jsonObject.get("c:Customer"); - Object obj = jsonObject.get("c:ReportItems"); - JSONArray jsonArray = new JSONArray(); - if (obj instanceof JSONObject) { - jsonArray.add(obj); - } else { - jsonArray = (JSONArray) obj; - // jsonArray = (JSONArray) jsonObject.get("c:ReportItems"); - } - if (jsonArray == null) { - continue; - } + finArray.close(); + finNonArray.close(); - // Creating the file in the filesystem for the ItemIdentifier as array object - String filePathArray = sarcsReportPathArray + "/SarcsARReport_" + issn + "_" - + simpleDateFormat.format(start.getTime()) + ".json"; - logger.info("Storing to file: " + filePathArray); - FSDataOutputStream finArray = dfs.create(new Path(filePathArray), true); + // Check the file size and if it is too big, delete it + File fileArray = new File(filePathArray); + if (fileArray.length() == 0) { + fileArray.delete(); + } + File fileNonArray = new File(filePathNonArray); + if (fileNonArray.length() == 0) { + fileNonArray.delete(); + } - // Creating the file in the filesystem for the ItemIdentifier as array object - String filePathNonArray = sarcsReportPathNonArray + "/SarcsARReport_" + issn + "_" - + simpleDateFormat.format(start.getTime()) + ".json"; - logger.info("Storing to file: " + filePathNonArray); - FSDataOutputStream finNonArray = dfs.create(new Path(filePathNonArray), true); + } - for (Object aJsonArray : jsonArray) { + dfs.close(); + } + // ConnectDB.getHiveConnection().close(); + } - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - renameKeysRecursively(":", jsonObjectRow); - - if (jsonObjectRow.get("ItemIdentifier") instanceof JSONObject) { - finNonArray.write(jsonObjectRow.toJSONString().getBytes()); - finNonArray.writeChar('\n'); - } else { - finArray.write(jsonObjectRow.toJSONString().getBytes()); - finArray.writeChar('\n'); - } - } - - finArray.close(); - finNonArray.close(); - - // Check the file size and if it is too big, delete it - File fileArray = new File(filePathArray); - if (fileArray.length() == 0) - fileArray.delete(); - File fileNonArray = new File(filePathNonArray); - if (fileNonArray.length() == 0) - fileNonArray.delete(); - - } - - dfs.close(); - } - //ConnectDB.getHiveConnection().close(); - } - - private void renameKeysRecursively(String delimiter, JSONArray givenJsonObj) throws Exception { - for (Object jjval : givenJsonObj) { - if (jjval instanceof JSONArray) { - renameKeysRecursively(delimiter, (JSONArray) jjval); - } else if (jjval instanceof JSONObject) { - renameKeysRecursively(delimiter, (JSONObject) jjval); - } // All other types of vals - else + private void renameKeysRecursively(String delimiter, JSONArray givenJsonObj) throws Exception { + for (Object jjval : givenJsonObj) { + if (jjval instanceof JSONArray) { + renameKeysRecursively(delimiter, (JSONArray) jjval); + } else if (jjval instanceof JSONObject) { + renameKeysRecursively(delimiter, (JSONObject) jjval); + } // All other types of vals + else ; - } - } + } + } - private void renameKeysRecursively(String delimiter, JSONObject givenJsonObj) throws Exception { - Set jkeys = new HashSet(givenJsonObj.keySet()); - for (String jkey : jkeys) { + private void renameKeysRecursively(String delimiter, JSONObject givenJsonObj) throws Exception { + Set jkeys = new HashSet(givenJsonObj.keySet()); + for (String jkey : jkeys) { - String[] splitArray = jkey.split(delimiter); - String newJkey = splitArray[splitArray.length - 1]; + String[] splitArray = jkey.split(delimiter); + String newJkey = splitArray[splitArray.length - 1]; - Object jval = givenJsonObj.get(jkey); - givenJsonObj.remove(jkey); - givenJsonObj.put(newJkey, jval); + Object jval = givenJsonObj.get(jkey); + givenJsonObj.remove(jkey); + givenJsonObj.put(newJkey, jval); - if (jval instanceof JSONObject) { - renameKeysRecursively(delimiter, (JSONObject) jval); - } + if (jval instanceof JSONObject) { + renameKeysRecursively(delimiter, (JSONObject) jval); + } - if (jval instanceof JSONArray) { - renameKeysRecursively(delimiter, (JSONArray) jval); - } - } - } + if (jval instanceof JSONArray) { + renameKeysRecursively(delimiter, (JSONArray) jval); + } + } + } - private String getJson(String url) throws Exception { - // String cred=username+":"+password; - // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); - try { - URL website = new URL(url); - URLConnection connection = website.openConnection(); - // connection.setRequestProperty ("Authorization", "Basic "+encoded); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); - response.append("\n"); - } - } - return response.toString(); - } catch (Exception e) { + private String getJson(String url) throws Exception { + // String cred=username+":"+password; + // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); + try { + URL website = new URL(url); + URLConnection connection = website.openConnection(); + // connection.setRequestProperty ("Authorization", "Basic "+encoded); + StringBuilder response; + try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { + response = new StringBuilder(); + String inputLine; + while ((inputLine = in.readLine()) != null) { + response.append(inputLine); + response.append("\n"); + } + } + return response.toString(); + } catch (Exception e) { - // Logging error and silently continuing - logger.error("Failed to get URL: " + e); - System.out.println("Failed to get URL: " + e); + // Logging error and silently continuing + logger.error("Failed to get URL: " + e); + System.out.println("Failed to get URL: " + e); // return null; // throw new Exception("Failed to get URL: " + e.toString(), e); - } - return ""; - } + } + return ""; + } } diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java index bf2187569..07e15605f 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/java/eu/dnetlib/oa/graph/usagerawdata/export/UsageStatsExporter.java @@ -13,7 +13,7 @@ import org.slf4j.LoggerFactory; /** * Main class for downloading and processing Usage statistics - * + * * @author D. Pierrakos, S. Zoupanos */ public class UsageStatsExporter { @@ -51,19 +51,13 @@ public class UsageStatsExporter { logger.info("Initialising DB properties"); ConnectDB.init(); -// runImpalaQuery(); - PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); logger.info("Re-creating database and tables"); - if (ExecuteWorkflow.recreateDbAndTables){ + if (ExecuteWorkflow.recreateDbAndTables) { piwikstatsdb.recreateDBAndTables(); - logger.info("DB-Tables-TmpTables are created "); - } -// else { -// piwikstatsdb.createTmpTables(); -// logger.info("TmpTables are created "); -// } + logger.info("DB-Tables-TmpTables are created "); + } logger.info("Initializing the download logs module"); PiwikDownloadLogs piwd = new PiwikDownloadLogs(ExecuteWorkflow.matomoBaseURL, ExecuteWorkflow.matomoAuthToken); @@ -106,9 +100,8 @@ public class UsageStatsExporter { lrf.GetLaReferenciaRepos(ExecuteWorkflow.lareferenciaLogPath); logger.info("Downloaded LaReferencia logs"); } - - LaReferenciaStats lastats = new LaReferenciaStats(ExecuteWorkflow.lareferenciaLogPath); + LaReferenciaStats lastats = new LaReferenciaStats(ExecuteWorkflow.lareferenciaLogPath); if (ExecuteWorkflow.processLaReferenciaLogs) { logger.info("Processing LaReferencia logs"); @@ -116,7 +109,6 @@ public class UsageStatsExporter { logger.info("LaReferencia logs done"); } - IrusStats irusstats = new IrusStats(ExecuteWorkflow.irusUKBaseURL); if (ExecuteWorkflow.irusCreateTablesEmptyDirs) { logger.info("Creating Irus Stats tables"); @@ -132,14 +124,11 @@ public class UsageStatsExporter { irusstats.getIrusRRReport(ExecuteWorkflow.irusUKReportPath); } - - if (ExecuteWorkflow.irusProcessStats) { + if (ExecuteWorkflow.irusProcessStats) { irusstats.processIrusStats(); logger.info("Irus done"); } - - SarcStats sarcStats = new SarcStats(); if (ExecuteWorkflow.sarcCreateTablesEmptyDirs) { sarcStats.reCreateLogDirs(); @@ -148,51 +137,70 @@ public class UsageStatsExporter { sarcStats.getAndProcessSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); } - - if (ExecuteWorkflow.sarcProcessStats) { + if (ExecuteWorkflow.sarcProcessStats) { sarcStats.processSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); - sarcStats.finalizeSarcStats(); + sarcStats.updateSarcLogs(); } logger.info("Sarc done"); - - -/* // finalize usagestats + + logger.info("Dropping tmp tables"); if (ExecuteWorkflow.finalizeStats) { piwikstatsdb.finalizeStats(); - logger.info("Finalized stats"); + logger.info("Dropped tmp tables"); } -*/ -/* - // Make the tables available to Impala - if (ExecuteWorkflow.finalTablesVisibleToImpala) { - logger.info("Making tables visible to Impala"); - invalidateMetadata(); - } -*/ - - logger.info("End"); + logger.info("Raw Data Download End"); } - private void invalidateMetadata() throws SQLException { - Statement stmt = null; + public void createdDBWithTablesOnly() throws Exception { + logger.info("Initialising DB properties"); + ConnectDB.init(); - stmt = ConnectDB.getImpalaConnection().createStatement(); + PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); + piwikstatsdb.recreateDBAndTables(); - String sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; + piwikstatsdb.createPedocsOldUsageData(); + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + + logger.info("Creating LaReferencia tables"); + String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + + "stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableLareferenciaLog); + logger.info("Created LaReferencia tables"); + + logger.info("Creating sushilog"); + + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog(source STRING, " + + "repository STRING, rid STRING, date STRING, metric_type STRING, count INT) clustered by (source, " + + "repository, rid, date, metric_type) into 100 buckets stored as orc tblproperties('transactional'='true')"; + stmt.executeUpdate(sqlCreateTableSushiLog); + logger.info("Created sushilog"); + + logger.info("Updating piwiklog"); + String sql = "insert into " + ConnectDB.getUsageStatsDBSchema() + + ".piwiklog select * from openaire_prod_usage_raw.piwiklog"; stmt.executeUpdate(sql); - sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; + logger.info("Updating lareferencialog"); + sql = "insert into " + ConnectDB.getUsageStatsDBSchema() + + ".lareferencialog select * from openaire_prod_usage_raw.lareferencialog"; stmt.executeUpdate(sql); - sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; + logger.info("Updating sushilog"); + sql = "insert into " + ConnectDB.getUsageStatsDBSchema() + + ".sushilog select * from openaire_prod_usage_raw.sushilog"; stmt.executeUpdate(sql); - sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; - stmt.executeUpdate(sql); - - stmt.close(); + stmt.close(); ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } + } diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json index 988c23b48..1aa5ad6f8 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/export/usagerawdata_parameters.json @@ -125,12 +125,6 @@ "paramDescription": "Starting log period", "paramRequired": true }, - { - "paramName": "elp", - "paramLongName": "endingLogPeriod", - "paramDescription": "Ending log period", - "paramRequired": true - }, { "paramName": "npidd", "paramLongName": "numberOfPiwikIdsToDownload", @@ -216,12 +210,6 @@ "paramDescription": "Create the usage_stats table?", "paramRequired": true }, - { - "paramName": "ftvi", - "paramLongName": "finalTablesVisibleToImpala", - "paramDescription": "Make the usage_stats, views_stats and downloads_stats tables visible to Impala", - "paramRequired": true - }, { "paramName": "nodt", "paramLongName": "numberOfDownloadThreads", diff --git a/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml index a6600516d..022a107ab 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml @@ -63,7 +63,6 @@ --downloadPiwikLogs${downloadPiwikLogs} --processPiwikLogs${processPiwikLogs} --startingLogPeriod${startingLogPeriod} - --endingLogPeriod${endingLogPeriod} --numberOfPiwikIdsToDownload${numberOfPiwikIdsToDownload} --numberOfSiteIdsToDownload${numberOfSiteIdsToDownload} --laReferenciaEmptyDirs${laReferenciaEmptyDirs} @@ -78,7 +77,6 @@ --sarcProcessStats${sarcProcessStats} --sarcNumberOfIssnToDownload${sarcNumberOfIssnToDownload} --finalizeStats${finalizeStats} - --finalTablesVisibleToImpala${finalTablesVisibleToImpala} --numberOfDownloadThreads${numberOfDownloadThreads} diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index f400239f5..79fabb603 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -23,7 +23,35 @@ 4.0.0 dhp-usage-stats-build - + + + + pl.project13.maven + git-commit-id-plugin + 2.1.15 + + + + revision + + + + + ${project.basedir}/../.git + + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.6.1 + + 1.8 + 1.8 + + + + UTF-8 UTF-8 diff --git a/dhp-workflows/dhp-usage-stats-build/runworkflow.sh b/dhp-workflows/dhp-usage-stats-build/runworkflow.sh new file mode 100755 index 000000000..191fb24c6 --- /dev/null +++ b/dhp-workflows/dhp-usage-stats-build/runworkflow.sh @@ -0,0 +1 @@ +mvn clean package -Poozie-package,deploy,run -Dworkflow.source.dir=eu/dnetlib/dhp/oa/graph/usagestatsbuild \ No newline at end of file diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ConnectDB.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ConnectDB.java index 8f0f8eae7..e53709f1a 100644 --- a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ConnectDB.java +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ConnectDB.java @@ -3,12 +3,17 @@ * To change this template file, choose Tools | Templates * and open the template in the editor. */ + package eu.dnetlib.oa.graph.usagestatsbuild.export; import java.sql.Connection; import java.sql.DriverManager; import java.sql.SQLException; import java.sql.Statement; +import java.text.DateFormat; +import java.text.SimpleDateFormat; +import java.util.Calendar; +import java.util.Date; import java.util.Properties; import org.apache.log4j.Logger; @@ -23,108 +28,120 @@ import com.mchange.v2.c3p0.ComboPooledDataSource; public abstract class ConnectDB { - public static Connection DB_HIVE_CONNECTION; - public static Connection DB_IMPALA_CONNECTION; + public static Connection DB_HIVE_CONNECTION; + public static Connection DB_IMPALA_CONNECTION; - private static String dbHiveUrl; - private static String dbImpalaUrl; - private static String usageRawDataDBSchema; - private static String usageStatsDBSchema; - private static String statsDBSchema; - private final static Logger log = Logger.getLogger(ConnectDB.class); + private static String dbHiveUrl; + private static String dbImpalaUrl; + private static String usageRawDataDBSchema; + private static String usageStatsDBSchema; + private static String usagestatsPermanentDBSchema; + private static String statsDBSchema; + private final static Logger log = Logger.getLogger(ConnectDB.class); - static void init() throws ClassNotFoundException { + static void init() throws ClassNotFoundException { - dbHiveUrl = ExecuteWorkflow.dbHiveUrl; - dbImpalaUrl = ExecuteWorkflow.dbImpalaUrl; - usageStatsDBSchema = ExecuteWorkflow.usageStatsDBSchema; - statsDBSchema = ExecuteWorkflow.statsDBSchema; - usageRawDataDBSchema = ExecuteWorkflow.usageRawDataDBSchema; + dbHiveUrl = ExecuteWorkflow.dbHiveUrl; + dbImpalaUrl = ExecuteWorkflow.dbImpalaUrl; + usageStatsDBSchema = ExecuteWorkflow.usageStatsDBSchema; + statsDBSchema = ExecuteWorkflow.statsDBSchema; + usageRawDataDBSchema = ExecuteWorkflow.usageRawDataDBSchema; + usagestatsPermanentDBSchema = ExecuteWorkflow.usagestatsPermanentDBSchema; - Class.forName("org.apache.hive.jdbc.HiveDriver"); - } + Class.forName("org.apache.hive.jdbc.HiveDriver"); + } - public static Connection getHiveConnection() throws SQLException { - if (DB_HIVE_CONNECTION != null && !DB_HIVE_CONNECTION.isClosed()) { - return DB_HIVE_CONNECTION; - } else { - DB_HIVE_CONNECTION = connectHive(); + public static Connection getHiveConnection() throws SQLException { + if (DB_HIVE_CONNECTION != null && !DB_HIVE_CONNECTION.isClosed()) { + return DB_HIVE_CONNECTION; + } else { + DB_HIVE_CONNECTION = connectHive(); - return DB_HIVE_CONNECTION; - } - } + return DB_HIVE_CONNECTION; + } + } - public static Connection getImpalaConnection() throws SQLException { - if (DB_IMPALA_CONNECTION != null && !DB_IMPALA_CONNECTION.isClosed()) { - return DB_IMPALA_CONNECTION; - } else { - DB_IMPALA_CONNECTION = connectImpala(); + public static Connection getImpalaConnection() throws SQLException { + if (DB_IMPALA_CONNECTION != null && !DB_IMPALA_CONNECTION.isClosed()) { + return DB_IMPALA_CONNECTION; + } else { + DB_IMPALA_CONNECTION = connectImpala(); - return DB_IMPALA_CONNECTION; - } - } + return DB_IMPALA_CONNECTION; + } + } - public static String getUsageRawDataDBSchema() { - return usageRawDataDBSchema; - } + public static String getUsageRawDataDBSchema() { + return ConnectDB.usageRawDataDBSchema; + } - public static String getUsageStatsDBSchema() { - return ConnectDB.usageStatsDBSchema; - } + public static String getUsageStatsDBSchema() { + String datePattern = "YYYYMMdd"; + DateFormat df = new SimpleDateFormat(datePattern); +// Get the today date using Calendar object. + Date today = Calendar.getInstance().getTime(); + String todayAsString = df.format(today); - public static String getStatsDBSchema() { - return ConnectDB.statsDBSchema; - } + return ConnectDB.usageStatsDBSchema + "_" + todayAsString; + } - private static Connection connectHive() throws SQLException { - /* + public static String getStatsDBSchema() { + return ConnectDB.statsDBSchema; + } + + public static String getUsagestatsPermanentDBSchema() { + return ConnectDB.usagestatsPermanentDBSchema; + } + + private static Connection connectHive() throws SQLException { + /* * Connection connection = DriverManager.getConnection(dbHiveUrl); Statement stmt = * connection.createStatement(); log.debug("Opened database successfully"); return connection; - */ - ComboPooledDataSource cpds = new ComboPooledDataSource(); - cpds.setJdbcUrl(dbHiveUrl); - cpds.setAcquireIncrement(1); - cpds.setMaxPoolSize(100); - cpds.setMinPoolSize(1); - cpds.setInitialPoolSize(1); - cpds.setMaxIdleTime(300); - cpds.setMaxConnectionAge(36000); + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbHiveUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); - cpds.setAcquireRetryAttempts(30); - cpds.setAcquireRetryDelay(2000); - cpds.setBreakAfterAcquireFailure(false); + cpds.setAcquireRetryAttempts(30); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); - cpds.setCheckoutTimeout(0); - cpds.setPreferredTestQuery("SELECT 1"); - cpds.setIdleConnectionTestPeriod(60); - return cpds.getConnection(); + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); + return cpds.getConnection(); - } + } - private static Connection connectImpala() throws SQLException { - /* + private static Connection connectImpala() throws SQLException { + /* * Connection connection = DriverManager.getConnection(dbImpalaUrl); Statement stmt = * connection.createStatement(); log.debug("Opened database successfully"); return connection; - */ - ComboPooledDataSource cpds = new ComboPooledDataSource(); - cpds.setJdbcUrl(dbImpalaUrl); - cpds.setAcquireIncrement(1); - cpds.setMaxPoolSize(100); - cpds.setMinPoolSize(1); - cpds.setInitialPoolSize(1); - cpds.setMaxIdleTime(300); - cpds.setMaxConnectionAge(36000); + */ + ComboPooledDataSource cpds = new ComboPooledDataSource(); + cpds.setJdbcUrl(dbImpalaUrl); + cpds.setAcquireIncrement(1); + cpds.setMaxPoolSize(100); + cpds.setMinPoolSize(1); + cpds.setInitialPoolSize(1); + cpds.setMaxIdleTime(300); + cpds.setMaxConnectionAge(36000); - cpds.setAcquireRetryAttempts(30); - cpds.setAcquireRetryDelay(2000); - cpds.setBreakAfterAcquireFailure(false); + cpds.setAcquireRetryAttempts(30); + cpds.setAcquireRetryDelay(2000); + cpds.setBreakAfterAcquireFailure(false); - cpds.setCheckoutTimeout(0); - cpds.setPreferredTestQuery("SELECT 1"); - cpds.setIdleConnectionTestPeriod(60); + cpds.setCheckoutTimeout(0); + cpds.setPreferredTestQuery("SELECT 1"); + cpds.setIdleConnectionTestPeriod(60); - return cpds.getConnection(); + return cpds.getConnection(); - } + } } diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ExecuteWorkflow.java index 3f958abba..26e44b1f6 100644 --- a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ExecuteWorkflow.java +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/ExecuteWorkflow.java @@ -3,6 +3,7 @@ * To change this template file, choose Tools | Templates * and open the template in the editor. */ + package eu.dnetlib.oa.graph.usagestatsbuild.export; import java.text.SimpleDateFormat; @@ -11,162 +12,142 @@ import java.util.Date; import org.apache.commons.io.IOUtils; import org.apache.log4j.BasicConfigurator; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + /** * @author D. Pierrakos, S. Zoupanos */ public class ExecuteWorkflow { - static String matomoAuthToken; - static String matomoBaseURL; - static String repoLogPath; - static String portalLogPath; - static String portalMatomoID; - static String irusUKBaseURL; - static String irusUKReportPath; - static String sarcsReportPathArray; - static String sarcsReportPathNonArray; - static String lareferenciaLogPath; - static String lareferenciaBaseURL; - static String lareferenciaAuthToken; - static String dbHiveUrl; - static String dbImpalaUrl; - static String usageRawDataDBSchema; - static String usageStatsDBSchema; - static String statsDBSchema; - static boolean recreateDbAndTables; +// static String matomoAuthToken; + static String matomoBaseURL; + static String repoLogPath; + static String portalLogPath; + static String portalMatomoID; +// static String irusUKBaseURL; + static String irusUKReportPath; + static String sarcsReportPathArray; + static String sarcsReportPathNonArray; + static String lareferenciaLogPath; +// static String lareferenciaBaseURL; +// static String lareferenciaAuthToken; + static String dbHiveUrl; + static String dbImpalaUrl; + static String usageRawDataDBSchema; + static String usageStatsDBSchema; + static String usagestatsPermanentDBSchema; + static String statsDBSchema; + static boolean recreateDbAndTables; - static boolean piwikEmptyDirs; - static boolean downloadPiwikLogs; - static boolean processPiwikLogs; + static boolean processPiwikLogs; + static boolean processLaReferenciaLogs; - static Calendar startingLogPeriod; - static Calendar endingLogPeriod; - static int numberOfPiwikIdsToDownload; - static int numberOfSiteIdsToDownload; + static boolean irusProcessStats; - static boolean laReferenciaEmptyDirs; - static boolean downloadLaReferenciaLogs; - static boolean processLaReferenciaLogs; + static boolean sarcProcessStats; - static boolean irusCreateTablesEmptyDirs; - static boolean irusDownloadReports; - static boolean irusProcessStats; - static int irusNumberOfOpendoarsToDownload; + static boolean finalizeStats; + static boolean finalTablesVisibleToImpala; - static boolean sarcCreateTablesEmptyDirs; - static boolean sarcDownloadReports; - static boolean sarcProcessStats; - static int sarcNumberOfIssnToDownload; + static int numberOfDownloadThreads; - static boolean finalizeStats; - static boolean finalTablesVisibleToImpala; + private static final Logger logger = LoggerFactory.getLogger(PiwikStatsDB.class); - static int numberOfDownloadThreads; + public static void main(String args[]) throws Exception { - private static final Logger logger = LoggerFactory.getLogger(PiwikStatsDB.class); + // Sending the logs to the console + BasicConfigurator.configure(); - public static void main(String args[]) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + UsageStatsExporter.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json"))); + parser.parseArgument(args); - // Sending the logs to the console - BasicConfigurator.configure(); + // Setting up the initial parameters +// matomoAuthToken = parser.get("matomoAuthToken"); +// matomoBaseURL = parser.get("matomoBaseURL"); + repoLogPath = parser.get("repoLogPath"); + portalLogPath = parser.get("portalLogPath"); + portalMatomoID = parser.get("portalMatomoID"); +// irusUKBaseURL = parser.get("irusUKBaseURL"); + irusUKReportPath = parser.get("irusUKReportPath"); + sarcsReportPathArray = parser.get("sarcsReportPathArray"); + sarcsReportPathNonArray = parser.get("sarcsReportPathNonArray"); + lareferenciaLogPath = parser.get("lareferenciaLogPath"); +// lareferenciaBaseURL = parser.get("lareferenciaBaseURL"); +// lareferenciaAuthToken = parser.get("lareferenciaAuthToken"); - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - UsageStatsExporter.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json"))); - parser.parseArgument(args); + dbHiveUrl = parser.get("dbHiveUrl"); + dbImpalaUrl = parser.get("dbImpalaUrl"); + usageRawDataDBSchema = parser.get("usageRawDataDBSchema"); + usageStatsDBSchema = parser.get("usageStatsDBSchema"); + usagestatsPermanentDBSchema = parser.get("usagestatsPermanentDBSchema"); + statsDBSchema = parser.get("statsDBSchema"); - // Setting up the initial parameters - matomoAuthToken = parser.get("matomoAuthToken"); - matomoBaseURL = parser.get("matomoBaseURL"); - repoLogPath = parser.get("repoLogPath"); - portalLogPath = parser.get("portalLogPath"); - portalMatomoID = parser.get("portalMatomoID"); - irusUKBaseURL = parser.get("irusUKBaseURL"); - irusUKReportPath = parser.get("irusUKReportPath"); - sarcsReportPathArray = parser.get("sarcsReportPathArray"); - sarcsReportPathNonArray = parser.get("sarcsReportPathNonArray"); - lareferenciaLogPath = parser.get("lareferenciaLogPath"); - lareferenciaBaseURL = parser.get("lareferenciaBaseURL"); - lareferenciaAuthToken = parser.get("lareferenciaAuthToken"); + if (parser.get("processPiwikLogs").toLowerCase().equals("true")) { + processPiwikLogs = true; + } else { + processPiwikLogs = false; + } - dbHiveUrl = parser.get("dbHiveUrl"); - dbImpalaUrl = parser.get("dbImpalaUrl"); - usageRawDataDBSchema = parser.get("usageRawDataDBSchema"); - usageStatsDBSchema = parser.get("usageStatsDBSchema"); - statsDBSchema = parser.get("statsDBSchema"); +// String startingLogPeriodStr = parser.get("startingLogPeriod"); +// Date startingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(startingLogPeriodStr); +// startingLogPeriod = startingLogPeriodStr(startingLogPeriodDate); +// +// String endingLogPeriodStr = parser.get("endingLogPeriod"); +// Date endingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(endingLogPeriodStr); +// endingLogPeriod = startingLogPeriodStr(endingLogPeriodDate); - if (parser.get("processPiwikLogs").toLowerCase().equals("true")) { - processPiwikLogs = true; - } else { - processPiwikLogs = false; - } + if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) { + recreateDbAndTables = true; + } else { + recreateDbAndTables = false; + } - String startingLogPeriodStr = parser.get("startingLogPeriod"); - Date startingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(startingLogPeriodStr); - startingLogPeriod = startingLogPeriodStr(startingLogPeriodDate); + if (parser.get("processLaReferenciaLogs").toLowerCase().equals("true")) { + processLaReferenciaLogs = true; + } else { + processLaReferenciaLogs = false; + } - String endingLogPeriodStr = parser.get("endingLogPeriod"); - Date endingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(endingLogPeriodStr); - endingLogPeriod = startingLogPeriodStr(endingLogPeriodDate); + if (parser.get("irusProcessStats").toLowerCase().equals("true")) { + irusProcessStats = true; + } else { + irusProcessStats = false; + } - numberOfPiwikIdsToDownload = Integer.parseInt(parser.get("numberOfPiwikIdsToDownload")); - numberOfSiteIdsToDownload = Integer.parseInt(parser.get("numberOfSiteIdsToDownload")); + if (parser.get("sarcProcessStats").toLowerCase().equals("true")) { + sarcProcessStats = true; + } else { + sarcProcessStats = false; + } - if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) { - recreateDbAndTables = true; - } else { - recreateDbAndTables = false; - } + if (parser.get("finalizeStats").toLowerCase().equals("true")) { + finalizeStats = true; + } else { + finalizeStats = false; + } + if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) { + finalTablesVisibleToImpala = true; + } else { + numberOfDownloadThreads = Integer.parseInt(parser.get("numberOfDownloadThreads")); + } - if (parser.get("processLaReferenciaLogs").toLowerCase().equals("true")) { - processLaReferenciaLogs = true; - } else { - processLaReferenciaLogs = false; - } + UsageStatsExporter usagestatsExport = new UsageStatsExporter(); + usagestatsExport.export(); + } - if (parser.get("irusProcessStats").toLowerCase().equals("true")) { - irusProcessStats = true; - } else { - irusProcessStats = false; - } + private static Calendar startingLogPeriodStr(Date date) { - irusNumberOfOpendoarsToDownload = Integer.parseInt(parser.get("irusNumberOfOpendoarsToDownload")); + Calendar calendar = Calendar.getInstance(); + calendar.setTime(date); + return calendar; - if (parser.get("sarcProcessStats").toLowerCase().equals("true")) { - sarcProcessStats = true; - } else { - sarcProcessStats = false; - } - sarcNumberOfIssnToDownload = Integer.parseInt(parser.get("sarcNumberOfIssnToDownload")); - - if (parser.get("finalizeStats").toLowerCase().equals("true")) { - finalizeStats = true; - } else { - finalizeStats = false; - } - if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) { - finalTablesVisibleToImpala = true; - } else { - numberOfDownloadThreads = Integer.parseInt(parser.get("numberOfDownloadThreads")); - } - - UsageStatsExporter usagestatsExport = new UsageStatsExporter(); - usagestatsExport.export(); - } - - private static Calendar startingLogPeriodStr(Date date) { - - Calendar calendar = Calendar.getInstance(); - calendar.setTime(date); - return calendar; - - } + } } diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/IrusStats.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/IrusStats.java index 4f34adc04..4439f848e 100644 --- a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/IrusStats.java +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/IrusStats.java @@ -1,3 +1,4 @@ + package eu.dnetlib.oa.graph.usagestatsbuild.export; import java.io.*; @@ -27,45 +28,42 @@ import org.slf4j.LoggerFactory; */ public class IrusStats { - private String irusUKURL; + private String irusUKURL; - private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); + private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); - public IrusStats() throws Exception { - } + public IrusStats() throws Exception { + } - - public void processIrusStats() throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); + public void processIrusStats() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + logger.info("Creating irus_downloads_stats_tmp table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".irus_downloads_stats_tmp " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmt.executeUpdate(createDownloadsStats); + logger.info("Created irus_downloads_stats_tmp table"); - logger.info("Creating irus_downloads_stats_tmp table"); - String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".irus_downloads_stats_tmp " - + "(`source` string, " - + "`repository_id` string, " - + "`result_id` string, " - + "`date` string, " - + "`count` bigint, " - + "`openaire` bigint)"; - stmt.executeUpdate(createDownloadsStats); - logger.info("Created irus_downloads_stats_tmp table"); + logger.info("Inserting into irus_downloads_stats_tmp"); + String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_downloads_stats_tmp " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(YEAR(date), '/', LPAD(MONTH(date), 2, '0')) as date, s.count, '0' " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".sushilog s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE s.repository=d.oid AND s.rid=ro.oid AND metric_type='ft_total' AND s.source='IRUS-UK'"; + stmt.executeUpdate(insertDStats); + logger.info("Inserted into irus_downloads_stats_tmp"); - logger.info("Inserting into irus_downloads_stats_tmp"); - String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_downloads_stats_tmp " - + "SELECT s.source, d.id AS repository_id, " - + "ro.id as result_id, CONCAT(YEAR(date), '/', LPAD(MONTH(date), 2, '0')) as date, s.count, '0' " - + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".sushilog s, " - + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " - + ConnectDB.getStatsDBSchema() + ".result_oids ro " - + "WHERE s.repository=d.oid AND s.rid=ro.oid AND metric_type='ft_total' AND s.source='IRUS-UK'"; - stmt.executeUpdate(insertDStats); - logger.info("Inserted into irus_downloads_stats_tmp"); + stmt.close(); + // ConnectDB.getHiveConnection().close(); + } - stmt.close(); - //ConnectDB.getHiveConnection().close(); - } - - } diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/LaReferenciaStats.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/LaReferenciaStats.java index ea3ac5948..0d34ebef3 100644 --- a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/LaReferenciaStats.java +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/LaReferenciaStats.java @@ -41,8 +41,6 @@ public class LaReferenciaStats { public LaReferenciaStats() throws Exception { } - - public void processLogs() throws Exception { try { logger.info("LaReferencia creating viewsStats"); @@ -62,7 +60,6 @@ public class LaReferenciaStats { } } - public void viewsStats() throws Exception { Statement stmt = ConnectDB.getHiveConnection().createStatement(); @@ -101,7 +98,7 @@ public class LaReferenciaStats { logger.info("Created la_views_stats_tmp table"); stmt.close(); - ConnectDB.getHiveConnection().close(); + // ConnectDB.getHiveConnection().close(); } private void downloadsStats() throws Exception { @@ -142,8 +139,7 @@ public class LaReferenciaStats { logger.info("Created la_downloads_stats_tmp table"); stmt.close(); - //ConnectDB.getHiveConnection().close(); + // ConnectDB.getHiveConnection().close(); } - } diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/PiwikStatsDB.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/PiwikStatsDB.java index a165c6eab..253dc03b5 100644 --- a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/PiwikStatsDB.java +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/PiwikStatsDB.java @@ -1,22 +1,15 @@ package eu.dnetlib.oa.graph.usagestatsbuild.export; -import java.io.*; -import java.net.URLDecoder; import java.sql.Connection; import java.sql.SQLException; import java.sql.Statement; +import java.sql.Timestamp; import java.text.SimpleDateFormat; import java.util.*; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.LocatedFileStatus; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.fs.RemoteIterator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.sql.Timestamp; /** * @author D. Pierrakos, S. Zoupanos @@ -29,37 +22,51 @@ public class PiwikStatsDB { private static final Logger logger = LoggerFactory.getLogger(PiwikStatsDB.class); - public PiwikStatsDB() throws Exception { } - public void recreateDBAndTables() throws Exception { this.createDatabase(); // The piwiklog table is not needed since it is built // on top of JSON files - ////////////this.createTmpTables(); + //////////// this.createTmpTables(); } private void createDatabase() throws Exception { + +// try { +// +// stmt = ConnectDB.getHiveConnection().createStatement(); +// +// logger.info("Dropping usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); +// String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + " CASCADE"; +// stmt.executeUpdate(dropDatabase); +// } catch (Exception e) { +// logger.error("Failed to drop database: " + e); +// throw new Exception("Failed to drop database: " + e.toString(), e); +// } +// try { stmt = ConnectDB.getHiveConnection().createStatement(); + logger.info("Creating usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); + String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema(); + stmt.executeUpdate(createDatabase); + logger.info("Usagestats DB created: " + ConnectDB.getUsageStatsDBSchema()); - logger.info("Dropping usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); - String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + " CASCADE"; - stmt.executeUpdate(dropDatabase); } catch (Exception e) { - logger.error("Failed to drop database: " + e); - throw new Exception("Failed to drop database: " + e.toString(), e); + logger.error("Failed to create database: " + e); + throw new Exception("Failed to create database: " + e.toString(), e); } try { stmt = ConnectDB.getHiveConnection().createStatement(); - logger.info("Creating usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); - String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema(); - stmt.executeUpdate(createDatabase); + logger.info("Creating permanent usagestats DB: " + ConnectDB.getUsagestatsPermanentDBSchema()); + String createPermanentDatabase = "CREATE DATABASE IF NOT EXISTS " + + ConnectDB.getUsagestatsPermanentDBSchema(); + stmt.executeUpdate(createPermanentDatabase); + logger.info("Created permanent usagestats DB: " + ConnectDB.getUsagestatsPermanentDBSchema()); } catch (Exception e) { logger.error("Failed to create database: " + e); @@ -67,17 +74,16 @@ public class PiwikStatsDB { } } - public void processLogs() throws Exception { try { - logger.info("ViewsStats processing starts at: "+new Timestamp(System.currentTimeMillis())); + logger.info("ViewsStats processing starts at: " + new Timestamp(System.currentTimeMillis())); viewsStats(); - logger.info("ViewsStats processing ends at: "+new Timestamp(System.currentTimeMillis())); + logger.info("ViewsStats processing ends at: " + new Timestamp(System.currentTimeMillis())); - logger.info("DownloadsStats processing starts at: "+new Timestamp(System.currentTimeMillis())); + logger.info("DownloadsStats processing starts at: " + new Timestamp(System.currentTimeMillis())); downloadsStats(); - logger.info("DownloadsStats processing ends at: "+new Timestamp(System.currentTimeMillis())); + logger.info("DownloadsStats processing ends at: " + new Timestamp(System.currentTimeMillis())); } catch (Exception e) { logger.error("Failed to process logs: " + e); @@ -85,68 +91,68 @@ public class PiwikStatsDB { } } - - public void viewsStats() throws Exception { Statement stmt = ConnectDB.getHiveConnection().createStatement(); ConnectDB.getHiveConnection().setAutoCommit(false); logger.info("Dropping openaire_result_views_monthly_tmp view"); - String drop_result_views_monthly = "DROP VIEW IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".openaire_piwikresult_views_monthly_tmp"; + String drop_result_views_monthly = "DROP VIEW IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_piwikresult_views_monthly_tmp"; stmt.executeUpdate(drop_result_views_monthly); logger.info("Dropped openaire_result_views_monthly_tmp view"); logger.info("Creating openaire_result_views_monthly_tmp view"); String create_result_views_monthly = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() - + ".openaire_result_views_monthly_tmp " + - "AS SELECT entity_id AS id, " + - "COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) " + - "AS openaire_referrer, " + - "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + - "FROM " + ConnectDB.getUsageRawDataDBSchema() - + ".piwiklog where action='action' and (source_item_type='oaItem' or " + - "source_item_type='repItem') " + - "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), " + - "source ORDER BY source, entity_id"; + + ".openaire_result_views_monthly_tmp " + + "AS SELECT entity_id, " + + "reflect('java.net.URLDecoder', 'decode', entity_id) AS id," + + "COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) " + + "AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + + ".piwiklog where action='action' and (source_item_type='oaItem' or " + + "source_item_type='repItem') " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), " + + "source ORDER BY source, entity_id"; stmt.executeUpdate(create_result_views_monthly); logger.info("Created openaire_result_views_monthly_tmp table"); logger.info("Dropping openaire_views_stats_tmp table"); - String drop_views_stats = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".openaire_views_stats_tmp"; + String drop_views_stats = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_views_stats_tmp"; stmt.executeUpdate(drop_views_stats); logger.info("Dropped openaire_views_stats_tmp table"); logger.info("Creating openaire_views_stats_tmp table"); String create_views_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".openaire_views_stats_tmp " + - "AS SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + - "max(views) AS count, max(openaire_referrer) AS openaire " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_views_monthly_tmp p, " + - ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + - "WHERE p.source=d.piwik_id AND p.id=ro.oid " + - "GROUP BY d.id, ro.id, month " + - "ORDER BY d.id, ro.id, month "; + + ".openaire_views_stats_tmp " + + "AS SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(views) AS count, max(openaire_referrer) AS openaire " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_views_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=d.piwik_id AND p.id=ro.oid AND ro.oid!='200' " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month "; stmt.executeUpdate(create_views_stats); logger.info("Created openaire_views_stats_tmp table"); logger.info("Creating openaire_pageviews_stats_tmp table"); String create_pageviews_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".openaire_pageviews_stats_tmp AS SELECT " + - "'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, max(views) AS count " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_views_monthly_tmp p, " + - ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + - "WHERE p.source=" + ExecuteWorkflow.portalMatomoID + " AND p.source=d.piwik_id and p.id=ro.id \n" + - "GROUP BY d.id, ro.id, month " + - "ORDER BY d.id, ro.id, month "; + + ".openaire_pageviews_stats_tmp AS SELECT " + + "'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, max(views) AS count " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_views_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=" + ExecuteWorkflow.portalMatomoID + + " AND p.source=d.piwik_id and p.id=ro.id AND ro.oid!='200' " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month "; stmt.executeUpdate(create_pageviews_stats); logger.info("Created pageviews_stats table"); stmt.close(); - //ConnectDB.getHiveConnection().close(); + // ConnectDB.getHiveConnection().close(); } private void downloadsStats() throws Exception { @@ -154,152 +160,315 @@ public class PiwikStatsDB { ConnectDB.getHiveConnection().setAutoCommit(false); logger.info("Dropping openaire_result_downloads_monthly_tmp view"); - String drop_result_downloads_monthly = "DROP VIEW IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".openaire_result_downloads_monthly_tmp"; + String drop_result_downloads_monthly = "DROP VIEW IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_result_downloads_monthly_tmp"; stmt.executeUpdate(drop_result_downloads_monthly); logger.info("Dropped openaire_result_downloads_monthly_tmp view"); logger.info("Creating openaire_result_downloads_monthly_tmp view"); - String sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_downloads_monthly_tmp " + - "AS SELECT entity_id AS id, COUNT(entity_id) as downloads, " + - "SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) AS openaire_referrer, " + - "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + - "FROM " + ConnectDB.getUsageRawDataDBSchema()+ ".piwiklog where action='download' " + - "AND (source_item_type='oaItem' OR source_item_type='repItem') " + - "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) , source " + - "ORDER BY source, entity_id, month"; + String sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + + ".openaire_result_downloads_monthly_tmp " + + "AS SELECT entity_id, " + + "reflect('java.net.URLDecoder', 'decode', entity_id) AS id," + + "COUNT(entity_id) as downloads, " + + "SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".piwiklog where action='download' " + + "AND (source_item_type='oaItem' OR source_item_type='repItem') " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) , source " + + "ORDER BY source, entity_id, month"; stmt.executeUpdate(sql); logger.info("Created openaire_result_downloads_monthly_tmp view"); logger.info("Dropping openaire_downloads_stats_tmp table"); - String drop_views_stats = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".openaire_downloads_stats_tmp"; + String drop_views_stats = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".openaire_downloads_stats_tmp"; stmt.executeUpdate(drop_views_stats); logger.info("Dropped openaire_downloads_stats_tmp table"); logger.info("Creating openaire_downloads_stats_tmp table"); - sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp AS " + - "SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + - "max(downloads) AS count, max(openaire_referrer) AS openaire " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_downloads_monthly_tmp p, " + - ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + - "WHERE p.source=d.piwik_id and p.id=ro.oid " + - "GROUP BY d.id, ro.id, month " + - "ORDER BY d.id, ro.id, month "; + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp AS " + + "SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(downloads) AS count, max(openaire_referrer) AS openaire " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_downloads_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE p.source=d.piwik_id and p.id=ro.oid AND ro.oid!='200' " + + "GROUP BY d.id, ro.id, month " + + "ORDER BY d.id, ro.id, month "; stmt.executeUpdate(sql); logger.info("Created downloads_stats table"); - logger.info("Dropping openaire_result_downloads_monthly_tmp view"); - sql = "DROP VIEW IF EXISTS "+ConnectDB.getUsageStatsDBSchema() + ".openaire_result_downloads_monthly_tmp"; + sql = "DROP VIEW IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".openaire_result_downloads_monthly_tmp"; logger.info("Dropped openaire_result_downloads_monthly_tmp view "); stmt.executeUpdate(sql); stmt.close(); - //ConnectDB.getHiveConnection().close(); + // ConnectDB.getHiveConnection().close(); + } + + public void uploadOldPedocs() throws Exception { + stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + // Dropping Pedocs pedocs_views_stats_tmp table + logger.info("Dropping Pedocs pedocs_views_stats_tmp table"); + String sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_views_stats_tmp"; + logger.info("Dropped pedocs_views_stats_tmp table "); + stmt.executeUpdate(sql); + + // Dropping Pedocs pedocs_downloads_stats table + logger.info("Dropping pedocs_downloads_stats table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_downloads_stats"; + logger.info("Dropped pedocs_downloads_stats table "); + stmt.executeUpdate(sql); + + // Creating Pedocs pedocs_views_stats_tmp table + logger.info("Creating Pedocs pedocs_views_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_views_stats_tmp AS " + + "SELECT 'OpenAIRE' as source, 'opendoar____::ab1a4d0dd4d48a2ba1077c4494791306' as repository_id," + + "r.id as result_id,date,counter_abstract as count, 0 as openaire " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".pedocsoldviews p, " + ConnectDB.getStatsDBSchema() + + ".result_oids r where r.oid=p.identifier"; + stmt.executeUpdate(sql); + logger.info("Created pedocs_views_stats_tmp table "); + + // Creating Pedocs pedocs_downloads_stats_tmp table + logger.info("Creating Pedocs pedocs_downloads_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_downloads_stats_tmp AS " + + "SELECT 'OpenAIRE' as source, 'opendoar____::ab1a4d0dd4d48a2ba1077c4494791306' as repository_id," + + "r.id as result_id, date, counter as count, 0 as openaire " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".pedocsolddownloads p, " + ConnectDB.getStatsDBSchema() + + ".result_oids r where r.oid=p.identifier"; + stmt.executeUpdate(sql); + logger.info("Created pedocs_downloads_stats_tmp table "); + + } + + public void uploadTUDELFTStats() throws Exception { + stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); + + // Dropping TUDELFT tudelft_result_views_monthly_tmp view + logger.info("Dropping TUDELFT tudelft_result_views_monthly_tmp view"); + String sql = "DROP view IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_views_monthly_tmp"; + logger.info("Dropped tudelft_result_views_monthly_tmp view "); + stmt.executeUpdate(sql); + + // Dropping TUDELFT tudelft_result_views_monthly_tmp view + logger.info("Dropping TUDELFT tudelft_result_downloads_monthly_tmp view"); + sql = "DROP view IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_downloads_monthly_tmp"; + logger.info("Dropped tudelft_result_downloads_monthly_tmp view "); + stmt.executeUpdate(sql); + + // Dropping TUDELFT tudelft_views_stats_tmp table + logger.info("Dropping TUDELFT tudelft_views_stats_tmp table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_views_stats_tmp"; + logger.info("Dropped tudelft_views_stats_tmp table "); + stmt.executeUpdate(sql); + + // Dropping TUDELFT tudelft_downloads_stats_tmp table + logger.info("Dropping TUDELFT tudelft_downloads_stats_tmp table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_downloads_stats_tmp"; + logger.info("Dropped tudelft_downloads_stats_tmp table "); + stmt.executeUpdate(sql); + + // Creating TUDELFT tudelft_result_views_monthly_tmp view + logger.info("Creating TUDELFT tudelft_result_views_monthly_tmp view"); + sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_views_monthly_tmp " + + "AS SELECT entity_id, reflect('java.net.URLDecoder', 'decode', entity_id) AS id, " + + "COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".piwiklog " + + "WHERE action='action' and (source_item_type='oaItem' or source_item_type='repItem') and source=252 " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), source ORDER BY source, entity_id"; + stmt.executeUpdate(sql); + logger.info("Created tudelft_result_views_monthly_tmp view "); + + // Creating TUDELFT tudelft_views_stats_tmp table + logger.info("Creating TUDELFT tudelft_views_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_views_stats_tmp AS " + + "SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(views) AS count, max(openaire_referrer) AS openaire FROM " + ConnectDB.getUsageStatsDBSchema() + + ".tudelft_result_views_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE concat('tud:',p.id)=ro.oid and d.id='opendoar____::c9892a989183de32e976c6f04e700201' " + + "GROUP BY d.id, ro.id, month ORDER BY d.id, ro.id"; + stmt.executeUpdate(sql); + logger.info("Created TUDELFT tudelft_views_stats_tmp table"); + + // Creating TUDELFT tudelft_result_downloads_monthly_tmp view + logger.info("Creating TUDELFT tudelft_result_downloads_monthly_tmp view"); + sql = "CREATE OR REPLACE VIEW " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_downloads_monthly_tmp " + + "AS SELECT entity_id, reflect('java.net.URLDecoder', 'decode', entity_id) AS id, " + + "COUNT(entity_id) as views, SUM(CASE WHEN referrer_name LIKE '%openaire%' THEN 1 ELSE 0 END) AS openaire_referrer, " + + "CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')) AS month, source " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".piwiklog " + + "WHERE action='download' and (source_item_type='oaItem' or source_item_type='repItem') and source=252 " + + "GROUP BY entity_id, CONCAT(YEAR(timestamp), '/', LPAD(MONTH(timestamp), 2, '0')), source ORDER BY source, entity_id"; + stmt.executeUpdate(sql); + logger.info("Created tudelft_result_downloads_monthly_tmp view "); + + // Creating TUDELFT tudelft_downloads_stats_tmp table + logger.info("Creating TUDELFT tudelft_downloads_stats_tmp table"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_downloads_stats_tmp AS " + + "SELECT 'OpenAIRE' as source, d.id as repository_id, ro.id as result_id, month as date, " + + "max(views) AS count, max(openaire_referrer) AS openaire FROM " + ConnectDB.getUsageStatsDBSchema() + + ".tudelft_result_downloads_monthly_tmp p, " + + ConnectDB.getStatsDBSchema() + ".datasource d, " + ConnectDB.getStatsDBSchema() + ".result_oids ro " + + "WHERE concat('tud:',p.id)=ro.oid and d.id='opendoar____::c9892a989183de32e976c6f04e700201' " + + "GROUP BY d.id, ro.id, month ORDER BY d.id, ro.id"; + stmt.executeUpdate(sql); + logger.info("Created TUDELFT tudelft_downloads_stats_tmp table"); + + // Dropping TUDELFT tudelft_result_views_monthly_tmp view + logger.info("Dropping TUDELFT tudelft_result_views_monthly_tmp view"); + sql = "DROP view IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_views_monthly_tmp"; + logger.info("Dropped tudelft_result_views_monthly_tmp view "); + stmt.executeUpdate(sql); + + // Dropping TUDELFT tudelft_result_views_monthly_tmp view + logger.info("Dropping TUDELFT tudelft_result_downloads_monthly_tmp view"); + sql = "DROP view IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_result_downloads_monthly_tmp"; + logger.info("Dropped tudelft_result_downloads_monthly_tmp view "); + stmt.executeUpdate(sql); + } public void finalizeStats() throws Exception { stmt = ConnectDB.getHiveConnection().createStatement(); ConnectDB.getHiveConnection().setAutoCommit(false); - //Dropping views_stats table - logger.info("Dropping views_stats table"); - String sql = "DROP TABLE IF EXISTS "+ConnectDB.getUsageStatsDBSchema() + ".views_stats"; + // Dropping views_stats table + logger.info("Dropping views_stats table"); + String sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; logger.info("Dropped views_stats table "); stmt.executeUpdate(sql); - //Dropping downloads_stats table - logger.info("Dropping downloads_stats table"); - sql = "DROP TABLE IF EXISTS "+ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; + // Dropping downloads_stats table + logger.info("Dropping downloads_stats table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; logger.info("Dropped downloads_stats table "); stmt.executeUpdate(sql); - //Dropping page_views_stats table - logger.info("Dropping pageviews_stats table"); - sql = "DROP TABLE IF EXISTS "+ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; + // Dropping page_views_stats table + logger.info("Dropping pageviews_stats table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; logger.info("Dropped pageviews_stats table "); stmt.executeUpdate(sql); - //Creating views_stats table + // Dropping usage_stats table + logger.info("Dropping usage_stats table"); + sql = "DROP TABLE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; + logger.info("Dropped usage_stats table "); + stmt.executeUpdate(sql); + + // Creating views_stats table logger.info("Creating views_stats table"); - String createViewsStats = "CREATE TABLE IF NOT EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".views_stats " + - "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_views_stats_tmp STORED AS PARQUET"; + String createViewsStats = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".views_stats " + + "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_views_stats_tmp STORED AS PARQUET"; stmt.executeUpdate(createViewsStats); logger.info("Created views_stats table"); - - //Inserting OpenAIRE views stats - logger.info("Inserting Openaire data to views_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_views_stats_tmp"; - stmt.executeUpdate(sql); - logger.info("Openaire views updated to views_stats"); - //Inserting Lareferencia views stats - logger.info("Inserting LaReferencia data to views_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_views_stats_tmp"; + // Inserting OpenAIRE views stats + logger.info("Inserting Openaire data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_views_stats_tmp"; stmt.executeUpdate(sql); - logger.info("LaReferencia views updated to views_stats"); - + logger.info("Openaire views updated to views_stats"); + + // Inserting Pedocs old views stats + logger.info("Inserting Pedocs old data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_views_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Pedocs views updated to views_stats"); + + // Inserting TUDELFT views stats + logger.info("Inserting TUDELFT data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_views_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("TUDELFT views updated to views_stats"); + + // Inserting Lareferencia views stats + logger.info("Inserting LaReferencia data to views_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_views_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("LaReferencia views updated to views_stats"); logger.info("Creating downloads_stats table"); - String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".downloads_stats " + - "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp STORED AS PARQUET"; + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".downloads_stats " + + "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp STORED AS PARQUET"; stmt.executeUpdate(createDownloadsStats); logger.info("Created downloads_stats table"); - //Inserting OpenAIRE downloads stats + // Inserting OpenAIRE downloads stats logger.info("Inserting OpenAIRE data to downloads_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp"; + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_downloads_stats_tmp"; stmt.executeUpdate(sql); + logger.info("Inserted OpenAIRE data to downloads_stats"); - //Inserting Lareferencia downloads stats + // Inserting Pedocs old downloads stats + logger.info("Inserting PeDocs old data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".pedocs_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Inserted Pedocs data to downloads_stats"); + + // Inserting TUDELFT downloads stats + logger.info("Inserting TUDELFT old data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".tudelft_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("Inserted TUDELFT data to downloads_stats"); + + // Inserting Lareferencia downloads stats logger.info("Inserting LaReferencia data to downloads_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_downloads_stats_tmp"; + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".la_downloads_stats_tmp"; stmt.executeUpdate(sql); - logger.info("Lareferencia downloads updated to downloads_stats"); - - //Inserting IRUS downloads stats - logger.info("Inserting IRUS data to downloads_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_downloads_stats_tmp"; - stmt.executeUpdate(sql); - logger.info("IRUS downloads updated to downloads_stats"); + logger.info("Lareferencia downloads updated to downloads_stats"); - //Inserting SARC-OJS downloads stats - logger.info("Inserting SARC data to downloads_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_downloads_stats_tmp"; + // Inserting IRUS downloads stats + logger.info("Inserting IRUS data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_downloads_stats_tmp"; stmt.executeUpdate(sql); - logger.info("SARC-OJS downloads updated to downloads_stats"); - - - logger.info("Creating pageviews_stats table"); + logger.info("IRUS downloads updated to downloads_stats"); + + // Inserting SARC-OJS downloads stats + logger.info("Inserting SARC data to downloads_stats"); + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_downloads_stats_tmp"; + stmt.executeUpdate(sql); + logger.info("SARC-OJS downloads updated to downloads_stats"); + + logger.info("Creating pageviews_stats table"); String create_pageviews_stats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".pageviews_stats " + - "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_pageviews_stats_tmp STORED AS PARQUET"; + + ".pageviews_stats " + + "LIKE " + ConnectDB.getUsageStatsDBSchema() + ".openaire_pageviews_stats_tmp STORED AS PARQUET"; stmt.executeUpdate(create_pageviews_stats); logger.info("Created pageviews_stats table"); - - //Inserting OpenAIRE views stats from Portal + + // Inserting OpenAIRE views stats from Portal logger.info("Inserting data to page_views_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_pageviews_stats_tmp"; + sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats " + + "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".openaire_pageviews_stats_tmp"; stmt.executeUpdate(sql); - + logger.info("Dropping full_dates table"); - String dropFullDates = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".full_dates"; + String dropFullDates = "DROP TABLE IF EXISTS " + + ConnectDB.getUsageStatsDBSchema() + + ".full_dates"; stmt.executeUpdate(dropFullDates); logger.info("Dropped full_dates table"); @@ -310,35 +479,80 @@ public class PiwikStatsDB { int diffMonth = diffYear * 12 + endCalendar.get(Calendar.MONTH) - startCalendar.get(Calendar.MONTH); logger.info("Creating full_dates table"); - sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".full_dates AS " + - "SELECT from_unixtime(unix_timestamp(cast(add_months(from_date,i) AS DATE)), 'yyyy/MM') AS txn_date " + - "FROM (SELECT DATE '2016-01-01' AS from_date) p " + - "LATERAL VIEW " + - "posexplode(split(space(" + diffMonth + "),' ')) pe AS i,x"; + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".full_dates AS " + + "SELECT from_unixtime(unix_timestamp(cast(add_months(from_date,i) AS DATE)), 'yyyy/MM') AS txn_date " + + "FROM (SELECT DATE '2016-01-01' AS from_date) p " + + "LATERAL VIEW " + + "posexplode(split(space(" + diffMonth + "),' ')) pe AS i,x"; stmt.executeUpdate(sql); logger.info("Created full_dates table"); - - logger.info("Inserting data to usage_stats"); - sql = "CREATE TABLE IF NOT EXISTS "+ConnectDB.getUsageStatsDBSchema() + ".usage_stats AS " + - "SELECT coalesce(ds.source, vs.source) as source, " + - "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + - "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + - "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + - "coalesce(ds.openaire, 0) as openaire_downloads, " + - "coalesce(vs.openaire, 0) as openaire_views " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats AS ds FULL OUTER JOIN " + - ConnectDB.getUsageStatsDBSchema() + ".views_stats AS vs ON ds.source=vs.source " + - "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; - stmt.executeUpdate(sql); - logger.info("Inserted data to usage_stats"); + logger.info("Inserting data to usage_stats"); + sql = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats AS " + + "SELECT coalesce(ds.source, vs.source) as source, " + + "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + + "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + + "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + + "coalesce(ds.openaire, 0) as openaire_downloads, " + + "coalesce(vs.openaire, 0) as openaire_views " + + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats AS ds FULL OUTER JOIN " + + ConnectDB.getUsageStatsDBSchema() + ".views_stats AS vs ON ds.source=vs.source " + + "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; + stmt.executeUpdate(sql); + logger.info("Inserted data to usage_stats"); + logger.info("Building views at permanent DB starts at: " + new Timestamp(System.currentTimeMillis())); + + logger.info("Dropping view views_stats on permanent usagestats DB"); + sql = "DROP VIEW IF EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + logger.info("Dropped view views_stats on permanent usagestats DB"); + + logger.info("Create view views_stats on permanent usagestats DB"); + sql = "CREATE VIEW IF NOT EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".views_stats" + + " AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + logger.info("Created view views_stats on permanent usagestats DB"); + + logger.info("Dropping view pageviews_stats on permanent usagestats DB"); + sql = "DROP VIEW IF EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + logger.info("Dropped view pageviews_stats on permanent usagestats DB"); + + logger.info("Create view pageviews_stats on permanent usagestats DB"); + sql = "CREATE VIEW IF NOT EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".pageviews_stats" + + " AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + logger.info("Created view pageviews_stats on permanent usagestats DB"); + + logger.info("Dropping view downloads_stats on permanent usagestats DB"); + sql = "DROP VIEW IF EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); + logger.info("Dropped view on downloads_stats on permanent usagestats DB"); + + logger.info("Create view on downloads_stats on permanent usagestats DB"); + sql = "CREATE VIEW IF NOT EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".downloads_stats" + + " AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); + logger.info("Created view on downloads_stats on permanent usagestats DB"); + + logger.info("Dropping view usage_stats on permanent usagestats DB"); + sql = "DROP VIEW IF EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + logger.info("Dropped view on usage_stats on permanent usagestats DB"); + + logger.info("Create view on usage_stats on permanent usagestats DB"); + sql = "CREATE VIEW IF NOT EXISTS " + ConnectDB.getUsagestatsPermanentDBSchema() + ".usage_stats" + + " AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + logger.info("Created view on usage_stats on permanent usagestats DB"); + + logger.info("Building views at permanent DB ends at: " + new Timestamp(System.currentTimeMillis())); stmt.close(); ConnectDB.getHiveConnection().close(); } - private Connection getConnection() throws SQLException { return ConnectDB.getHiveConnection(); } diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/SarcStats.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/SarcStats.java index 2d224075f..880233f00 100644 --- a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/SarcStats.java +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/SarcStats.java @@ -1,3 +1,4 @@ + package eu.dnetlib.oa.graph.usagestatsbuild.export; import java.io.*; @@ -33,74 +34,74 @@ import org.slf4j.LoggerFactory; */ public class SarcStats { - private Statement stmtHive = null; - private Statement stmtImpala = null; + private Statement stmtHive = null; + private Statement stmtImpala = null; - private static final Logger logger = LoggerFactory.getLogger(SarcStats.class); + private static final Logger logger = LoggerFactory.getLogger(SarcStats.class); - public SarcStats() throws Exception { + public SarcStats() throws Exception { // createTables(); - } + } - private void createTables() throws Exception { - try { + private void createTables() throws Exception { + try { - stmtHive = ConnectDB.getHiveConnection().createStatement(); - String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilog(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; - stmtHive.executeUpdate(sqlCreateTableSushiLog); + stmtHive = ConnectDB.getHiveConnection().createStatement(); + String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilog(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; + stmtHive.executeUpdate(sqlCreateTableSushiLog); - // String sqlCopyPublicSushiLog="INSERT INTO sushilog SELECT * FROM public.sushilog;"; - // stmt.executeUpdate(sqlCopyPublicSushiLog); - String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " - + " ON INSERT TO sushilog " - + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," - + "sushilog.rid, sushilog.date " - + "FROM sushilog " - + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; - stmtHive.executeUpdate(sqlcreateRuleSushiLog); - String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; - stmtHive.executeUpdate(createSushiIndex); + // String sqlCopyPublicSushiLog="INSERT INTO sushilog SELECT * FROM public.sushilog;"; + // stmt.executeUpdate(sqlCopyPublicSushiLog); + String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " + + " ON INSERT TO sushilog " + + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," + + "sushilog.rid, sushilog.date " + + "FROM sushilog " + + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; + stmtHive.executeUpdate(sqlcreateRuleSushiLog); + String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; + stmtHive.executeUpdate(createSushiIndex); - stmtHive.close(); - ConnectDB.getHiveConnection().close(); - logger.info("Sushi Tables Created"); - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - } - } + stmtHive.close(); + ConnectDB.getHiveConnection().close(); + logger.info("Sushi Tables Created"); + } catch (Exception e) { + logger.error("Failed to create tables: " + e); + throw new Exception("Failed to create tables: " + e.toString(), e); + } + } - public void processSarc() throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); + public void processSarc() throws Exception { + Statement stmt = ConnectDB.getHiveConnection().createStatement(); + ConnectDB.getHiveConnection().setAutoCommit(false); - logger.info("Creating sarc_downloads_stats_tmp table"); - String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sarc_downloads_stats_tmp " - + "(`source` string, " - + "`repository_id` string, " - + "`result_id` string, " - + "`date` string, " - + "`count` bigint, " - + "`openaire` bigint)"; - stmt.executeUpdate(createDownloadsStats); - logger.info("Created sarc_downloads_stats_tmp table"); + logger.info("Creating sarc_downloads_stats_tmp table"); + String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + + ".sarc_downloads_stats_tmp " + + "(`source` string, " + + "`repository_id` string, " + + "`result_id` string, " + + "`date` string, " + + "`count` bigint, " + + "`openaire` bigint)"; + stmt.executeUpdate(createDownloadsStats); + logger.info("Created sarc_downloads_stats_tmp table"); - logger.info("Inserting into sarc_downloads_stats_tmp"); - String insertSarcStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_downloads_stats_tmp " - + "SELECT s.source, d.id AS repository_id, " - + "ro.id as result_id, CONCAT(CAST(YEAR(`date`) AS STRING), '/', " - + "LPAD(CAST(MONTH(`date`) AS STRING), 2, '0')) AS `date`, s.count, '0' " - + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".sushilog s, " - + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " - + ConnectDB.getStatsDBSchema() + ".result_pids ro " - + "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND d.id like CONCAT('%', 'sarcservicod', '%') " - + "AND s.rid=ro.pid AND ro.type='Digital Object Identifier' AND s.metric_type='ft_total' AND s.source='SARC-OJS'"; - stmt.executeUpdate(insertSarcStats); - logger.info("Inserted into sarc_downloads_stats_tmp"); - - stmt.close(); - //ConnectDB.getHiveConnection().close(); - } + logger.info("Inserting into sarc_downloads_stats_tmp"); + String insertSarcStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_downloads_stats_tmp " + + "SELECT s.source, d.id AS repository_id, " + + "ro.id as result_id, CONCAT(CAST(YEAR(`date`) AS STRING), '/', " + + "LPAD(CAST(MONTH(`date`) AS STRING), 2, '0')) AS `date`, s.count, '0' " + + "FROM " + ConnectDB.getUsageRawDataDBSchema() + ".sushilog s, " + + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " + + ConnectDB.getStatsDBSchema() + ".result_pids ro " + + "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND d.id like CONCAT('%', 'sarcservicod', '%') " + + "AND s.rid=ro.pid AND ro.type='Digital Object Identifier' AND s.metric_type='ft_total' AND s.source='SARC-OJS'"; + stmt.executeUpdate(insertSarcStats); + logger.info("Inserted into sarc_downloads_stats_tmp"); + + stmt.close(); + // ConnectDB.getHiveConnection().close(); + } } diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/UsageStatsExporter.java index 43abb1681..47986f52a 100644 --- a/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/UsageStatsExporter.java +++ b/dhp-workflows/dhp-usage-stats-build/src/main/java/eu/dnetlib/oa/graph/usagestatsbuild/export/UsageStatsExporter.java @@ -1,3 +1,4 @@ + package eu.dnetlib.oa.graph.usagestatsbuild.export; import java.io.IOException; @@ -17,90 +18,110 @@ import org.slf4j.LoggerFactory; */ public class UsageStatsExporter { - public UsageStatsExporter() { + public UsageStatsExporter() { - } + } - private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); + private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); - public void export() throws Exception { + public void export() throws Exception { - logger.info("Initialising DB properties"); - ConnectDB.init(); + logger.info("Initialising DB properties"); + ConnectDB.init(); // runImpalaQuery(); - PiwikStatsDB piwikstatsdb = new PiwikStatsDB(); + PiwikStatsDB piwikstatsdb = new PiwikStatsDB(); - logger.info("Re-creating database and tables"); - if (ExecuteWorkflow.recreateDbAndTables) { - piwikstatsdb.recreateDBAndTables(); - logger.info("DB-Tables are created "); - } + logger.info("Re-creating database and tables"); + if (ExecuteWorkflow.recreateDbAndTables) { + piwikstatsdb.recreateDBAndTables(); + logger.info("DB-Tables are created "); + } // else { // piwikstatsdb.createTmpTables(); // logger.info("TmpTables are created "); // } - if (ExecuteWorkflow.processPiwikLogs) { - logger.info("Processing logs"); - piwikstatsdb.processLogs(); - } + if (ExecuteWorkflow.processPiwikLogs) { + logger.info("Processing Piwik logs"); + piwikstatsdb.processLogs(); + logger.info("Piwik logs Done"); + logger.info("Processing Pedocs Old Stats"); + piwikstatsdb.uploadOldPedocs(); + logger.info("Processing Pedocs Old Stats Done"); + logger.info("Processing TUDELFT Stats"); + piwikstatsdb.uploadTUDELFTStats(); + logger.info("Processing TUDELFT Stats Done"); - LaReferenciaStats lastats = new LaReferenciaStats(); + } - if (ExecuteWorkflow.processLaReferenciaLogs) { - logger.info("Processing LaReferencia logs"); - lastats.processLogs(); - logger.info("LaReferencia logs done"); - } - - IrusStats irusstats = new IrusStats(); - - if (ExecuteWorkflow.irusProcessStats) { - logger.info("Processing IRUS"); - irusstats.processIrusStats(); - logger.info("Irus done"); - } + LaReferenciaStats lastats = new LaReferenciaStats(); - SarcStats sarcStats = new SarcStats(); + if (ExecuteWorkflow.processLaReferenciaLogs) { + logger.info("Processing LaReferencia logs"); + lastats.processLogs(); + logger.info("LaReferencia logs done"); + } - if (ExecuteWorkflow.sarcProcessStats) { - sarcStats.processSarc(); - } - logger.info("Sarc done"); + IrusStats irusstats = new IrusStats(); - // finalize usagestats - if (ExecuteWorkflow.finalizeStats) { - piwikstatsdb.finalizeStats(); - logger.info("Finalized stats"); - } + if (ExecuteWorkflow.irusProcessStats) { + logger.info("Processing IRUS"); + irusstats.processIrusStats(); + logger.info("Irus done"); + } - // Make the tables available to Impala - if (ExecuteWorkflow.finalTablesVisibleToImpala) { - logger.info("Making tables visible to Impala"); - invalidateMetadata(); - } + SarcStats sarcStats = new SarcStats(); - logger.info("End"); - } + if (ExecuteWorkflow.sarcProcessStats) { + sarcStats.processSarc(); + } + logger.info("Sarc done"); - private void invalidateMetadata() throws SQLException { - Statement stmt = null; + // finalize usagestats + if (ExecuteWorkflow.finalizeStats) { + piwikstatsdb.finalizeStats(); + logger.info("Finalized stats"); + } - stmt = ConnectDB.getImpalaConnection().createStatement(); + // Make the tables available to Impala + if (ExecuteWorkflow.finalTablesVisibleToImpala) { + logger.info("Making tables visible to Impala"); + invalidateMetadata(); + } - String sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; - stmt.executeUpdate(sql); + logger.info("End"); + } - sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; - stmt.executeUpdate(sql); + private void invalidateMetadata() throws SQLException { + Statement stmt = null; - sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; - stmt.executeUpdate(sql); + stmt = ConnectDB.getImpalaConnection().createStatement(); - sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; - stmt.executeUpdate(sql); + String sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); - stmt.close(); - ConnectDB.getHiveConnection().close(); - } + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsagestatsPermanentDBSchema() + ".downloads_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsagestatsPermanentDBSchema() + ".views_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsagestatsPermanentDBSchema() + ".usage_stats"; + stmt.executeUpdate(sql); + + sql = "INVALIDATE METADATA " + ConnectDB.getUsagestatsPermanentDBSchema() + ".pageviews_stats"; + stmt.executeUpdate(sql); + + stmt.close(); + ConnectDB.getHiveConnection().close(); + } } diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json index 3f121288e..407370ada 100644 --- a/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json +++ b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/export/usagestatsbuild_parameters.json @@ -1,237 +1,128 @@ [ - { - "paramName": "mat", - "paramLongName": "matomoAuthToken", - "paramDescription": "when true will stop SparkSession after job execution", - "paramRequired": false - }, - { - "paramName": "mbu", - "paramLongName": "matomoBaseURL", - "paramDescription": "URL of the isLookUp Service", - "paramRequired": true - }, - { - "paramName": "rlp", - "paramLongName": "repoLogPath", - "paramDescription": "nameNode of the source cluster", - "paramRequired": true - }, - { - "paramName": "plp", - "paramLongName": "portalLogPath", - "paramDescription": "namoNode of the target cluster", - "paramRequired": true - }, - { - "paramName": "pmi", - "paramLongName": "portalMatomoID", - "paramDescription": "namoNode of the target cluster", - "paramRequired": true - }, - { - "paramName": "iukbuw", - "paramLongName": "irusUKBaseURL", - "paramDescription": "working directory", - "paramRequired": true - }, - { - "paramName": "iukrp", - "paramLongName": "irusUKReportPath", - "paramDescription": "maximum number of map tasks used in the distcp process", - "paramRequired": true - }, - { - "paramName": "srpa", - "paramLongName": "sarcsReportPathArray", - "paramDescription": "memory for distcp action copying actionsets from remote cluster", - "paramRequired": true - }, - { - "paramName": "srpna", - "paramLongName": "sarcsReportPathNonArray", - "paramDescription": "timeout for distcp copying actions from remote cluster", - "paramRequired": true - }, - { - "paramName": "llp", - "paramLongName": "lareferenciaLogPath", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "lbu", - "paramLongName": "lareferenciaBaseURL", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "lat", - "paramLongName": "lareferenciaAuthToken", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "dbhu", - "paramLongName": "dbHiveUrl", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "dbiu", - "paramLongName": "dbImpalaUrl", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "urdbs", - "paramLongName": "usageRawDataDBSchema", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, { - "paramName": "usdbs", - "paramLongName": "usageStatsDBSchema", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "sdbs", - "paramLongName": "statsDBSchema", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "rdbt", - "paramLongName": "recreateDbAndTables", - "paramDescription": "Re-create database and initial tables?", - "paramRequired": true - }, - { - "paramName": "pwed", - "paramLongName": "piwikEmptyDirs", - "paramDescription": "Empty piwik directories?", - "paramRequired": true - }, - { - "paramName": "ppwl", - "paramLongName": "processPiwikLogs", - "paramDescription": "Process the piwiklogs (create & fill in the needed tables and process the data) based on the downloaded data", - "paramRequired": true - }, - { - "paramName": "dpwl", - "paramLongName": "downloadPiwikLogs", - "paramDescription": "download piwik logs?", - "paramRequired": true - }, - { - "paramName": "slp", - "paramLongName": "startingLogPeriod", - "paramDescription": "Starting log period", - "paramRequired": true - }, - { - "paramName": "elp", - "paramLongName": "endingLogPeriod", - "paramDescription": "Ending log period", - "paramRequired": true - }, - { - "paramName": "npidd", - "paramLongName": "numberOfPiwikIdsToDownload", - "paramDescription": "Limit the number of the downloaded piwikids to the first numberOfPiwikIdsToDownload", - "paramRequired": true - }, - { - "paramName": "nsidd", - "paramLongName": "numberOfSiteIdsToDownload", - "paramDescription": "Limit the number of the downloaded siteids (La Referencia logs) to the first numberOfSiteIdsToDownload", - "paramRequired": true - }, - { - "paramName": "lerd", - "paramLongName": "laReferenciaEmptyDirs", - "paramDescription": "Empty LaReferencia directories?", - "paramRequired": true - }, - { - "paramName": "plrl", - "paramLongName": "processLaReferenciaLogs", - "paramDescription": "Process the La Referencia logs (create & fill in the needed tables and process the data) based on the downloaded data", - "paramRequired": true - }, - { - "paramName": "dlrl", - "paramLongName": "downloadLaReferenciaLogs", - "paramDescription": "download La Referencia logs?", - "paramRequired": true - }, - { - "paramName": "icted", - "paramLongName": "irusCreateTablesEmptyDirs", - "paramDescription": "Irus section: Create tables and empty JSON directories?", - "paramRequired": true - }, - { - "paramName": "idr", - "paramLongName": "irusDownloadReports", - "paramDescription": "Irus section: Download reports?", - "paramRequired": true - }, - { - "paramName": "ipr", - "paramLongName": "irusProcessStats", - "paramDescription": "Irus section: Process stats?", - "paramRequired": true - }, - { - "paramName": "inod", - "paramLongName": "irusNumberOfOpendoarsToDownload", - "paramDescription": "Limit the number of the downloaded Opendoars (Irus) to the first irusNumberOfOpendoarsToDownload", - "paramRequired": true - }, - { - "paramName": "icted", - "paramLongName": "sarcCreateTablesEmptyDirs", - "paramDescription": "Sarc section: Create tables and empty JSON directories?", - "paramRequired": true - }, - { - "paramName": "idr", - "paramLongName": "sarcDownloadReports", - "paramDescription": "Sarc section: Download reports?", - "paramRequired": true - }, - { - "paramName": "ipr", - "paramLongName": "sarcProcessStats", - "paramDescription": "Sarc section: Process stats?", - "paramRequired": true - }, - { - "paramName": "inod", - "paramLongName": "sarcNumberOfIssnToDownload", - "paramDescription": "Limit the number of the downloaded ISSN (Sarc) to the first sarcNumberOfIssnToDownload", - "paramRequired": true - }, - - { - "paramName": "fs", - "paramLongName": "finalizeStats", - "paramDescription": "Create the usage_stats table?", - "paramRequired": true - }, - { - "paramName": "ftvi", - "paramLongName": "finalTablesVisibleToImpala", - "paramDescription": "Make the usage_stats, views_stats and downloads_stats tables visible to Impala", - "paramRequired": true - }, - { - "paramName": "nodt", - "paramLongName": "numberOfDownloadThreads", - "paramDescription": "Number of download threads", - "paramRequired": true - } + "paramName": "rlp", + "paramLongName": "repoLogPath", + "paramDescription": "nameNode of the source cluster", + "paramRequired": true + }, + { + "paramName": "plp", + "paramLongName": "portalLogPath", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "pmi", + "paramLongName": "portalMatomoID", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "iukrp", + "paramLongName": "irusUKReportPath", + "paramDescription": "maximum number of map tasks used in the distcp process", + "paramRequired": true + }, + { + "paramName": "srpa", + "paramLongName": "sarcsReportPathArray", + "paramDescription": "memory for distcp action copying actionsets from remote cluster", + "paramRequired": true + }, + { + "paramName": "srpna", + "paramLongName": "sarcsReportPathNonArray", + "paramDescription": "timeout for distcp copying actions from remote cluster", + "paramRequired": true + }, + { + "paramName": "llp", + "paramLongName": "lareferenciaLogPath", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbhu", + "paramLongName": "dbHiveUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "dbiu", + "paramLongName": "dbImpalaUrl", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "urdbs", + "paramLongName": "usageRawDataDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "usdbs", + "paramLongName": "usageStatsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "sdbs", + "paramLongName": "statsDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "uspdbs", + "paramLongName": "usagestatsPermanentDBSchema", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + }, + { + "paramName": "rdbt", + "paramLongName": "recreateDbAndTables", + "paramDescription": "Re-create database and initial tables?", + "paramRequired": true + }, + { + "paramName": "ppwl", + "paramLongName": "processPiwikLogs", + "paramDescription": "Process the piwiklogs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "plrl", + "paramLongName": "processLaReferenciaLogs", + "paramDescription": "Process the La Referencia logs (create & fill in the needed tables and process the data) based on the downloaded data", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "irusProcessStats", + "paramDescription": "Irus section: Process stats?", + "paramRequired": true + }, + { + "paramName": "ipr", + "paramLongName": "sarcProcessStats", + "paramDescription": "Sarc section: Process stats?", + "paramRequired": true + }, + { + "paramName": "fs", + "paramLongName": "finalizeStats", + "paramDescription": "Create the usage_stats table?", + "paramRequired": true + }, + { + "paramName": "ftvi", + "paramLongName": "finalTablesVisibleToImpala", + "paramDescription": "Make the usage_stats, views_stats and downloads_stats tables visible to Impala", + "paramRequired": true + }, + { + "paramName": "nodt", + "paramLongName": "numberOfDownloadThreads", + "paramDescription": "Number of download threads", + "paramRequired": true + } ] diff --git a/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/workflow.xml b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/workflow.xml index 37700539b..71e8a50d6 100644 --- a/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-usage-stats-build/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestatsbuild/oozie_app/workflow.xml @@ -42,42 +42,24 @@ eu.dnetlib.oa.graph.usagestatsbuild.export.ExecuteWorkflow - --matomoAuthToken${matomoAuthToken} - --matomoBaseURL${matomoBaseURL} --repoLogPath${repoLogPath} --portalLogPath${portalLogPath} --portalMatomoID${portalMatomoID} - --irusUKBaseURL${irusUKBaseURL} --irusUKReportPath${irusUKReportPath} --sarcsReportPathArray${sarcsReportPathArray} --sarcsReportPathNonArray${sarcsReportPathNonArray} --lareferenciaLogPath${lareferenciaLogPath} - --lareferenciaBaseURL${lareferenciaBaseURL} - --lareferenciaAuthToken${lareferenciaAuthToken} --dbHiveUrl${hiveJdbcUrl} --dbImpalaUrl${impalaJdbcUrl} --usageRawDataDBSchema${usageRawDataDBSchema} --usageStatsDBSchema${usageStatsDBSchema} + --usagestatsPermanentDBSchema${usagestatsPermanentDBSchema} --statsDBSchema${statsDBSchema} --recreateDbAndTables${recreateDbAndTables} - --piwikEmptyDirs${piwikEmptyDirs} - --downloadPiwikLogs${downloadPiwikLogs} --processPiwikLogs${processPiwikLogs} - --startingLogPeriod${startingLogPeriod} - --endingLogPeriod${endingLogPeriod} - --numberOfPiwikIdsToDownload${numberOfPiwikIdsToDownload} - --numberOfSiteIdsToDownload${numberOfSiteIdsToDownload} - --laReferenciaEmptyDirs${laReferenciaEmptyDirs} - --downloadLaReferenciaLogs${downloadLaReferenciaLogs} --processLaReferenciaLogs${processLaReferenciaLogs} - --irusCreateTablesEmptyDirs${irusCreateTablesEmptyDirs} - --irusDownloadReports${irusDownloadReports} --irusProcessStats${irusProcessStats} - --irusNumberOfOpendoarsToDownload${irusNumberOfOpendoarsToDownload} - --sarcCreateTablesEmptyDirs${sarcCreateTablesEmptyDirs} - --sarcDownloadReports${sarcDownloadReports} --sarcProcessStats${sarcProcessStats} - --sarcNumberOfIssnToDownload${sarcNumberOfIssnToDownload} --finalizeStats${finalizeStats} --finalTablesVisibleToImpala${finalTablesVisibleToImpala} --numberOfDownloadThreads${numberOfDownloadThreads} From 399548f221eb252c381c58d7df77352620b048c8 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 14 Dec 2020 11:03:55 +0100 Subject: [PATCH 082/149] whitelist of topics --- .../dhp/broker/oa/GenerateEventsJob.java | 5 +- .../dhp/broker/oa/util/EventFinder.java | 9 +- .../oa/generate_all/oozie_app/workflow.xml | 6 + .../dhp/broker/oa/generate_events.json | 6 + .../oa/reindex/oozie_app/config-default.xml | 18 +++ .../broker/oa/reindex/oozie_app/workflow.xml | 116 ++++++++++++++++++ 6 files changed, 158 insertions(+), 2 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java index 457b82517..1ae241e34 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java @@ -59,6 +59,9 @@ public class GenerateEventsJob { final Set dsIdBlacklist = ClusterUtils.parseParamAsList(parser, "datasourceIdBlacklist"); log.info("datasourceIdBlacklist: {}", StringUtils.join(dsIdBlacklist, ",")); + final Set topicWhitelist = ClusterUtils.parseParamAsList(parser, "topicWhitelist"); + log.info("topicWhitelist: {}", StringUtils.join(topicWhitelist, ",")); + final SparkConf conf = new SparkConf(); runWithSparkSession(conf, isSparkSessionManaged, spark -> { @@ -75,7 +78,7 @@ public class GenerateEventsJob { final Dataset dataset = groups .map( g -> EventFinder - .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), + .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, topicWhitelist, accumulators), Encoders .bean(EventGroup.class)) .flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java index 1ab56cc34..103751f95 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java @@ -76,6 +76,7 @@ public class EventFinder { final Set dsIdWhitelist, final Set dsIdBlacklist, final Set dsTypeWhitelist, + final Set topicWhitelist, final Map accumulators) { final List> list = new ArrayList<>(); @@ -84,7 +85,13 @@ public class EventFinder { for (final OaBrokerRelatedDatasource targetDs : target.getDatasources()) { if (verifyTarget(targetDs, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) { for (final UpdateMatcher matcher : matchers) { - list.addAll(matcher.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators)); + for (final UpdateInfo info : matcher + .searchUpdatesForRecord(target, targetDs, results.getData(), accumulators)) { + if (topicWhitelist == null || topicWhitelist.isEmpty() + || topicWhitelist.contains(info.getTopic().getPath())) { + list.add(info); + } + } } } } diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index 1a1df418b..ea81c90d0 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -24,6 +24,11 @@ - a black list (comma separeted, - for empty list) of datasource ids + + topicWhitelist + * + a white list (comma separeted, * for all) of topics + esEventIndexName the elasticsearch index name for events @@ -447,6 +452,7 @@ --datasourceIdWhitelist${datasourceIdWhitelist} --datasourceTypeWhitelist${datasourceTypeWhitelist} --datasourceIdBlacklist${datasourceIdBlacklist} + --topicWhitelist${topicWhitelist} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json index a482ee2dc..e803bb5b9 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json @@ -28,5 +28,11 @@ "paramLongName": "datasourceIdBlacklist", "paramDescription": "a black list (comma separeted, - for empty list) of datasource ids", "paramRequired": true + }, + { + "paramName": "topicWhitelist", + "paramLongName": "topicWhitelist", + "paramDescription": "a white list (comma separeted, * for all) of topics", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml new file mode 100644 index 000000000..2e0ed9aee --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml @@ -0,0 +1,18 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml new file mode 100644 index 000000000..43c26f3a3 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml @@ -0,0 +1,116 @@ + + + + + outputDir + the path where the the generated data will be stored + + + esEventIndexName + the elasticsearch index name for events + + + esIndexHost + the elasticsearch host + + + maxIndexedEventsForDsAndTopic + the max number of events for each couple (ds/topic) + + + brokerApiBaseUrl + the url of the broker service api + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + IndexEventSubsetOnESJob + eu.dnetlib.dhp.broker.oa.IndexEventSubsetJob + dhp-broker-events-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.dynamicAllocation.maxExecutors="8" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --outputDir${outputDir} + --index${esEventIndexName} + --esHost${esIndexHost} + --maxEventsForTopic${maxIndexedEventsForDsAndTopic} + --brokerApiBaseUrl${brokerApiBaseUrl} + + + + + + + + + + \ No newline at end of file From d03756c962c31b8dc7929242dcca9e990b28a51a Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 14 Dec 2020 11:11:41 +0100 Subject: [PATCH 083/149] mkdir of output dir --- .../dhp/broker/oa/generate_all/oozie_app/workflow.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index ea81c90d0..250f928f8 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -116,15 +116,15 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + - + From 1506f49052655964bfbf8390c10361f92953b245 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 14 Dec 2020 11:14:03 +0100 Subject: [PATCH 084/149] Xml record serialization for author PIDs: 1) only one value per PID type is allowed; 2) orcid prevails over orcid_pending --- .../utils/AuthorPidTypeComparator.java | 52 +++++++++++++++++++ .../oa/provision/utils/XmlRecordFactory.java | 12 +++++ .../oa/provision/XmlRecordFactoryTest.java | 14 +++-- .../dnetlib/dhp/oa/provision/publication.json | 49 ++++++++--------- 4 files changed, 96 insertions(+), 31 deletions(-) create mode 100644 dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/AuthorPidTypeComparator.java diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/AuthorPidTypeComparator.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/AuthorPidTypeComparator.java new file mode 100644 index 000000000..7391569ed --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/AuthorPidTypeComparator.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.oa.provision.utils; + +import java.util.Comparator; +import java.util.Optional; + +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public class AuthorPidTypeComparator implements Comparator { + + @Override + public int compare(StructuredProperty left, StructuredProperty right) { + + String lClass = Optional + .ofNullable(left) + .map(StructuredProperty::getQualifier) + .map(Qualifier::getClassid) + .orElse(null); + + String rClass = Optional + .ofNullable(right) + .map(StructuredProperty::getQualifier) + .map(Qualifier::getClassid) + .orElse(null); + + if (lClass == null && rClass == null) + return 0; + if (lClass == null) + return 1; + if (rClass == null) + return -1; + + if (lClass.equals(rClass)) + return 0; + + if (lClass.equals(ModelConstants.ORCID)) + return -1; + if (rClass.equals(ModelConstants.ORCID)) + return 1; + + if (lClass.equals(ModelConstants.ORCID_PENDING)) + return -1; + if (rClass.equals(ModelConstants.ORCID_PENDING)) + return 1; + + return 0; + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index eba736228..9f16e99d8 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -254,6 +254,18 @@ public class XmlRecordFactory implements Serializable { p -> p, (p1, p2) -> p1)) .values() + .stream() + .collect( + Collectors + .groupingBy( + p -> p.getValue(), + Collectors + .mapping( + p -> p, + Collectors.minBy(new AuthorPidTypeComparator())))) + .values() + .stream() + .map(op -> op.get()) .forEach( sp -> { String pidType = getAuthorPidType(sp.getQualifier().getClassid()); diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 0f1912cc3..8ae8a55c3 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -14,6 +14,7 @@ import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; +import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; @@ -25,6 +26,9 @@ public class XmlRecordFactoryTest { private static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource"; + private static ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + @Test public void testXMLRecordFactory() throws IOException, DocumentException { @@ -33,7 +37,7 @@ public class XmlRecordFactoryTest { XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, otherDsTypeId); - Publication p = new ObjectMapper() + Publication p = OBJECT_MAPPER .readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class); String xml = xmlRecordFactory.build(new JoinedEntity<>(p)); @@ -44,10 +48,14 @@ public class XmlRecordFactoryTest { assertNotNull(doc); - // System.out.println(doc.asXML()); + System.out.println(doc.asXML()); - Assertions.assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid")); + Assertions.assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid")); Assertions.assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending")); + + Assertions.assertEquals("0000-0001-9613-9956", doc.valueOf("//creator[@rank = '2']/@orcid")); + Assertions.assertEquals("", doc.valueOf("//creator[@rank = '2']/@orcid_pending")); + // TODO add assertions based of values extracted from the XML record } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json index b6b183b15..ea7a30051 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -6,41 +6,15 @@ "name": "Jaehyun", "pid": [ { - "dataInfo": { - "deletedbyinference": false, - "inferenceprovenance": "", - "inferred": false, - "invisible": false, - "provenanceaction": { - "classid": "", - "classname": "", - "schemeid": "", - "schemename": "" - }, - "trust": "" - }, "qualifier": { "classid": "orcid", "classname": "Open Researcher and Contributor ID", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types" }, - "value": "0000-0001-9613-6639" + "value": "0000-0001-9613-6638" }, { - "dataInfo": { - "deletedbyinference": false, - "inferenceprovenance": "", - "inferred": false, - "invisible": false, - "provenanceaction": { - "classid": "", - "classname": "", - "schemeid": "", - "schemename": "" - }, - "trust": "" - }, "qualifier": { "classid": "orcid_pending", "classname": "Open Researcher and Contributor ID", @@ -57,7 +31,26 @@ "affiliation": [], "fullname": "Berrada, Salim", "name": "Salim", - "pid": [], + "pid": [ + { + "qualifier": { + "classid": "orcid", + "classname": "Open Researcher and Contributor ID", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "0000-0001-9613-9956" + }, + { + "qualifier": { + "classid": "orcid_pending", + "classname": "Open Researcher and Contributor ID", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "0000-0001-9613-9956" + } + ], "rank": 2, "surname": "Berrada" }, From a203aee32a61c67a20ebb2965ade8e150880089e Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 14 Dec 2020 12:02:33 +0100 Subject: [PATCH 085/149] ES wf properties --- .../dhp/broker/oa/IndexEventSubsetJob.java | 20 ++++++++++--- .../dhp/broker/oa/IndexNotificationsJob.java | 20 ++++++++++--- .../dnetlib/dhp/broker/oa/IndexOnESJob.java | 22 +++++++++++---- .../oa/generate_all/oozie_app/workflow.xml | 28 +++++++++++++++++++ .../eu/dnetlib/dhp/broker/oa/index_es.json | 24 ++++++++++++++++ .../dhp/broker/oa/index_event_subset.json | 24 ++++++++++++++++ .../dhp/broker/oa/index_notifications.json | 24 ++++++++++++++++ .../notifications_only/oozie_app/workflow.xml | 24 ++++++++++++++++ .../broker/oa/reindex/oozie_app/workflow.xml | 24 ++++++++++++++++ 9 files changed, 196 insertions(+), 14 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java index 72efc9e6b..e18a7ef56 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java @@ -55,6 +55,18 @@ public class IndexEventSubsetJob { final String indexHost = parser.get("esHost"); log.info("indexHost: {}", indexHost); + final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount"); + log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount); + + final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait"); + log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait); + + final String esBatchSizeEntries = parser.get("esBatchSizeEntries"); + log.info("esBatchSizeEntries: {}", esBatchSizeEntries); + + final String esNodesWanOnly = parser.get("esNodesWanOnly"); + log.info("esNodesWanOnly: {}", esNodesWanOnly); + final int maxEventsForTopic = NumberUtils.toInt(parser.get("maxEventsForTopic")); log.info("maxEventsForTopic: {}", maxEventsForTopic); @@ -86,10 +98,10 @@ public class IndexEventSubsetJob { esCfg.put("es.index.auto.create", "false"); esCfg.put("es.nodes", indexHost); esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY - esCfg.put("es.batch.write.retry.count", "8"); - esCfg.put("es.batch.write.retry.wait", "60s"); - esCfg.put("es.batch.size.entries", "200"); - esCfg.put("es.nodes.wan.only", "true"); + esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); + esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); + esCfg.put("es.batch.size.entries", esBatchSizeEntries); + esCfg.put("es.nodes.wan.only", esNodesWanOnly); log.info("*** Start indexing"); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index 29fc72d04..75f4eb066 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -63,6 +63,18 @@ public class IndexNotificationsJob { final String indexHost = parser.get("esHost"); log.info("indexHost: {}", indexHost); + final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount"); + log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount); + + final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait"); + log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait); + + final String esBatchSizeEntries = parser.get("esBatchSizeEntries"); + log.info("esBatchSizeEntries: {}", esBatchSizeEntries); + + final String esNodesWanOnly = parser.get("esNodesWanOnly"); + log.info("esNodesWanOnly: {}", esNodesWanOnly); + final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl"); log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl); @@ -92,10 +104,10 @@ public class IndexNotificationsJob { esCfg.put("es.index.auto.create", "false"); esCfg.put("es.nodes", indexHost); esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY - esCfg.put("es.batch.write.retry.count", "8"); - esCfg.put("es.batch.write.retry.wait", "60s"); - esCfg.put("es.batch.size.entries", "200"); - esCfg.put("es.nodes.wan.only", "true"); + esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); + esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); + esCfg.put("es.batch.size.entries", esBatchSizeEntries); + esCfg.put("es.nodes.wan.only", esNodesWanOnly); log.info("*** Start indexing"); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java index 006cde48c..380a689e4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java @@ -45,6 +45,18 @@ public class IndexOnESJob { final String indexHost = parser.get("esHost"); log.info("indexHost: {}", indexHost); + final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount"); + log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount); + + final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait"); + log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait); + + final String esBatchSizeEntries = parser.get("esBatchSizeEntries"); + log.info("esBatchSizeEntries: {}", esBatchSizeEntries); + + final String esNodesWanOnly = parser.get("esNodesWanOnly"); + log.info("esNodesWanOnly: {}", esNodesWanOnly); + final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); final JavaRDD inputRdd = ClusterUtils @@ -53,15 +65,13 @@ public class IndexOnESJob { .javaRDD(); final Map esCfg = new HashMap<>(); - // esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54"); - esCfg.put("es.index.auto.create", "false"); esCfg.put("es.nodes", indexHost); esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY - esCfg.put("es.batch.write.retry.count", "8"); - esCfg.put("es.batch.write.retry.wait", "60s"); - esCfg.put("es.batch.size.entries", "200"); - esCfg.put("es.nodes.wan.only", "true"); + esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); + esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); + esCfg.put("es.batch.size.entries", esBatchSizeEntries); + esCfg.put("es.nodes.wan.only", esNodesWanOnly); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); } diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index 250f928f8..d06eec87e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -41,6 +41,26 @@ esIndexHost the elasticsearch host + + esBatchWriteRetryCount + 8 + an ES configuration property + + + esBatchWriteRetryWait + 60s + an ES configuration property + + + esBatchSizeEntries + 200 + an ES configuration property + + + esNodesWanOnly + true + an ES configuration property + maxIndexedEventsForDsAndTopic the max number of events for each couple (ds/topic) @@ -478,6 +498,10 @@ --outputDir${outputDir} --index${esEventIndexName} --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} --maxEventsForTopic${maxIndexedEventsForDsAndTopic} --brokerApiBaseUrl${brokerApiBaseUrl} @@ -505,6 +529,10 @@ --outputDir${outputDir} --index${esNotificationsIndexName} --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} --brokerApiBaseUrl${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json index 079709ad8..f7e072d0f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json @@ -16,5 +16,29 @@ "paramLongName": "esHost", "paramDescription": "the ES host", "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryCount", + "paramLongName": "esBatchWriteRetryCount", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryWait", + "paramLongName": "esBatchWriteRetryWait", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchSizeEntries", + "paramLongName": "esBatchSizeEntries", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esNodesWanOnly", + "paramLongName": "esNodesWanOnly", + "paramDescription": "an ES configuration property", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json index 441249661..0046490bb 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json @@ -16,7 +16,31 @@ "paramLongName": "esHost", "paramDescription": "the ES host", "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryCount", + "paramLongName": "esBatchWriteRetryCount", + "paramDescription": "an ES configuration property", + "paramRequired": true }, + { + "paramName": "esBatchWriteRetryWait", + "paramLongName": "esBatchWriteRetryWait", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchSizeEntries", + "paramLongName": "esBatchSizeEntries", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esNodesWanOnly", + "paramLongName": "esNodesWanOnly", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, { "paramName": "n", "paramLongName": "maxEventsForTopic", diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json index 63e9b1263..370b48411 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json @@ -17,6 +17,30 @@ "paramDescription": "the ES host", "paramRequired": true }, + { + "paramName": "esBatchWriteRetryCount", + "paramLongName": "esBatchWriteRetryCount", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryWait", + "paramLongName": "esBatchWriteRetryWait", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchSizeEntries", + "paramLongName": "esBatchSizeEntries", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esNodesWanOnly", + "paramLongName": "esNodesWanOnly", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, { "paramName": "broker", "paramLongName": "brokerApiBaseUrl", diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml index c73b3fb52..248326d57 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml @@ -36,6 +36,26 @@ esIndexHost the elasticsearch host + + esBatchWriteRetryCount + 8 + an ES configuration property + + + esBatchWriteRetryWait + 60s + an ES configuration property + + + esBatchSizeEntries + 200 + an ES configuration property + + + esNodesWanOnly + true + an ES configuration property + maxIndexedEventsForDsAndTopic the max number of events for each couple (ds/topic) @@ -125,6 +145,10 @@ --outputDir${outputDir} --index${esNotificationsIndexName} --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} --brokerApiBaseUrl${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml index 43c26f3a3..9095004ad 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml @@ -13,6 +13,26 @@ esIndexHost the elasticsearch host + + esBatchWriteRetryCount + 8 + an ES configuration property + + + esBatchWriteRetryWait + 60s + an ES configuration property + + + esBatchSizeEntries + 200 + an ES configuration property + + + esNodesWanOnly + true + an ES configuration property + maxIndexedEventsForDsAndTopic the max number of events for each couple (ds/topic) @@ -102,6 +122,10 @@ --outputDir${outputDir} --index${esEventIndexName} --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} --maxEventsForTopic${maxIndexedEventsForDsAndTopic} --brokerApiBaseUrl${brokerApiBaseUrl} From 152916890f06763d1e562d54c81ab2cd75def7ac Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 14 Dec 2020 14:40:05 +0100 Subject: [PATCH 086/149] renamed test name --- .../resulttocommunityfromsemrel/ResultToCommunityJobTest.java | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java index a8e1ab841..7709e00a8 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java @@ -24,7 +24,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest; import eu.dnetlib.dhp.schema.oaf.Dataset; public class ResultToCommunityJobTest { @@ -66,7 +65,7 @@ public class ResultToCommunityJobTest { } @Test - public void test1() throws Exception { + public void testSparkResultToCommunityThroughSemRelJob() throws Exception { SparkResultToCommunityThroughSemRelJob .main( new String[] { From 7d325e2c5719a5ced2595229f4a8cb27cb276866 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 14 Dec 2020 14:40:54 +0100 Subject: [PATCH 087/149] using actual result subclasses instead of their parent class --- .../SparkResultToCommunityFromOrganizationJob.java | 2 +- .../SparkResultToCommunityThroughSemRelJob.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java index 66297e177..60ad43859 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java @@ -108,7 +108,7 @@ public class SparkResultToCommunityFromOrganizationJob { .stream() .map(con -> con.getId()) .collect(Collectors.toList()); - Result res = new Result(); + R res = (R) ret.getClass().newInstance(); res.setId(ret.getId()); List propagatedContexts = new ArrayList<>(); for (String cId : communitySet) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java index 0c613d1b4..5ac117693 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java @@ -130,7 +130,7 @@ public class SparkResultToCommunityThroughSemRelJob { }) .filter(Objects::nonNull) .collect(Collectors.toList()); - Result r = new Result(); + R r = (R) ret.getClass().newInstance(); r.setId(ret.getId()); r.setContext(contextList); ret.mergeFrom(r); From e8ef8c63d458fc0545bb7df79edd4d0255fe7e1a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 14 Dec 2020 15:04:44 +0100 Subject: [PATCH 088/149] delegate merging of OafEntity.dataInfo to the implementation of subclasses --- dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java | 2 -- .../src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java | 2 -- 2 files changed, 4 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index f4f5baa7b..494123fdf 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -62,8 +62,6 @@ public abstract class Oaf implements Serializable { .distinct() // relies on KeyValue.equals .collect(Collectors.toList())); - mergeOAFDataInfo(o); - setLastupdatetimestamp( Math .max( diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java index b698c957d..4be4d5d30 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java @@ -351,8 +351,6 @@ public class Project extends OafEntity implements Serializable { ? p.getFundedamount() : fundedamount; - // programme = mergeLists(programme, p.getProgramme()); - h2020classification = mergeLists(h2020classification, p.getH2020classification()); mergeOAFDataInfo(e); From b6f08ce226971f36df418c2b3edb93cdf01ea358 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 14 Dec 2020 15:07:31 +0100 Subject: [PATCH 089/149] re-adding the old junit:junit dep as solr-test-framework needs it --- dhp-workflows/dhp-graph-provision/pom.xml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index c8fab5207..0d44d8e5e 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -54,15 +54,18 @@ spark-solr + + + junit + junit + 4.12 + test + org.apache.solr solr-test-framework test - - junit - junit - com.carrotsearch * From 3e19cf7b4a214373c77ac2fd8cde52fceff0d478 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 14 Dec 2020 15:24:33 +0100 Subject: [PATCH 090/149] openaireId --- .../dhp/broker/oa/util/ConversionUtils.java | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index 053627a5f..085681488 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -74,7 +74,7 @@ public class ConversionUtils { } final OaBrokerRelatedDataset res = new OaBrokerRelatedDataset(); - res.setOpenaireId(d.getId()); + res.setOpenaireId(cleanOpenaireId(d.getId())); res.setOriginalId(first(d.getOriginalId())); res.setTitle(structPropValue(d.getTitle())); res.setPids(mappedList(d.getPid(), ConversionUtils::oafPidToBrokerPid)); @@ -89,7 +89,7 @@ public class ConversionUtils { } final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication(); - res.setOpenaireId(p.getId()); + res.setOpenaireId(cleanOpenaireId(p.getId())); res.setOriginalId(first(p.getOriginalId())); res.setTitle(structPropValue(p.getTitle())); res.setPids(mappedList(p.getPid(), ConversionUtils::oafPidToBrokerPid)); @@ -106,7 +106,7 @@ public class ConversionUtils { final OaBrokerMainEntity res = new OaBrokerMainEntity(); - res.setOpenaireId(result.getId()); + res.setOpenaireId(cleanOpenaireId(result.getId())); res.setOriginalId(first(result.getOriginalId())); res.setTypology(classId(result.getResulttype())); res.setTitles(structPropList(result.getTitle())); @@ -129,6 +129,10 @@ public class ConversionUtils { return res; } + private static String cleanOpenaireId(final String id) { + return id.contains("|") ? StringUtils.substringAfter(id, "|") : id; + } + private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) { if (author == null) { return null; @@ -188,7 +192,7 @@ public class ConversionUtils { } final OaBrokerProject res = new OaBrokerProject(); - res.setOpenaireId(p.getId()); + res.setOpenaireId(cleanOpenaireId(p.getId())); res.setTitle(fieldValue(p.getTitle())); res.setAcronym(fieldValue(p.getAcronym())); res.setCode(fieldValue(p.getCode())); @@ -214,7 +218,7 @@ public class ConversionUtils { } final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware(); - res.setOpenaireId(sw.getId()); + res.setOpenaireId(cleanOpenaireId(sw.getId())); res.setName(structPropValue(sw.getTitle())); res.setDescription(fieldValue(sw.getDescription())); res.setRepository(fieldValue(sw.getCodeRepositoryUrl())); @@ -230,7 +234,7 @@ public class ConversionUtils { final OaBrokerRelatedDatasource res = new OaBrokerRelatedDatasource(); res.setName(StringUtils.defaultIfBlank(fieldValue(ds.getOfficialname()), fieldValue(ds.getEnglishname()))); - res.setOpenaireId(ds.getId()); + res.setOpenaireId(cleanOpenaireId(ds.getId())); res.setType(classId(ds.getDatasourcetype())); return res; } From 991e675dc6b04b834bd62642a9eebf77bb106b35 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 14 Dec 2020 15:41:25 +0100 Subject: [PATCH 091/149] validation in claim rels --- .../raw/MigrateDbEntitiesApplication.java | 58 +++++++++++-------- .../dnetlib/dhp/oa/graph/sql/queryClaims.sql | 2 +- 2 files changed, 36 insertions(+), 24 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index b6210013c..3adbd244c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -23,7 +23,15 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM; -import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.*; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.asString; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.dataInfo; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.journal; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listFields; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listKeyValues; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.qualifier; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty; import java.io.Closeable; import java.io.IOException; @@ -462,44 +470,48 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i return Arrays.asList(r); } else { + final String validationDate = rs.getString("curation_date"); + final String sourceId = createOpenaireId(rs.getString(SOURCE_TYPE), rs.getString("source_id"), false); final String targetId = createOpenaireId(rs.getString(TARGET_TYPE), rs.getString("target_id"), false); final Relation r1 = new Relation(); final Relation r2 = new Relation(); - if (rs.getString(SOURCE_TYPE).equals("project")) { - r1.setCollectedfrom(collectedFrom); - r1.setRelType(RESULT_PROJECT); - r1.setSubRelType(OUTCOME); - r1.setRelClass(PRODUCES); - - r2.setCollectedfrom(collectedFrom); - r2.setRelType(RESULT_PROJECT); - r2.setSubRelType(OUTCOME); - r2.setRelClass(IS_PRODUCED_BY); - } else { - r1.setCollectedfrom(collectedFrom); - r1.setRelType(RESULT_RESULT); - r1.setSubRelType(RELATIONSHIP); - r1.setRelClass(IS_RELATED_TO); - - r2.setCollectedfrom(collectedFrom); - r2.setRelType(RESULT_RESULT); - r2.setSubRelType(RELATIONSHIP); - r2.setRelClass(IS_RELATED_TO); - } - + r1.setValidated(true); + r1.setValidationDate(validationDate); + r1.setCollectedfrom(collectedFrom); r1.setSource(sourceId); r1.setTarget(targetId); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); + r2.setValidationDate(validationDate); + r2.setValidated(true); + r2.setCollectedfrom(collectedFrom); r2.setSource(targetId); r2.setTarget(sourceId); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); + if (rs.getString(SOURCE_TYPE).equals("project")) { + r1.setRelType(RESULT_PROJECT); + r1.setSubRelType(OUTCOME); + r1.setRelClass(PRODUCES); + + r2.setRelType(RESULT_PROJECT); + r2.setSubRelType(OUTCOME); + r2.setRelClass(IS_PRODUCED_BY); + } else { + r1.setRelType(RESULT_RESULT); + r1.setSubRelType(RELATIONSHIP); + r1.setRelClass(IS_RELATED_TO); + + r2.setRelType(RESULT_RESULT); + r2.setSubRelType(RELATIONSHIP); + r2.setRelClass(IS_RELATED_TO); + } + return Arrays.asList(r1, r2); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql index 0390c11aa..f912d3ce9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql @@ -1 +1 @@ -SELECT source_type, source_id, target_type, target_id, semantics FROM claim WHERE approved=TRUE; \ No newline at end of file +SELECT source_type, source_id, target_type, target_id, semantics, curation_date::text FROM claim WHERE approved=TRUE; \ No newline at end of file From 12fa5d122ae959842c9d28602144ffe7514eeeaa Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 15 Dec 2020 08:30:26 +0100 Subject: [PATCH 092/149] fixed a problem with join --- .../eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java | 2 +- .../dhp/broker/oa/PrepareRelatedDatasetsJob.java | 5 +++-- .../dhp/broker/oa/PrepareRelatedProjectsJob.java | 2 +- .../broker/oa/PrepareRelatedPublicationsJob.java | 5 +++-- .../dhp/broker/oa/PrepareRelatedSoftwaresJob.java | 2 +- .../eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java | 11 +++++++++++ .../dnetlib/dhp/broker/oa/util/ConversionUtils.java | 2 +- .../oa/util/DatasourceRelationsAccumulator.java | 13 +++++++++++-- 8 files changed, 32 insertions(+), 10 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java index a575328e8..dc156cbcf 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java @@ -63,7 +63,7 @@ public class PrepareGroupsJob { .readPath(spark, workingDir + "/joinedEntities_step4", OaBrokerMainEntity.class); final Dataset mergedRels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); final TypedColumn, ResultGroup> aggr = new ResultAggregator() diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java index 8c2879b38..9bdf32a64 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java @@ -62,7 +62,7 @@ public class PrepareRelatedDatasetsJob { .map(ConversionUtils::oafDatasetToBrokerDataset, Encoders.bean(OaBrokerRelatedDataset.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass())) @@ -72,7 +72,8 @@ public class PrepareRelatedDatasetsJob { final Dataset dataset = rels .joinWith(datasets, datasets.col("openaireId").equalTo(rels.col("target")), "inner") .map(t -> { - final RelatedDataset rel = new RelatedDataset(t._1.getSource(), t._2); + final RelatedDataset rel = new RelatedDataset(t._1.getSource(), + t._2); rel.getRelDataset().setRelType(t._1.getRelClass()); return rel; }, Encoders.bean(RelatedDataset.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java index 1952b5d9c..9498c0f33 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java @@ -64,7 +64,7 @@ public class PrepareRelatedProjectsJob { .map(ConversionUtils::oafProjectToBrokerProject, Encoders.bean(OaBrokerProject.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT)) .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java index d6ac27fc5..8270500fd 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java @@ -65,7 +65,7 @@ public class PrepareRelatedPublicationsJob { Encoders.bean(OaBrokerRelatedPublication.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass())) @@ -75,7 +75,8 @@ public class PrepareRelatedPublicationsJob { final Dataset dataset = rels .joinWith(pubs, pubs.col("openaireId").equalTo(rels.col("target")), "inner") .map(t -> { - final RelatedPublication rel = new RelatedPublication(t._1.getSource(), t._2); + final RelatedPublication rel = new RelatedPublication( + t._1.getSource(), t._2); rel.getRelPublication().setRelType(t._1.getRelClass()); return rel; }, Encoders.bean(RelatedPublication.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java index c4ccf4af6..16b450733 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java @@ -64,7 +64,7 @@ public class PrepareRelatedSoftwaresJob { .map(ConversionUtils::oafSoftwareToBrokerSoftware, Encoders.bean(OaBrokerRelatedSoftware.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java index 04985a6ab..9ce64f6bd 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java @@ -17,6 +17,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.oaf.Relation; public class ClusterUtils { @@ -30,6 +31,16 @@ public class ClusterUtils { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } + public static Dataset loadRelations(final String graphPath, final SparkSession spark) { + return ClusterUtils + .readPath(spark, graphPath + "/relation", Relation.class) + .map(r -> { + r.setSource(ConversionUtils.cleanOpenaireId(r.getSource())); + r.setTarget(ConversionUtils.cleanOpenaireId(r.getTarget())); + return r; + }, Encoders.bean(Relation.class)); + } + public static Dataset readPath( final SparkSession spark, final String inputPath, diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index 085681488..ecbfd821e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -129,7 +129,7 @@ public class ConversionUtils { return res; } - private static String cleanOpenaireId(final String id) { + public static String cleanOpenaireId(final String id) { return id.contains("|") ? StringUtils.substringAfter(id, "|") : id; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java index 75c4625ce..c693be93c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java @@ -59,9 +59,18 @@ public class DatasourceRelationsAccumulator implements Serializable { final DatasourceRelationsAccumulator res = new DatasourceRelationsAccumulator(); collectedFromSet .stream() - .map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.COLLECTED_FROM_REL)) + .map( + s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s), + BrokerConstants.COLLECTED_FROM_REL)) .forEach(res::addTuple); - hostedBySet.stream().map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.HOSTED_BY_REL)).forEach(res::addTuple); + + hostedBySet + .stream() + .map( + s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s), + BrokerConstants.HOSTED_BY_REL)) + .forEach(res::addTuple); + return res; } From 1f6c8a9e83be2dfcc0942e423e03c712dcda308b Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 15 Dec 2020 11:47:15 +0100 Subject: [PATCH 093/149] added orcid_pending type to records coming from Crossref --- .../main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala | 3 ++- .../main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala index 9c9221b27..8d906fa15 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala @@ -35,7 +35,8 @@ object DoiBoostMappingUtil { //STATIC STRING val MAG = "microsoft" val MAG_NAME = "Microsoft Academic Graph" - val ORCID = "ORCID" + val ORCID = "orcid" + val ORCID_PENDING = "orcid_pending" val CROSSREF = "Crossref" val UNPAYWALL = "UnpayWall" val GRID_AC = "grid.ac" diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 5ba01357e..d1ceb9a07 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -200,7 +200,7 @@ case object Crossref2Oaf { a.setSurname(family) a.setFullname(s"$given $family") if (StringUtils.isNotBlank(orcid)) - a.setPid(List(createSP(orcid, ORCID, PID_TYPES, generateDataInfo())).asJava) + a.setPid(List(createSP(orcid, ORCID_PENDING, PID_TYPES, generateDataInfo())).asJava) a } From f9dc1e45fd0559a3cd57d56f411b89bc97fedaa4 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 15 Dec 2020 14:54:11 +0100 Subject: [PATCH 094/149] fixed a bug with invalid subject topic --- .../matchers/simple/EnrichMissingSubject.java | 19 ++++++++++++++++++- .../oa/matchers/simple/EnrichMoreSubject.java | 19 ++++++++++++++++++- 2 files changed, 36 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java index 26ebbb7c0..cb3ea5464 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java @@ -16,7 +16,24 @@ public class EnrichMissingSubject extends UpdateMatcher { public EnrichMissingSubject() { super(20, - s -> Topic.fromPath("ENRICH/MISSING/SUBJECT/" + s.getType()), + s -> { + switch (s.getType().toLowerCase()) { + case "acm": + return Topic.ENRICH_MISSING_SUBJECT_ACM; + case "arxiv": + return Topic.ENRICH_MISSING_SUBJECT_ARXIV; + case "ddc": + return Topic.ENRICH_MISSING_SUBJECT_DDC; + case "jel": + return Topic.ENRICH_MISSING_SUBJECT_JEL; + case "mesh": + return Topic.ENRICH_MISSING_SUBJECT_MESHEUROPMC; + case "rvk": + return Topic.ENRICH_MISSING_SUBJECT_RVK; + default: + return null; + } + }, (p, s) -> p.getSubjects().add(s), s -> subjectAsString(s)); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java index bbe6609d7..1f6edf96e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java @@ -16,7 +16,24 @@ public class EnrichMoreSubject extends UpdateMatcher { public EnrichMoreSubject() { super(20, - s -> Topic.fromPath("ENRICH/MORE/SUBJECT/" + s.getType()), + s -> { + switch (s.getType().toLowerCase()) { + case "acm": + return Topic.ENRICH_MORE_SUBJECT_ACM; + case "arxiv": + return Topic.ENRICH_MORE_SUBJECT_ARXIV; + case "ddc": + return Topic.ENRICH_MORE_SUBJECT_DDC; + case "jel": + return Topic.ENRICH_MORE_SUBJECT_JEL; + case "mesh": + return Topic.ENRICH_MORE_SUBJECT_MESHEUROPMC; + case "rvk": + return Topic.ENRICH_MORE_SUBJECT_RVK; + default: + return null; + } + }, (p, s) -> p.getSubjects().add(s), s -> subjectAsString(s)); } From 4766495f5bf76d49b31d664519fe51706a0ecb4a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 17 Dec 2020 09:15:50 +0100 Subject: [PATCH 095/149] [orcid_to_result_from_semrel_propagation] fixed typo in SQL --- .../PrepareResultOrcidAssociationStep1.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java index dd8342980..b3ef3a112 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java @@ -104,7 +104,7 @@ public class PrepareResultOrcidAssociationStep1 { + " LATERAL VIEW EXPLODE (author) a AS MyT " + " LATERAL VIEW EXPLODE (MyT.pid) p AS MyP " + " WHERE lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID + "' or " - + " lower(MyP.qalifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp " + + " lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp " + " GROUP BY id) r_t " + " JOIN (" + " SELECT source, target " From f9a8fd8bbd13e18926e3c0ffda88c160c5aa6587 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Thu, 17 Dec 2020 11:59:45 +0100 Subject: [PATCH 096/149] updated test record for textgrid --- .../eu/dnetlib/dhp/oa/graph/raw/textgrid.xml | 58 ++++++++++--------- 1 file changed, 30 insertions(+), 28 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml index eddbc1ec4..7ad7c4d6b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml @@ -6,29 +6,29 @@ xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> - r3f52792889d::000051aa1f61d77d2c0b340091f8024e - textgrid:q9cv.0 - 2020-11-17T09:34:11.128+01:00 + r3f52792889d::00002412cb25f2f3047712d00ab2c8eb + hdl:11858/00-1734-0000-0003-EE73-2 + 2020-12-16T10:04:03.148Z r3f52792889d - textgrid:q9cv.0 - 2012-01-21T13:35:20Z - 2020-11-17T19:08:56.703+01:00 + textgrid:rn8z.0 + 2012-01-29T20:54:12Z + 2020-12-16T16:02:37.562Z - hdl:11858/00-1734-0000-0003-7664-F + hdl:11858/00-1734-0000-0003-EE73-2 - Hoffmann von Fallersleben, August Heinrich - 118552589 + Liliencron, Detlev von + 118572954 - Mailied - August Heinrich Hoffmann von Fallersleben: Unpolitische Lieder von Hoffmann von Fallersleben, 1. + 2. Theil, 1. Theil, Hamburg: Hoffmann und Campe, 1841. + Auf dem Trocknen + Detlev von Liliencron: Gute Nacht. Hinterlassene Gedichte, Berlin: Schuster & Loeffler, 1909. TextGrid 2012 @@ -38,21 +38,21 @@ Digitale Bibliothek - TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c + TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c - 2012-01-21T13:35:20Z - 2012-01-21T13:35:20Z - 2012-01-21T13:35:20Z + 2012-01-29T20:54:12Z + 2012-01-29T20:54:12Z + 2012-01-29T20:54:12Z - textgrid:q9cv.0 - http://hdl.handle.net/hdl:11858/00-1734-0000-0003-7664-F + textgrid:rn8z.0 + http://hdl.handle.net/hdl:11858/00-1734-0000-0003-EE73-2 - hdl:11858/00-1734-0000-0003-7666-B + hdl:11858/00-1734-0000-0003-EE72-4 527 Bytes @@ -77,17 +77,18 @@ Hamburg + xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">Berlin - hdl:11858/00-1734-0000-0003-7664-F + hdl:11858/00-1734-0000-0003-EE73-2 0021 0002 - 2012-01-21 + 2012-01-29 OPEN http://creativecommons.org/licenses/by/3.0/de/legalcode und + DE @@ -95,11 +96,11 @@ xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> - + https%3A%2F%2Fdev.textgridlab.org%2F1.0%2Ftgoaipmh%2Foai - textgrid:q9cv.0 - 2012-01-21T13:35:20Z - http://schema.datacite.org/oai/oai-1.0/ + textgrid:rn8z.0 + 2012-01-29T20:54:12Z + @@ -107,9 +108,10 @@ false 0.9 - - \ No newline at end of file + + From 03319d3bd95912d83068c9a120bc4614de52b51d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 17 Dec 2020 12:23:58 +0100 Subject: [PATCH 097/149] Revert "Merge pull request 'Creation of the action set to include the bipFinder! score' (#62) from miriam.baglioni/dnet-hadoop:bipFinder into master" This reverts commit add7e1693b3d103ee5101aee4454d022264b06b6, reversing changes made to f9a8fd8bbd13e18926e3c0ffda88c160c5aa6587. --- .../eu/dnetlib/dhp/schema/oaf/Measure.java | 5 +- .../bipfinder/BipDeserialize.java | 28 - .../dhp/actionmanager/bipfinder/BipScore.java | 30 - .../bipfinder/CollectAndSave.java | 85 -- .../dhp/actionmanager/bipfinder/KeyValue.java | 26 - .../bipfinder/PreparedResult.java | 28 - .../dhp/actionmanager/bipfinder/Score.java | 30 - .../bipfinder/SparkAtomicActionScoreJob.java | 200 --- .../bipfinder/input_actionset_parameter.json | 20 - .../bipfinder/input_parameters.json | 32 - .../bipfinder/oozie_app/config-default.xml | 58 - .../bipfinder/oozie_app/workflow.xml | 171 --- .../SparkAtomicActionScoreJobTest.java | 331 ----- .../actionmanager/bipfinder/bip_scores.json | 1101 ----------------- .../actionmanager/bipfinder/publication.json | 18 - .../bipfinder/publication_2.json | 18 - .../bipfinder/publication_3.json | 18 - 17 files changed, 2 insertions(+), 2197 deletions(-) delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java delete mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json delete mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json delete mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json delete mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java index 78a4c6801..c0c14d10d 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.schema.oaf; -import java.io.Serializable; import java.util.List; import com.google.common.base.Objects; @@ -9,7 +8,7 @@ import com.google.common.base.Objects; /** * Represent a measure, must be further described by a system available resource providing name and descriptions. */ -public class Measure implements Serializable { +public class Measure { /** * Unique measure identifier. @@ -17,7 +16,7 @@ public class Measure implements Serializable { private String id; /** - * List of units associated with this measure. KeyValue provides a pair to store the label (key) and the value, plus + * List of units associated with this measure. KeyValue provides a pair to store the laber (key) and the value, plus * common provenance information. */ private List unit; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java deleted file mode 100644 index d5b2ced7c..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java +++ /dev/null @@ -1,28 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.bipfinder; - -import java.io.Serializable; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; - -/** - * Class that maps the model of the bipFinder! input data. - * Only needed for deserialization purposes - */ - -public class BipDeserialize extends HashMap> implements Serializable { - - public BipDeserialize() { - super(); - } - - public List get(String key) { - - if (super.get(key) == null) { - return new ArrayList<>(); - } - return super.get(key); - } - -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java deleted file mode 100644 index da9a4bd0c..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.bipfinder; - -import java.io.Serializable; -import java.util.List; - -/** - * Rewriting of the bipFinder input data by extracting the identifier of the result (doi) - */ - -public class BipScore implements Serializable { - private String id; //doi - private List scoreList; //unit as given in the inputfile - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = id; - } - - public List getScoreList() { - return scoreList; - } - - public void setScoreList(List scoreList) { - this.scoreList = scoreList; - } -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java deleted file mode 100644 index 0bebe2fb0..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java +++ /dev/null @@ -1,85 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.bipfinder; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.io.Text; -import org.apache.hadoop.mapred.SequenceFileOutputFormat; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.schema.oaf.Result; - -/** - * Just collects all the atomic actions produced for the different results and saves them in - * outputpath for the ActionSet - */ -public class CollectAndSave implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - - String jsonConfiguration = IOUtils - .toString( - CollectAndSave.class - .getResourceAsStream( - "/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("inputPath"); - log.info("inputPath {}: ", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath {}: ", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - removeOutputDir(spark, outputPath); - collectAndSave(spark, inputPath, outputPath); - }); - } - - private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) { - JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - sc - .sequenceFile(inputPath + "/publication", Text.class, Text.class) - .union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)) - .union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)) - .union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class)) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); - ; - } - - private static void removeOutputDir(SparkSession spark, String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } - -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java deleted file mode 100644 index 6909a9634..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java +++ /dev/null @@ -1,26 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.bipfinder; - -import java.io.Serializable; - -public class KeyValue implements Serializable { - - private String key; - private String value; - - public String getKey() { - return key; - } - - public void setKey(String key) { - this.key = key; - } - - public String getValue() { - return value; - } - - public void setValue(String value) { - this.value = value; - } -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java deleted file mode 100644 index 493e94417..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java +++ /dev/null @@ -1,28 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.bipfinder; - -import java.io.Serializable; - -/** - * Subset of the information of the generic results that are needed to create the atomic action - */ -public class PreparedResult implements Serializable { - private String id; // openaire id - private String value; // doi - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = id; - } - - public String getValue() { - return value; - } - - public void setValue(String value) { - this.value = value; - } -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java deleted file mode 100644 index 7cc21b44d..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.bipfinder; - -import java.io.Serializable; -import java.util.List; - -/** - * represents the score in the input file - */ -public class Score implements Serializable { - - private String id; - private List unit; - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = id; - } - - public List getUnit() { - return unit; - } - - public void setUnit(List unit) { - this.unit = unit; - } -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java deleted file mode 100644 index 23764f38e..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ /dev/null @@ -1,200 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.bipfinder; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.io.Text; -import org.apache.hadoop.mapred.SequenceFileOutputFormat; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.schema.action.AtomicAction; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import scala.Tuple2; - -/** - * created the Atomic Action for each tipe of results - */ -public class SparkAtomicActionScoreJob implements Serializable { - - private static String DOI = "doi"; - private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJob.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - - String jsonConfiguration = IOUtils - .toString( - SparkAtomicActionScoreJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("inputPath"); - log.info("inputPath {}: ", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath {}: ", outputPath); - - final String bipScorePath = parser.get("bipScorePath"); - log.info("bipScorePath: {}", bipScorePath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - Class inputClazz = (Class) Class.forName(resultClassName); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - removeOutputDir(spark, outputPath); - prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz); - }); - } - - private static void prepareResults(SparkSession spark, String inputPath, String outputPath, - String bipScorePath, Class inputClazz) { - - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - - JavaRDD bipDeserializeJavaRDD = sc - .textFile(bipScorePath) - .map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class)); - - Dataset bipScores = spark - .createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> { - BipScore bs = new BipScore(); - bs.setId(key); - bs.setScoreList(entry.get(key)); - return bs; - }).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class)); - - System.out.println(bipScores.count()); - - Dataset results = readPath(spark, inputPath, inputClazz); - - results.createOrReplaceTempView("result"); - - Dataset preparedResult = spark - .sql( - "select pIde.value value, id " + - "from result " + - "lateral view explode (pid) p as pIde " + - "where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'") - .as(Encoders.bean(PreparedResult.class)); - - bipScores - .joinWith( - preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")), - "inner") - .map((MapFunction, BipScore>) value -> { - BipScore ret = value._1(); - ret.setId(value._2().getId()); - return ret; - }, Encoders.bean(BipScore.class)) - .groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, it) -> { - Result ret = inputClazz.newInstance(); - BipScore first = it.next(); - ret.setId(first.getId()); - - ret.setMeasures(getMeasure(first)); - it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value))); - - return (I) ret; - }, Encoders.bean(inputClazz)) - .toJavaRDD() - .map(p -> new AtomicAction(inputClazz, p)) - .mapToPair( - aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); - - } - - - private static List getMeasure(BipScore value) { - return value - .getScoreList() - .stream() - .map(score -> { - Measure m = new Measure(); - m.setId(score.getId()); - m - .setUnit( - score - .getUnit() - .stream() - .map(unit -> { - KeyValue kv = new KeyValue(); - kv.setValue(unit.getValue()); - kv.setKey(unit.getKey()); - kv.setDataInfo(getDataInfo()); - return kv; - }) - .collect(Collectors.toList())); - return m; - }) - .collect(Collectors.toList()); - } - - private static DataInfo getDataInfo() { - DataInfo di = new DataInfo(); - di.setInferred(false); - di.setInvisible(false); - di.setDeletedbyinference(false); - di.setTrust(""); - Qualifier qualifier = new Qualifier(); - qualifier.setClassid("sysimport:actionset"); - qualifier.setClassname("Harvested"); - qualifier.setSchemename("dnet:provenanceActions"); - qualifier.setSchemeid("dnet:provenanceActions"); - di.setProvenanceaction(qualifier); - return di; - } - - private static void removeOutputDir(SparkSession spark, String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } - - public static Dataset readPath( - SparkSession spark, String inputPath, Class clazz) { - return spark - .read() - .textFile(inputPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); - } - -} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json deleted file mode 100644 index 67911eef1..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json +++ /dev/null @@ -1,20 +0,0 @@ -[ - { - "paramName": "issm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "when true will stop SparkSession after job execution", - "paramRequired": false -}, -{ -"paramName": "ip", -"paramLongName": "inputPath", -"paramDescription": "the URL from where to get the programme file", -"paramRequired": true -}, -{ -"paramName": "o", -"paramLongName": "outputPath", -"paramDescription": "the path of the new ActionSet", -"paramRequired": true -} -] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json deleted file mode 100644 index ae844a0c9..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json +++ /dev/null @@ -1,32 +0,0 @@ -[ - { - "paramName": "issm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "when true will stop SparkSession after job execution", - "paramRequired": false -}, -{ -"paramName": "ip", -"paramLongName": "inputPath", -"paramDescription": "the URL from where to get the programme file", -"paramRequired": true -}, -{ -"paramName": "o", -"paramLongName": "outputPath", -"paramDescription": "the path of the new ActionSet", -"paramRequired": true -}, - { - "paramName": "rtn", - "paramLongName": "resultTableName", - "paramDescription": "the path of the new ActionSet", - "paramRequired": true - }, - { - "paramName": "bsp", - "paramLongName": "bipScorePath", - "paramDescription": "the path of the new ActionSet", - "paramRequired": true - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/config-default.xml deleted file mode 100644 index a1755f329..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/config-default.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - - - oozie.launcher.mapreduce.user.classpath.first - true - - - sparkExecutorNumber - 4 - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - sparkDriverMemory - 15G - - - sparkExecutorMemory - 6G - - - sparkExecutorCores - 1 - - \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml deleted file mode 100644 index ea2e9f58a..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml +++ /dev/null @@ -1,171 +0,0 @@ - - - - inputPath - the input path of the resources to be extended - - - - bipScorePath - the path where to find the bipFinder scores - - - outputPath - the path where to store the actionset - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - - - - - - - - yarn - cluster - Produces the atomic action with the bip finder scores for publications - eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --inputPath${inputPath}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/publication - --bipScorePath${bipScorePath} - - - - - - - - yarn - cluster - Produces the atomic action with the bip finder scores for datasets - eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --inputPath${inputPath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/dataset - --bipScorePath${bipScorePath} - - - - - - - - yarn - cluster - Produces the atomic action with the bip finder scores for orp - eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --inputPath${inputPath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/otherresearchproduct - --bipScorePath${bipScorePath} - - - - - - - - yarn - cluster - Produces the atomic action with the bip finder scores for software - eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --inputPath${inputPath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/software - --bipScorePath${bipScorePath} - - - - - - - - - - yarn - cluster - saves all the aa produced for the several types of results in the as output path - eu.dnetlib.dhp.actionmanager.bipfinder.CollectAndSave - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --inputPath${workingDir} - --outputPath${outputPath} - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java deleted file mode 100644 index 4b02e7485..000000000 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java +++ /dev/null @@ -1,331 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.bipfinder; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; -import java.util.stream.Collectors; - -import org.apache.commons.io.FileUtils; -import org.apache.hadoop.io.Text; -import org.apache.hadoop.mapred.SequenceFileOutputFormat; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.action.AtomicAction; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import scala.Tuple2; - -public class SparkAtomicActionScoreJobTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(SparkAtomicActionScoreJobTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(SparkAtomicActionScoreJobTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(SparkAtomicActionScoreJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void matchOne() throws Exception { - String bipScoresPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") - .getPath(); - String inputPath = getClass() - .getResource( - "/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json") - .getPath(); - - SparkAtomicActionScoreJob - .main( - new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-inputPath", - inputPath, - "-bipScorePath", - bipScoresPath, - "-resultTableName", - "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", - workingDir.toString() + "/actionSet" - }); - - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) - .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) - .map(aa -> ((Publication) aa.getPayload())); - - Assertions.assertTrue(tmp.count() == 1); - - Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - verificationDataset.createOrReplaceTempView("publication"); - - Dataset execVerification = spark - .sql( - "Select p.id oaid, mes.id, mUnit.value from publication p " + - "lateral view explode(measures) m as mes " + - "lateral view explode(mes.unit) u as mUnit "); - - Assertions.assertEquals(2, execVerification.count()); - - Assertions - .assertEquals( - "50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", - execVerification.select("oaid").collectAsList().get(0).getString(0)); - - Assertions - .assertEquals( - "1.47565045883e-08", - execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0)); - - Assertions - .assertEquals( - "0.227515392", - execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0)); - - } - - @Test - public void matchOneWithTwo() throws Exception { - String bipScoresPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") - .getPath(); - String inputPath = getClass() - .getResource( - "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json") - .getPath(); - - SparkAtomicActionScoreJob - .main( - new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-inputPath", - inputPath, - "-bipScorePath", - bipScoresPath, - "-resultTableName", - "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", - workingDir.toString() + "/actionSet" - }); - - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) - .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) - .map(aa -> ((Publication) aa.getPayload())); - - Assertions.assertTrue(tmp.count() == 1); - - Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - verificationDataset.createOrReplaceTempView("publication"); - - Dataset execVerification = spark - .sql( - "Select p.id oaid, mes.id, mUnit.value from publication p " + - "lateral view explode(measures) m as mes " + - "lateral view explode(mes.unit) u as mUnit "); - - Assertions.assertEquals(4, execVerification.count()); - - Assertions - .assertEquals( - "50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", - execVerification.select("oaid").collectAsList().get(0).getString(0)); - - Assertions - .assertEquals( - 2, - execVerification.filter("id = 'influence'").count()); - - Assertions - .assertEquals( - 2, - execVerification.filter("id = 'popularity'").count()); - - List tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList(); - String tmp_influence = tmp_ds.get(0).getString(0); - Assertions - .assertTrue( - "1.47565045883e-08".equals(tmp_influence) || - "1.98956540239e-08".equals(tmp_influence)); - - tmp_influence = tmp_ds.get(1).getString(0); - Assertions - .assertTrue( - "1.47565045883e-08".equals(tmp_influence) || - "1.98956540239e-08".equals(tmp_influence)); - - Assertions.assertTrue(!tmp_ds.get(0).getString(0).equals(tmp_ds.get(1).getString(0))); - - } - - @Test - public void matchTwo() throws Exception { - String bipScoresPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") - .getPath(); - String inputPath = getClass() - .getResource( - "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json") - .getPath(); - - SparkAtomicActionScoreJob - .main( - new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-inputPath", - inputPath, - "-bipScorePath", - bipScoresPath, - "-resultTableName", - "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", - workingDir.toString() + "/actionSet" - }); - - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) - .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) - .map(aa -> ((Publication) aa.getPayload())); - - Assertions.assertTrue(tmp.count() == 2); - - Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - verificationDataset.createOrReplaceTempView("publication"); - - Dataset execVerification = spark - .sql( - "Select p.id oaid, mes.id, mUnit.value from publication p " + - "lateral view explode(measures) m as mes " + - "lateral view explode(mes.unit) u as mUnit "); - - Assertions.assertEquals(4, execVerification.count()); - - Assertions - .assertEquals( - 2, - execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count()); - - Assertions - .assertEquals( - 2, - execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count()); - - Assertions - .assertEquals( - 2, - execVerification.filter("id = 'influence'").count()); - - Assertions - .assertEquals( - 2, - execVerification.filter("id = 'popularity'").count()); - - Assertions - .assertEquals( - "1.47565045883e-08", - execVerification - .filter( - "oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + - "and id = 'influence'") - .select("value") - .collectAsList() - .get(0) - .getString(0)); - - Assertions - .assertEquals( - "1.98956540239e-08", - execVerification - .filter( - "oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + - "and id = 'influence'") - .select("value") - .collectAsList() - .get(0) - .getString(0)); - - Assertions - .assertEquals( - "0.282046161584", - execVerification - .filter( - "oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + - "and id = 'popularity'") - .select("value") - .collectAsList() - .get(0) - .getString(0)); - - Assertions - .assertEquals( - "0.227515392", - execVerification - .filter( - "oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + - "and id = 'popularity'") - .select("value") - .collectAsList() - .get(0) - .getString(0)); - - } - -} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json deleted file mode 100644 index a4f3fa8b8..000000000 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json +++ /dev/null @@ -1,1101 +0,0 @@ -{"10.1001/10-v4n2-hsf10003": [{"id": "influence", "unit": [{"value": "1.62759106106e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.22519296", "key": "score"}]}]} -{"10.1001/2012.jama.10456": [{"id": "influence", "unit": [{"value": "1.66083991022e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.8690688", "key": "score"}]}]} -{"10.1001/2013.jamadermatol.729": [{"id": "influence", "unit": [{"value": "2.0769133069e-08", "key": "score"}]}, {"id": 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In natural materials, such as nacre, there are examples of multifunctional macromolecules that have combined binding affinities for different materials within the same molecule, thereby bridging these materials and acting as a molecular glue. Here, we describe the use of a designed multifunctional protein that is used for self-assembly of nanofibrillar cellulose. Recent advances in the production of cellulose nanofibrils have given inspiration for new uses of cellulosic materials. Cellulose nanofibrils have mechanical and structural features that open new possibilities for performance in composites and other nanoscale materials. Functionalisation was realised through a bi-functional fusion protein having both an ability to bind to cellulose and a second functionality of surface activity. The cellulose-binding function was obtained using cellulose-binding domains from cellulolytic enzymes and the surface activity through the use of a surface active protein called hydrophobin. Using the bi-functional protein, cellulose nanofibrils could be assembled into tightly packed thin films at the air/water interface and at the oil/water interface. It was shown that the combination of protein and cellulose nanofibrils resulted in a synergistic improvement in the formation and stability of oil-in-water emulsions resulting in emulsions that were stable for several months. 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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reentry"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"value":"629.8"}],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Cadre de travail généralisé de compensation non-linéaire robuste : application à la rentrée atmosphérique"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"A generalized framework for robust nonlinear compensation : application to an atmospheric reentry control problem"}]} \ No newline at end of file From 2e503ee101bca19d610b51ad1738cc0c0c12ad0e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 17 Dec 2020 13:47:38 +0100 Subject: [PATCH 098/149] code formatting --- .../java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java | 4 ++-- .../actionmanager/bipfinder/SparkAtomicActionScoreJob.java | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java index da9a4bd0c..247546694 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java @@ -9,8 +9,8 @@ import java.util.List; */ public class BipScore implements Serializable { - private String id; //doi - private List scoreList; //unit as given in the inputfile + private String id; // doi + private List scoreList; // unit as given in the inputfile public String getId() { return id; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 23764f38e..50bda898c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -144,7 +144,6 @@ public class SparkAtomicActionScoreJob implements Serializable { } - private static List getMeasure(BipScore value) { return value .getScoreList() From 47270d9af59ab3a5b1fe0fd93466315ca5560062 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 18 Dec 2020 15:38:59 +0100 Subject: [PATCH 099/149] lenient mock can be lenient --- .../dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 9cf75f208..0d1ec1ad1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -35,7 +35,7 @@ public class MigrateDbEntitiesApplicationTest { private MigrateDbEntitiesApplication app; - @Mock + @Mock(lenient = true) private ResultSet rs; @Mock From 2a074c3b2b37519f42698661c772f034633e9813 Mon Sep 17 00:00:00 2001 From: antleb Date: Fri, 18 Dec 2020 18:40:48 +0200 Subject: [PATCH 100/149] Changed typo in script names --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index dcd034166..7bd9ce1b6 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -259,7 +259,7 @@ ${hive_jdbc_url} - + stats_db_name=${stats_db_name} stats_db_shadow_name=${stats_db_shadow_name} @@ -288,7 +288,7 @@ impala-shell.sh ${stats_db_shadow_name} computeProductionStats.sql - ${wf:appPath()}/scripts/computeProductionStats.sql + ${wf:appPath()}/scripts/step19.sql impala-shell.sh From 6cb0dc3f433d385739cac12049b44a9d128b220c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 21 Dec 2020 11:40:17 +0100 Subject: [PATCH 101/149] extended OCRID cleaning procedure --- .../dhp/oa/graph/clean/CleaningFunctions.java | 29 +++++++++++++++---- 1 file changed, 23 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index fbb20f143..798eae4dd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -16,7 +16,7 @@ import eu.dnetlib.dhp.schema.oaf.*; public class CleaningFunctions { public static final String DOI_URL_PREFIX_REGEX = "(^http(s?):\\/\\/)(((dx\\.)?doi\\.org)|(handle\\.test\\.datacite\\.org))\\/"; - public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/"; + public static final String ORCID_CLEANING_REGEX = ".*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9x]{4})"; public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)"; public static final Set PID_BLACKLIST = new HashSet<>(); @@ -211,14 +211,31 @@ public class CleaningFunctions { .map(Qualifier::getClassid) .orElse("")) .orElse(""); - if (pidProvenance.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) { - p.getQualifier().setClassid(ModelConstants.ORCID); - } else { - p.getQualifier().setClassid(ModelConstants.ORCID_PENDING); + if (p + .getQualifier() + .getClassid() + .toLowerCase() + .contains(ModelConstants.ORCID)) { + if (pidProvenance + .equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) { + p.getQualifier().setClassid(ModelConstants.ORCID); + } else { + p.getQualifier().setClassid(ModelConstants.ORCID_PENDING); + } + final String orcid = p + .getValue() + .trim() + .toLowerCase() + .replaceAll(ORCID_CLEANING_REGEX, "$1-$2-$3-$4"); + if (orcid.length() == 19) { + p.setValue(orcid); + } else { + p.setValue(""); + } } - p.setValue(p.getValue().trim().replaceAll(ORCID_PREFIX_REGEX, "")); return p; }) + .filter(p -> StringUtils.isNotBlank(p.getValue())) .collect( Collectors .toMap( From 794e22b09cff59a48459c7574e61b07cdfbba1f4 Mon Sep 17 00:00:00 2001 From: miconis Date: Mon, 21 Dec 2020 17:51:42 +0100 Subject: [PATCH 102/149] bug fix in the authormerge: now authors with higher size have priority, normalization of author name fixed --- .../eu/dnetlib/dhp/oa/merge/AuthorMerger.java | 48 +++++++-- .../dhp/oa/merge/AuthorMergerTest.java | 97 +++++++++++++++++++ .../oa/merge/publications_with_authors.json | 3 + 3 files changed, 138 insertions(+), 10 deletions(-) create mode 100644 dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java create mode 100644 dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java index 17482c019..5ad4598a6 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.merge; import java.text.Normalizer; import java.util.*; import java.util.stream.Collectors; +import java.util.stream.Stream; import org.apache.commons.lang3.StringUtils; @@ -32,6 +33,24 @@ public class AuthorMerger { } + public static List mergeAuthor(final List a, final List b, Double threshold) { + int pa = countAuthorsPids(a); + int pb = countAuthorsPids(b); + List base, enrich; + int sa = authorsSize(a); + int sb = authorsSize(b); + + if (sa == sb) { + base = pa > pb ? a : b; + enrich = pa > pb ? b : a; + } else { + base = sa > sb ? a : b; + enrich = sa > sb ? b : a; + } + enrichPidFromList(base, enrich, threshold); + return base; + } + public static List mergeAuthor(final List a, final List b) { int pa = countAuthorsPids(a); int pb = countAuthorsPids(b); @@ -39,20 +58,22 @@ public class AuthorMerger { int sa = authorsSize(a); int sb = authorsSize(b); - if (pa == pb) { - base = sa > sb ? a : b; - enrich = sa > sb ? b : a; - } else { + if (sa == sb) { base = pa > pb ? a : b; enrich = pa > pb ? b : a; + } else { + base = sa > sb ? a : b; + enrich = sa > sb ? b : a; } - enrichPidFromList(base, enrich); + enrichPidFromList(base, enrich, THRESHOLD); return base; } - private static void enrichPidFromList(List base, List enrich) { + private static void enrichPidFromList(List base, List enrich, Double threshold) { if (base == null || enrich == null) return; + + // (if an Author has more than 1 pid, it appears 2 times in the list) final Map basePidAuthorMap = base .stream() .filter(a -> a.getPid() != null && a.getPid().size() > 0) @@ -63,6 +84,7 @@ public class AuthorMerger { .map(p -> new Tuple2<>(pidToComparableString(p), a))) .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); + // (list of pid that are missing in the other list) final List> pidToEnrich = enrich .stream() .filter(a -> a.getPid() != null && a.getPid().size() > 0) @@ -74,6 +96,7 @@ public class AuthorMerger { .map(p -> new Tuple2<>(p, a))) .collect(Collectors.toList()); + pidToEnrich .forEach( a -> { @@ -83,10 +106,10 @@ public class AuthorMerger { .max(Comparator.comparing(Tuple2::_1)); if (simAuthor.isPresent()) { - double th = THRESHOLD; + double th = threshold; // increase the threshold if the surname is too short if (simAuthor.get()._2().getSurname() != null - && simAuthor.get()._2().getSurname().length() <= 3) + && simAuthor.get()._2().getSurname().length() <= 3 && threshold > 0.0) th = 0.99; if (simAuthor.get()._1() > th) { @@ -156,7 +179,7 @@ public class AuthorMerger { } private static String normalize(final String s) { - return nfd(s) + String[] normalized = nfd(s) .toLowerCase() // do not compact the regexes in a single expression, would cause StackOverflowError // in case @@ -166,7 +189,12 @@ public class AuthorMerger { .replaceAll("(\\p{Punct})+", " ") .replaceAll("(\\d)+", " ") .replaceAll("(\\n)+", " ") - .trim(); + .trim() + .split(" "); + + Arrays.sort(normalized); + + return String.join(" ", normalized); } private static String nfd(final String s) { diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java new file mode 100644 index 000000000..1ff9753be --- /dev/null +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java @@ -0,0 +1,97 @@ +package eu.dnetlib.dhp.oa.merge; + +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.pace.util.MapDocumentUtil; +import org.codehaus.jackson.map.ObjectMapper; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import scala.Tuple2; + +import java.io.BufferedReader; +import java.io.FileReader; +import java.io.IOException; +import java.nio.file.Paths; +import java.util.ArrayList; +import java.util.List; +import java.util.stream.Collectors; + +public class AuthorMergerTest { + + String publicationsBasePath; + + List> authors; + + @BeforeEach + public void setUp() throws Exception { + + publicationsBasePath = Paths + .get(AuthorMergerTest.class.getResource("/eu/dnetlib/dhp/oa/merge").toURI()) + .toFile() + .getAbsolutePath(); + + authors = + readSample(publicationsBasePath + "/publications_with_authors.json", Publication.class) + .stream() + .map(p -> p._2().getAuthor()).collect(Collectors.toList()); + + } + + @Test + public void mergeTest() { //used in the dedup: threshold set to 0.95 + + for (List authors1: authors){ + System.out.println("List " + (authors.indexOf(authors1)+1)); + for (Author author: authors1){ + System.out.println(authorToString(author)); + } + } + + List merge = AuthorMerger.merge(authors); + + System.out.println("Merge "); + for (Author author: merge) { + System.out.println(authorToString(author)); + } + + Assertions.assertEquals(7, merge.size()); + + } + + public List> readSample(String path, Class clazz) { + List> res = new ArrayList<>(); + BufferedReader reader; + try { + reader = new BufferedReader(new FileReader(path)); + String line = reader.readLine(); + while (line != null) { + res + .add( + new Tuple2<>( + MapDocumentUtil.getJPathString("$.id", line), + new ObjectMapper().readValue(line, clazz))); + // read next line + line = reader.readLine(); + } + reader.close(); + } catch (IOException e) { + e.printStackTrace(); + } + + return res; + } + + public String authorToString(Author a){ + + String print = "Fullname = "; + print += a.getFullname() + " pid = ["; + if (a.getPid() != null) + for (StructuredProperty sp : a.getPid()) { + print += sp.toComparableString() + " "; + } + print += "]"; + return print; + } +} diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json new file mode 100644 index 000000000..600181ba5 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json @@ -0,0 +1,3 @@ +{ "journal":{ "dataInfo":null, "conferenceplace":null, "issnPrinted":"0009-9260", "issnOnline":null, "issnLinking":null, "ep":"636", "iss":null, "sp":"632", "vol":"55", "edition":null, "conferencedate":null, "name":"Clinical Radiology" }, "measures":null, "author":[ { "rank":null, "fullname":"KARL TURETSCHEK", "affiliation":null, "pid":null, "surname":"TURETSCHEK", "name":"KARL" }, { "rank":null, "fullname":"WOLFGANG EBNER", "affiliation":null, "pid":null, "surname":"EBNER", "name":"WOLFGANG" }, { "rank":null, "fullname":"DOMINIK FLEISCHMANN", "affiliation":null, "pid":null, "surname":"FLEISCHMANN", "name":"DOMINIK" }, { "rank":null, "fullname":"PATRICK WUNDERBALDINGER", "affiliation":null, "pid":null, "surname":"WUNDERBALDINGER", "name":"PATRICK" }, { "rank":null, "fullname":"LUDWIG ERLACHER", "affiliation":null, "pid":null, "surname":"ERLACHER", "name":"LUDWIG" }, { "rank":null, "fullname":"THOMAS ZONTSICH", "affiliation":null, "pid":null, "surname":"ZONTSICH", "name":"THOMAS" }, { "rank":null, "fullname":"ALEXANDER A. 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"collectedfrom":[ { "dataInfo":null, "value":"ORCID", "key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a" } ], "dataInfo":{ "trust":"0.9", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "lastupdatetimestamp":null } +{ "journal":{ "dataInfo":null, "conferenceplace":null, "issnPrinted":"0009-9260", "issnOnline":null, "issnLinking":null, "ep":"636", "iss":"8", "sp":"632", "vol":"55", "edition":null, "conferencedate":null, "name":"Clinical Radiology" }, "measures":null, "author":[ { "rank":null, "fullname":"T. Zontsich", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL"}, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/1966908432" } ], "surname":null, "name":null }, { "rank":null, "fullname":"L Erlacher", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL"}, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/687931320" } ], "surname":null, "name":null }, { "rank":null, "fullname":"Dominik Fleischmann", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL"}, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/2156559961" } ], "surname":null, "name":null }, { "rank":null, "fullname":"Alexander A. Bankier", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL"}, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/1107971609" } ], "surname":null, "name":null }, { "rank":null, "fullname":"Patrick Wunderbaldinger", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL" }, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/2422340537" } ], "surname":null, "name":null }, { "rank":null, "fullname":"Wolfgang Ebner", "affiliation":null, "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL" }, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/2186462571" } ], "surname":null, "name":null }, { "rank":null, "fullname":"K. Turetschek", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL" }, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/321765676" } ], "surname":null, "name":null } ], "resulttype":{ "classid":"publication", "schemeid":"dnet:result_typologies", "schemename":"dnet:result_typologies", "classname":"publication" }, "title":[ { "qualifier":{ "classid":"main title", "schemeid":"dnet:dataCite_title", "schemename":"dnet:dataCite_title", "classname":"main title" }, "dataInfo":null, "value":"early pulmonary involvement in ankylosing spondylitis assessment with thin section ct" }, { "qualifier":{ "classid":"alternative title", "schemeid":"dnet:dataCite_title", "schemename":"dnet:dataCite_title", "classname":"alternative title" }, "dataInfo":null, "value":"Early pulmonary involvement in ankylosing spondylitis: assessment with thin-section CT." } ], "relevantdate":null, "dateofacceptance":{ "dataInfo":null, "value":"2000-08-01" }, "publisher":{ "dataInfo":null, "value":"Elsevier" }, "embargoenddate":null, "fulltext":null, "contributor":null, "resourcetype":null, "coverage":null, "bestaccessright":null, "externalReference":null, "format":null, "description":[ { "dataInfo":null, "value":"Abstract AIM: To determine the frequency and the distribution of early pulmonary lesions in patients with ankylosing spondylitis (AS) and a normal chest X-ray on thin-section CT and to correlate the CT findings with the results of pulmonary function tests and clinical data. MATERIALS AND METHODS: Twenty-five patients with clinically proven AS and no history of smoking underwent clinical examinations, pulmonary function tests (PFT), chest radiography, and thin-section CT. Four of 25 patients (16%), who had obvious signs on plain films suggestive of pre-existing disorders unrelated to AS were excluded. RESULTS: Fifteen of 21 patients (71%) had abnormalities on thin-section CT. The most frequent abnormalities were thickening of the interlobular septa in seven of 21 patients (33%), mild bronchial wall thickening in (6/21, 29%), pleural thickening and pleuropulmonary irregularities (both 29%) and linear septal thickening (6/21, 29%). In six patients there were no signs of pleuropulmonary involvement. Eight of 15 patients (53%) with abnormal and four of six patients (67%) with normal CT findings revealed mild restrictive lung function impairment. CONCLUSION: Patients with AS but a normal chest radiograph frequently have abnormalities on thin-section CT. As these abnormalities are usually subtle and their extent does not correlate with functional and clinical data, the overall routine impact of thin-section CT in the diagnosis of AS is limited. Turetschek, K , (2000) Clinical Radiology53, 632–636." } ], "source":[ { "dataInfo":null, "value":null } ], "subject":[ { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Complication" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Chest radiograph" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.580897", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine.diagnostic_test" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.580897", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"In patient" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Radiography" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.4582326", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"business.industry" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.4582326", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"business" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Thin section ct" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Respiratory disease" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.49358836", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine.disease" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.49358836", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Ankylosing spondylitis" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.49937168", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine.disease" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.49937168", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Radiology" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.4573571", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine.medical_specialty" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.4573571", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.40295774", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, 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"instance":[ { "processingchargecurrency":null, "refereed":null, "instancetype":null, "hostedby":null, "distributionlocation":null, "processingchargeamount":null, "license":null, "accessright":null, "dateofacceptance":null, "collectedfrom":{ "dataInfo":null, "value":"Microsoft Academic Graph", "key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a" }, "url":[ "https://www.ncbi.nlm.nih.gov/pubmed/10964736", "https://www.sciencedirect.com/science/article/pii/S0009926000904987", "https://academic.microsoft.com/#/detail/1990704599" ] } ], "context":null, "country":null, "originalId":[ "1990704599", "10.1053/crad.2000.0498" ], "pid":[ { "qualifier":{ "classid":"doi", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"doi" }, "dataInfo":null, "value":"10.1053/crad.2000.0498" } ], "dateofcollection":null, "dateoftransformation":null, "oaiprovenance":null, "extraInfo":null, "id":"50|doiboost____::994b7e47b9e225ab6d5e14841cb45a7f", "collectedfrom":[ { "dataInfo":null, "value":"Microsoft Academic Graph", "key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a" } ], "dataInfo":{ "trust":"0.9", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset"} }, "lastupdatetimestamp":null } \ No newline at end of file From be5969a8c2e6b2edfaee0f2bf43d9f250b0f05c1 Mon Sep 17 00:00:00 2001 From: antleb Date: Tue, 22 Dec 2020 13:33:32 +0200 Subject: [PATCH 103/149] Changed typo in script names --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index 7bd9ce1b6..ceaa47794 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -287,7 +287,7 @@ ${nameNode} impala-shell.sh ${stats_db_shadow_name} - computeProductionStats.sql + step19.sql ${wf:appPath()}/scripts/step19.sql impala-shell.sh From d8b5f43a7e923544510a8f15d384ec8ed00015e9 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 22 Dec 2020 14:59:03 +0100 Subject: [PATCH 104/149] code formatting --- .../eu/dnetlib/dhp/oa/merge/AuthorMerger.java | 5 +- .../dhp/oa/merge/AuthorMergerTest.java | 140 +++++++++--------- 2 files changed, 73 insertions(+), 72 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java index 5ad4598a6..b3d84c40f 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java @@ -73,7 +73,7 @@ public class AuthorMerger { if (base == null || enrich == null) return; - // (if an Author has more than 1 pid, it appears 2 times in the list) + // (if an Author has more than 1 pid, it appears 2 times in the list) final Map basePidAuthorMap = base .stream() .filter(a -> a.getPid() != null && a.getPid().size() > 0) @@ -84,7 +84,7 @@ public class AuthorMerger { .map(p -> new Tuple2<>(pidToComparableString(p), a))) .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); - // (list of pid that are missing in the other list) + // (list of pid that are missing in the other list) final List> pidToEnrich = enrich .stream() .filter(a -> a.getPid() != null && a.getPid().size() > 0) @@ -96,7 +96,6 @@ public class AuthorMerger { .map(p -> new Tuple2<>(p, a))) .collect(Collectors.toList()); - pidToEnrich .forEach( a -> { diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java index 1ff9753be..02e694770 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java @@ -1,14 +1,5 @@ -package eu.dnetlib.dhp.oa.merge; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import eu.dnetlib.pace.util.MapDocumentUtil; -import org.codehaus.jackson.map.ObjectMapper; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import scala.Tuple2; +package eu.dnetlib.dhp.oa.merge; import java.io.BufferedReader; import java.io.FileReader; @@ -18,80 +9,91 @@ import java.util.ArrayList; import java.util.List; import java.util.stream.Collectors; +import org.codehaus.jackson.map.ObjectMapper; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.pace.util.MapDocumentUtil; +import scala.Tuple2; + public class AuthorMergerTest { - String publicationsBasePath; + String publicationsBasePath; - List> authors; + List> authors; - @BeforeEach - public void setUp() throws Exception { + @BeforeEach + public void setUp() throws Exception { - publicationsBasePath = Paths - .get(AuthorMergerTest.class.getResource("/eu/dnetlib/dhp/oa/merge").toURI()) - .toFile() - .getAbsolutePath(); + publicationsBasePath = Paths + .get(AuthorMergerTest.class.getResource("/eu/dnetlib/dhp/oa/merge").toURI()) + .toFile() + .getAbsolutePath(); - authors = - readSample(publicationsBasePath + "/publications_with_authors.json", Publication.class) - .stream() - .map(p -> p._2().getAuthor()).collect(Collectors.toList()); + authors = readSample(publicationsBasePath + "/publications_with_authors.json", Publication.class) + .stream() + .map(p -> p._2().getAuthor()) + .collect(Collectors.toList()); - } + } - @Test - public void mergeTest() { //used in the dedup: threshold set to 0.95 + @Test + public void mergeTest() { // used in the dedup: threshold set to 0.95 - for (List authors1: authors){ - System.out.println("List " + (authors.indexOf(authors1)+1)); - for (Author author: authors1){ - System.out.println(authorToString(author)); - } - } + for (List authors1 : authors) { + System.out.println("List " + (authors.indexOf(authors1) + 1)); + for (Author author : authors1) { + System.out.println(authorToString(author)); + } + } - List merge = AuthorMerger.merge(authors); + List merge = AuthorMerger.merge(authors); - System.out.println("Merge "); - for (Author author: merge) { - System.out.println(authorToString(author)); - } + System.out.println("Merge "); + for (Author author : merge) { + System.out.println(authorToString(author)); + } - Assertions.assertEquals(7, merge.size()); + Assertions.assertEquals(7, merge.size()); - } + } - public List> readSample(String path, Class clazz) { - List> res = new ArrayList<>(); - BufferedReader reader; - try { - reader = new BufferedReader(new FileReader(path)); - String line = reader.readLine(); - while (line != null) { - res - .add( - new Tuple2<>( - MapDocumentUtil.getJPathString("$.id", line), - new ObjectMapper().readValue(line, clazz))); - // read next line - line = reader.readLine(); - } - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } + public List> readSample(String path, Class clazz) { + List> res = new ArrayList<>(); + BufferedReader reader; + try { + reader = new BufferedReader(new FileReader(path)); + String line = reader.readLine(); + while (line != null) { + res + .add( + new Tuple2<>( + MapDocumentUtil.getJPathString("$.id", line), + new ObjectMapper().readValue(line, clazz))); + // read next line + line = reader.readLine(); + } + reader.close(); + } catch (IOException e) { + e.printStackTrace(); + } - return res; - } + return res; + } - public String authorToString(Author a){ + public String authorToString(Author a) { - String print = "Fullname = "; - print += a.getFullname() + " pid = ["; - if (a.getPid() != null) - for (StructuredProperty sp : a.getPid()) { - print += sp.toComparableString() + " "; - } - print += "]"; - return print; - } + String print = "Fullname = "; + print += a.getFullname() + " pid = ["; + if (a.getPid() != null) + for (StructuredProperty sp : a.getPid()) { + print += sp.toComparableString() + " "; + } + print += "]"; + return print; + } } From 6848d0c3d7fa5230efd26b28c9e3d25e3465a45c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 23 Dec 2020 12:21:58 +0100 Subject: [PATCH 105/149] trivial: avoid duplicated code --- .../eu/dnetlib/dhp/oa/merge/AuthorMerger.java | 16 +--------------- .../dnetlib/dhp/oa/merge/AuthorMergerTest.java | 4 ++-- 2 files changed, 3 insertions(+), 17 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java index b3d84c40f..0b602b774 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java @@ -52,21 +52,7 @@ public class AuthorMerger { } public static List mergeAuthor(final List a, final List b) { - int pa = countAuthorsPids(a); - int pb = countAuthorsPids(b); - List base, enrich; - int sa = authorsSize(a); - int sb = authorsSize(b); - - if (sa == sb) { - base = pa > pb ? a : b; - enrich = pa > pb ? b : a; - } else { - base = sa > sb ? a : b; - enrich = sa > sb ? b : a; - } - enrichPidFromList(base, enrich, THRESHOLD); - return base; + return mergeAuthor(a, b, THRESHOLD); } private static void enrichPidFromList(List base, List enrich, Double threshold) { diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java index 02e694770..d7b3bc36f 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java @@ -22,9 +22,9 @@ import scala.Tuple2; public class AuthorMergerTest { - String publicationsBasePath; + private String publicationsBasePath; - List> authors; + private List> authors; @BeforeEach public void setUp() throws Exception { From 723b01f9e96a95e4d6c6fb77916962cef146e250 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 23 Dec 2020 12:22:48 +0100 Subject: [PATCH 106/149] trivial: the less magic numbers and values around, the better --- .../dhp/oa/graph/clean/CleaningFunctions.java | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index 798eae4dd..859fc074c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -16,7 +16,10 @@ import eu.dnetlib.dhp.schema.oaf.*; public class CleaningFunctions { public static final String DOI_URL_PREFIX_REGEX = "(^http(s?):\\/\\/)(((dx\\.)?doi\\.org)|(handle\\.test\\.datacite\\.org))\\/"; + public static final String ORCID_CLEANING_REGEX = ".*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9x]{4})"; + public static final int ORCID_LEN = 19; + public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)"; public static final Set PID_BLACKLIST = new HashSet<>(); @@ -86,7 +89,7 @@ public class CleaningFunctions { } else if (value instanceof Organization) { Organization o = (Organization) value; if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) { - o.setCountry(qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_COUNTRY_TYPE)); + o.setCountry(qualifier(ModelConstants.UNKNOWN, "Unknown", ModelConstants.DNET_COUNTRY_TYPE)); } } else if (value instanceof Relation) { // nothing to clean here @@ -153,12 +156,14 @@ public class CleaningFunctions { if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) { r .setResourcetype( - qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE)); + qualifier(ModelConstants.UNKNOWN, "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE)); } if (Objects.nonNull(r.getInstance())) { for (Instance i : r.getInstance()) { if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) { - i.setAccessright(qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES)); + i + .setAccessright( + qualifier(ModelConstants.UNKNOWN, "not available", ModelConstants.DNET_ACCESS_MODES)); } if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) { i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY); @@ -173,7 +178,7 @@ public class CleaningFunctions { if (Objects.isNull(bestaccessrights)) { r .setBestaccessright( - qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES)); + qualifier(ModelConstants.UNKNOWN, "not available", ModelConstants.DNET_ACCESS_MODES)); } else { r.setBestaccessright(bestaccessrights); } @@ -227,7 +232,7 @@ public class CleaningFunctions { .trim() .toLowerCase() .replaceAll(ORCID_CLEANING_REGEX, "$1-$2-$3-$4"); - if (orcid.length() == 19) { + if (orcid.length() == ORCID_LEN) { p.setValue(orcid); } else { p.setValue(""); From 60649ac7d25bb2ddeac0f94593e6ffd48e06336d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 23 Dec 2020 12:26:04 +0100 Subject: [PATCH 107/149] swapped expected and actual in tests, updated expected number of authors --- .../test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index 30cfebe79..882483e22 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -100,8 +100,8 @@ public class EntityMergerTest implements Serializable { assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30"); // verify authors - assertEquals(pub_merged.getAuthor().size(), 9); - assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4); + assertEquals(13, pub_merged.getAuthor().size()); + assertEquals(4, AuthorMerger.countAuthorsPids(pub_merged.getAuthor())); // verify title int count = 0; From 28460c2cd12c4d963a9b3493e8b8ec6578b67187 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 23 Dec 2020 16:59:52 +0100 Subject: [PATCH 108/149] using com.fasterxml.jackson.databind.ObjectMapper instead of org.codehaus.jackson.map.ObjectMapper --- .../dnetlib/dhp/oa/merge/AuthorMergerTest.java | 3 ++- .../dhp/schema/common/ModelConstants.java | 2 ++ .../dnetlib/dhp/oa/dedup/EntityMergerTest.java | 3 ++- .../dedup/SparkCreateConnectedComponent.java | 3 +-- .../eu/dnetlib/dedup/SparkCreateSimRels.java | 3 ++- .../dnetlib/doiboost/DoiBoostMappingUtil.scala | 9 +-------- .../doiboost/SparkGenerateDoiBoost.scala | 3 ++- .../eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala | 4 ++-- .../orcid/SparkDownloadOrcidAuthors.java | 16 ++++++---------- .../doiboost/orcid/MappingORCIDToOAFTest.scala | 2 +- .../dhp/oa/graph/clean/CleaningFunctions.java | 2 +- .../common/AbstractMigrationApplication.java | 3 ++- .../java/eu/dnetlib/dhp/export/DLIToOAF.scala | 6 +++--- .../export/SparkExportContentForOpenAire.scala | 17 ++--------------- .../dhp/provision/DropAndCreateESIndex.java | 3 ++- .../provision/SparkConvertDatasetToJson.scala | 2 +- 16 files changed, 32 insertions(+), 49 deletions(-) diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java index d7b3bc36f..9c4e62214 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java @@ -9,11 +9,12 @@ import java.util.ArrayList; import java.util.List; import java.util.stream.Collectors; -import org.codehaus.jackson.map.ObjectMapper; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java index 1efa86586..bff92ecf9 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java @@ -105,6 +105,8 @@ public class ModelConstants { public static final KeyValue UNKNOWN_REPOSITORY = keyValue( "10|openaire____::55045bd2a65019fd8e6741a755395c8c", "Unknown Repository"); + public static final Qualifier UNKNOWN_COUNTRY = qualifier(UNKNOWN, "Unknown", DNET_COUNTRY_TYPE, DNET_COUNTRY_TYPE); + private static Qualifier qualifier( final String classid, final String classname, diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index 882483e22..c35bbf424 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -10,10 +10,11 @@ import java.io.Serializable; import java.nio.file.Paths; import java.util.*; -import org.codehaus.jackson.map.ObjectMapper; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.pace.util.MapDocumentUtil; diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java index 8646ac742..9bc90d51d 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java @@ -7,7 +7,6 @@ import java.util.List; import org.apache.commons.io.IOUtils; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.PairFunction; @@ -16,8 +15,8 @@ import org.apache.spark.rdd.RDD; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; -import org.codehaus.jackson.map.ObjectMapper; +import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.hash.Hashing; import eu.dnetlib.dedup.graph.ConnectedComponent; diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java index 572824e3d..7adf992cd 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java @@ -10,7 +10,8 @@ import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; -import org.codehaus.jackson.map.ObjectMapper; + +import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Oaf; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala index 8d906fa15..683986de2 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala @@ -4,14 +4,13 @@ import eu.dnetlib.dhp.schema.action.AtomicAction import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty} import eu.dnetlib.dhp.utils.DHPUtils import org.apache.commons.lang3.StringUtils -import org.codehaus.jackson.map.ObjectMapper +import com.fasterxml.jackson.databind.ObjectMapper import org.json4s import org.json4s.DefaultFormats import org.json4s.jackson.JsonMethods.parse import org.slf4j.{Logger, LoggerFactory} import scala.collection.JavaConverters._ -import scala.io.Source case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {} @@ -19,17 +18,11 @@ case class HostedByItemType(id: String, officialname: String, issn: String, eiss case class DoiBoostAffiliation(PaperId:Long, AffiliationId:Long, GridId:Option[String], OfficialPage:Option[String], DisplayName:Option[String]){} object DoiBoostMappingUtil { - def getUnknownCountry(): Qualifier = { - createQualifier("UNKNOWN","UNKNOWN","dnet:countries","dnet:countries") - } - - def generateMAGAffiliationId(affId: String): String = { s"20|microsoft___$SEPARATOR${DHPUtils.md5(affId)}" } - val logger: Logger = LoggerFactory.getLogger(getClass) //STATIC STRING diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 860254527..19a512ac6 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -2,6 +2,7 @@ package eu.dnetlib.doiboost import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.oa.merge.AuthorMerger +import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset} import eu.dnetlib.doiboost.mag.ConversionUtil import org.apache.commons.io.IOUtils @@ -132,7 +133,7 @@ object SparkGenerateDoiBoost { o.setLegalname(DoiBoostMappingUtil.asField(affiliation.DisplayName.get)) if (affiliation.OfficialPage.isDefined) o.setWebsiteurl(DoiBoostMappingUtil.asField(affiliation.OfficialPage.get)) - o.setCountry(DoiBoostMappingUtil.getUnknownCountry()) + o.setCountry(ModelConstants.UNKNOWN_COUNTRY) o } else diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala index f7255e559..e9773dbbb 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala @@ -1,11 +1,11 @@ package eu.dnetlib.doiboost.orcid +import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication} import eu.dnetlib.dhp.schema.orcid.OrcidDOI import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier} import org.apache.commons.lang.StringUtils -import org.codehaus.jackson.map.ObjectMapper import org.slf4j.{Logger, LoggerFactory} import scala.collection.JavaConverters._ @@ -18,7 +18,7 @@ case class ORCIDItem(oid:String,name:String,surname:String,creditName:String,err case class ORCIDElement(doi:String, authors:List[ORCIDItem]) {} object ORCIDToOAF { val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass) - val mapper = new ObjectMapper + val mapper = new ObjectMapper() def isJsonValid(inputStr: String): Boolean = { import java.io.IOException diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java index 598835a00..1422a0840 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java @@ -3,10 +3,8 @@ package eu.dnetlib.doiboost.orcid; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import java.io.IOException; import java.text.SimpleDateFormat; import java.util.Date; -import java.util.List; import java.util.Optional; import org.apache.commons.io.IOUtils; @@ -18,11 +16,9 @@ import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; -import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.Function; import org.apache.spark.util.LongAccumulator; -import org.mortbay.log.Log; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -36,7 +32,7 @@ public class SparkDownloadOrcidAuthors { static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; static final String lastUpdate = "2020-09-29 00:00:00"; - public static void main(String[] args) throws IOException, Exception { + public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils @@ -51,12 +47,12 @@ public class SparkDownloadOrcidAuthors { .orElse(Boolean.TRUE); logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String workingPath = parser.get("workingPath"); - logger.info("workingPath: ", workingPath); + logger.info("workingPath: {}", workingPath); final String outputPath = parser.get("outputPath"); - logger.info("outputPath: ", outputPath); + logger.info("outputPath: {}", outputPath); final String token = parser.get("token"); final String lambdaFileName = parser.get("lambdaFileName"); - logger.info("lambdaFileName: ", lambdaFileName); + logger.info("lambdaFileName: {}", lambdaFileName); SparkConf conf = new SparkConf(); runWithSparkSession( @@ -171,8 +167,8 @@ public class SparkDownloadOrcidAuthors { } private static boolean isModified(String orcidId, String modifiedDate) { - Date modifiedDateDt = null; - Date lastUpdateDt = null; + Date modifiedDateDt; + Date lastUpdateDt; try { if (modifiedDate.length() != 19) { modifiedDate = modifiedDate.substring(0, 19); diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala index 0222b393d..a1b3d06b7 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -1,9 +1,9 @@ package eu.dnetlib.doiboost.orcid +import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.schema.oaf.Publication import eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF.getClass import org.apache.spark.sql.{Encoder, Encoders, SparkSession} -import org.codehaus.jackson.map.ObjectMapper import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.Test import org.slf4j.{Logger, LoggerFactory} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index 859fc074c..885d761c5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -89,7 +89,7 @@ public class CleaningFunctions { } else if (value instanceof Organization) { Organization o = (Organization) value; if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) { - o.setCountry(qualifier(ModelConstants.UNKNOWN, "Unknown", ModelConstants.DNET_COUNTRY_TYPE)); + o.setCountry(ModelConstants.UNKNOWN_COUNTRY); } } else if (value instanceof Relation) { // nothing to clean here diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java index f7579c0a0..a0ce4f5a6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java @@ -11,7 +11,8 @@ import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; -import org.codehaus.jackson.map.ObjectMapper; + +import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.oaf.Oaf; diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala index 705160a2b..8043236e0 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala @@ -1,15 +1,15 @@ package eu.dnetlib.dhp.export +import com.fasterxml.jackson.databind.ObjectMapper + import java.time.LocalDateTime import java.time.format.DateTimeFormatter - import eu.dnetlib.dhp.common.PacePerson import eu.dnetlib.dhp.schema.action.AtomicAction -import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty} +import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty} import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} import eu.dnetlib.dhp.utils.DHPUtils import org.apache.commons.lang3.StringUtils -import org.codehaus.jackson.map.ObjectMapper import eu.dnetlib.dhp.schema.scholexplorer.OafUtils._ import scala.collection.JavaConverters._ diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala index f1e374f95..3f632af22 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala @@ -1,27 +1,21 @@ package eu.dnetlib.dhp.`export` import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.{Instance, Publication, Relation, Dataset => OafDataset} +import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset} import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} import org.apache.commons.io.IOUtils import org.apache.hadoop.io.Text import org.apache.hadoop.io.compress.GzipCodec import org.apache.hadoop.mapred.SequenceFileOutputFormat -import org.apache.spark.rdd.RDD import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.apache.spark.sql.functions._ import org.apache.spark.sql.expressions.Window -import org.apache.spark.{SparkConf, SparkContext} -import org.codehaus.jackson.map.ObjectMapper +import org.apache.spark.SparkConf import scala.collection.mutable.ArrayBuffer -import scala.collection.JavaConverters._ object SparkExportContentForOpenAire { - - - def main(args: Array[String]): Unit = { val conf: SparkConf = new SparkConf() val parser = new ArgumentApplicationParser(IOUtils.toString(SparkExportContentForOpenAire.getClass.getResourceAsStream("input_export_content_parameters.json"))) @@ -178,11 +172,4 @@ object SparkExportContentForOpenAire { fRels.union(fpubs).union(fdats).rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingPath/export/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec]) } - - - - - - - } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java index 1b5849f35..7598fd957 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java @@ -10,7 +10,8 @@ import org.apache.http.client.methods.HttpPut; import org.apache.http.entity.StringEntity; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; -import org.codehaus.jackson.map.ObjectMapper; + +import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala index 81bdb2941..8133666a6 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala @@ -1,5 +1,6 @@ package eu.dnetlib.dhp.provision +import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.provision.scholix.Scholix import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary @@ -7,7 +8,6 @@ import org.apache.commons.io.IOUtils import org.apache.hadoop.io.compress.GzipCodec import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SparkSession} -import org.codehaus.jackson.map.ObjectMapper object SparkConvertDatasetToJson { From 71851589428e12d286ec2d05a0d3d40eb92625ad Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 29 Dec 2020 11:06:28 +0100 Subject: [PATCH 109/149] ignore missing properties --- .../dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java index 9c80528e3..e2ff90d7b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java @@ -10,6 +10,7 @@ import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.DeserializationFeature; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; @@ -44,7 +45,8 @@ public class GroupEntitiesAndRelationsSparkJob { private final static String SOURCE_JPATH = "$.source"; - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); public static void main(String[] args) throws Exception { From b0dc92786f83c428498ab4c64102ca53d39fb54b Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Mon, 4 Jan 2021 17:01:35 +0100 Subject: [PATCH 110/149] defined a single oozie workflow for the generation of doiboost --- .../SparkGenerateDOIBoostActionSet.scala | 3 +- .../doiboost/generate_doiboost_as_params.json | 3 +- .../dhp/doiboost/oozie_app/config-default.xml | 42 +++ .../dhp/doiboost/oozie_app/workflow.xml | 326 ++++++++++++++++++ 4 files changed, 372 insertions(+), 2 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala index 7a6cd3faa..da9da22b6 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala @@ -39,6 +39,7 @@ object SparkGenerateDOIBoostActionSet { val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath") val dbOrganizationPath = parser.get("dbOrganizationPath") val workingDirPath = parser.get("targetPath") + val sequenceFilePath = parser.get("sFilePath") spark.read.load(dbDatasetPath).as[OafDataset] .map(d =>DoiBoostMappingUtil.fixResult(d)) @@ -65,7 +66,7 @@ object SparkGenerateDOIBoostActionSet { val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)] - d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec]) + d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec]) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json index 6eb1ec6f1..0cf9955c9 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json @@ -5,5 +5,6 @@ {"paramName": "cr", "paramLongName":"crossRefRelation", "paramDescription": "the UnpayWall Publication Path", "paramRequired": true}, {"paramName": "da", "paramLongName":"dbaffiliationRelationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true}, {"paramName": "do", "paramLongName":"dbOrganizationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true}, - {"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true} + {"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true}, + {"paramName": "sp", "paramLongName":"sFilePath", "paramDescription": "the Sequence file Path", "paramRequired": true}, ] diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml new file mode 100644 index 000000000..508202e30 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml @@ -0,0 +1,42 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml new file mode 100644 index 000000000..d77972512 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml @@ -0,0 +1,326 @@ + + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorIntersectionMemory + memory for individual executor + + + + sparkExecutorCores + number of cores used by single executor + + + + + + workingPath + the working Path + + + + hostedByMapPath + the hostedByMap Path + + + outputPath + the Path of the sequence file action set + + + + + + + inputPathCrossref + the Crossref input path + + + crossrefTimestamp + Timestamp for the Crossref incremental Harvesting + + + + + inputPathMAG + the MAG working path + + + + + + inputPathUnpayWall + the UnpayWall working path + + + + + inputPathOrcid + the ORCID working path + + + + + + + + + + + + ${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'} + ${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'} + ${wf:conf('resumeFrom') eq 'PreprocessMag'} + ${wf:conf('resumeFrom') eq 'PreprocessUW'} + ${wf:conf('resumeFrom') eq 'PreprocessORCID'} + ${wf:conf('resumeFrom') eq 'CreateDOIBoost'} + ${wf:conf('resumeFrom') eq 'GenerateActionSet'} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.crossref.CrossrefImporter + -t${inputPathCrossref}/index_update + -n${nameNode} + -ts${timestamp} + + + + + + + + + + + yarn-cluster + cluster + GenerateCrossrefDataset + eu.dnetlib.doiboost.crossref.CrossrefDataset + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --workingPath${inputPathCrossref} + --masteryarn-cluster + + + + + + + + + + + + + + + + + + yarn-cluster + cluster + ConvertCrossrefToOAF + eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${inputPathCrossref}/crossref_ds + --targetPath${workingPath} + --masteryarn-cluster + + + + + + + + + + + + + + + + + + + + + yarn-cluster + cluster + Convert Mag to Dataset + eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + ${sparkExtraOPT} + + --sourcePath${inputPathMAG}/input + --targetPath${inputPathMAG}/dataset + --masteryarn-cluster + + + + + + + + + + yarn-cluster + cluster + Convert Mag to OAF Dataset + eu.dnetlib.doiboost.mag.SparkPreProcessMAG + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${inputPathMAG}/dataset + --workingPath${inputPathMAG}/process + --targetPath${workingPath} + --masteryarn-cluster + + + + + + + + + + yarn-cluster + cluster + Convert UnpayWall to Dataset + eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${inputPathUnpayWall}/uw_extracted + --targetPath${workingPath} + --masteryarn-cluster + + + + + + + + + + + yarn-cluster + cluster + Convert ORCID to Dataset + eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --sourcePath${inputPathOrcid} + --targetPath${workingPath} + --masteryarn-cluster + + + + + + + + + yarn-cluster + cluster + Create DOIBoost Infospace + eu.dnetlib.doiboost.SparkGenerateDoiBoost + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --hostedByMapPath${hostedByMapPath} + --affiliationPath${inputPathMAG}/process/Affiliations + --paperAffiliationPath${inputPathMAG}/process/PaperAuthorAffiliations + --workingDirPath${workingPath} + --masteryarn-cluster + + + + + + + + + yarn-cluster + cluster + Generate DOIBoost ActionSet + eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorIntersectionMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --dbPublicationPath${workingPath}/doiBoostPublicationFiltered + --dbDatasetPath${workingPath}/crossrefDataset + --crossRefRelation${workingPath}/crossrefRelation + --dbaffiliationRelationPath${workingPath}/doiBoostPublicationAffiliation + -do${workingPath}/doiBoostOrganization + --targetPath${workingPath}/actionDataSet + --sFilePath${outputPath} + --masteryarn-cluster + + + + + + + \ No newline at end of file From 8765020b85acf0f88a252197de04de4dbb9735fc Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Mon, 4 Jan 2021 17:37:08 +0100 Subject: [PATCH 111/149] minor fix --- .../doiboost/SparkGenerateDoiBoost.scala | 2 +- ...ProcessMAG.scala => SparkProcessMAG.scala} | 2 +- .../doiboost/generate_doiboost_params.json | 2 +- .../dhp/doiboost/oozie_app/workflow.xml | 20 ++++++++----------- 4 files changed, 11 insertions(+), 15 deletions(-) rename dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/{SparkPreProcessMAG.scala => SparkProcessMAG.scala} (99%) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 19a512ac6..11f9828db 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -31,7 +31,7 @@ object SparkGenerateDoiBoost { import spark.implicits._ val hostedByMapPath = parser.get("hostedByMapPath") - val workingDirPath = parser.get("workingDirPath") + val workingDirPath = parser.get("workingPath") implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala similarity index 99% rename from dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala rename to dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala index 02dc4979a..780e65c1e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala @@ -11,7 +11,7 @@ import org.slf4j.{Logger, LoggerFactory} import scala.collection.JavaConverters._ -object SparkPreProcessMAG { +object SparkProcessMAG { def main(args: Array[String]): Unit = { val logger: Logger = LoggerFactory.getLogger(getClass) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json index ea08f47d4..1ff63dd0e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json @@ -3,5 +3,5 @@ {"paramName": "hb", "paramLongName":"hostedByMapPath", "paramDescription": "the hosted By Map Path", "paramRequired": true}, {"paramName": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true}, {"paramName": "pa", "paramLongName":"paperAffiliationPath", "paramDescription": "the paperAffiliation Path", "paramRequired": true}, - {"paramName": "w", "paramLongName":"workingDirPath", "paramDescription": "the Working Path", "paramRequired": true} + {"paramName": "w", "paramLongName":"workingPath", "paramDescription": "the Working Path", "paramRequired": true} ] diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml index d77972512..c116d07b1 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml @@ -166,9 +166,9 @@ - - - + + + @@ -191,18 +191,16 @@ --targetPath${inputPathMAG}/dataset --masteryarn-cluster - + - - - + yarn-cluster cluster Convert Mag to OAF Dataset - eu.dnetlib.doiboost.mag.SparkPreProcessMAG + eu.dnetlib.doiboost.mag.SparkProcessMAG dhp-doiboost-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} @@ -244,8 +242,6 @@ - - @@ -269,7 +265,7 @@ - + yarn-cluster @@ -287,7 +283,7 @@ --hostedByMapPath${hostedByMapPath} --affiliationPath${inputPathMAG}/process/Affiliations --paperAffiliationPath${inputPathMAG}/process/PaperAuthorAffiliations - --workingDirPath${workingPath} + --workingPath${workingPath} --masteryarn-cluster From e79445a8b44111404e3796a03181442726a28297 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Mon, 4 Jan 2021 17:39:25 +0100 Subject: [PATCH 112/149] minor fix for claudio polemica --- .../resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml index c116d07b1..bc859d0e0 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml @@ -309,7 +309,7 @@ --dbDatasetPath${workingPath}/crossrefDataset --crossRefRelation${workingPath}/crossrefRelation --dbaffiliationRelationPath${workingPath}/doiBoostPublicationAffiliation - -do${workingPath}/doiBoostOrganization + --dbOrganizationPath${workingPath}/doiBoostOrganization --targetPath${workingPath}/actionDataSet --sFilePath${outputPath} --masteryarn-cluster From 7834a357683cf3a340794e03945825dd780f0c19 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Mon, 4 Jan 2021 17:54:57 +0100 Subject: [PATCH 113/149] avoid to save intermediate dataset before generation of Sequence file --- .../SparkGenerateDOIBoostActionSet.scala | 26 +++++++++++-------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala index da9da22b6..78477ae4d 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala @@ -41,30 +41,34 @@ object SparkGenerateDOIBoostActionSet { val workingDirPath = parser.get("targetPath") val sequenceFilePath = parser.get("sFilePath") - spark.read.load(dbDatasetPath).as[OafDataset] + val asDataset = spark.read.load(dbDatasetPath).as[OafDataset] .map(d =>DoiBoostMappingUtil.fixResult(d)) .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) - .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet") +// .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet") - spark.read.load(dbPublicationPath).as[Publication] + val asPublication =spark.read.load(dbPublicationPath).as[Publication] .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) - .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") - spark.read.load(dbOrganizationPath).as[Organization] + val asOrganization = spark.read.load(dbOrganizationPath).as[Organization] .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) - .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") - spark.read.load(crossRefRelation).as[Relation] + val asCRelation = spark.read.load(crossRefRelation).as[Relation] .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) - .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") - spark.read.load(dbaffiliationRelationPath).as[Relation] + val asRelAffiliation = spark.read.load(dbaffiliationRelationPath).as[Relation] .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) - .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") +// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet") - val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)] + + + val d: Dataset[(String, String)] = asDataset.union(asPublication).union(asOrganization).union(asCRelation).union(asRelAffiliation) + +// spark.read.load(s"$workingDirPath/actionSet").as[(String,String)] d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec]) From 26e9d55c13e7eebc3be2e997b8b7a3fea180d1cf Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 5 Jan 2021 09:59:26 +0100 Subject: [PATCH 114/149] code formatting --- .../dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java index e2ff90d7b..3186f828c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java @@ -10,7 +10,6 @@ import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; -import com.fasterxml.jackson.databind.DeserializationFeature; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; @@ -22,6 +21,7 @@ import org.apache.spark.sql.expressions.Aggregator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import com.jayway.jsonpath.Configuration; import com.jayway.jsonpath.DocumentContext; @@ -46,7 +46,7 @@ public class GroupEntitiesAndRelationsSparkJob { private final static String SOURCE_JPATH = "$.source"; private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() - .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); public static void main(String[] args) throws Exception { From 8879704ba0e243bea120673c0d14ce76bb59afd0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 5 Jan 2021 10:00:13 +0100 Subject: [PATCH 115/149] [DOIBoost] configurable ES server url and index name in crossref importer --- .../doiboost/crossref/CrossrefImporter.java | 46 ++++++++------ .../dnetlib/doiboost/crossref/ESClient.java | 63 ++++++++----------- .../dnetlib/dhp/doiboost/import_from_es.json | 8 ++- .../dhp/doiboost/oozie_app/workflow.xml | 35 +++++++---- 4 files changed, 81 insertions(+), 71 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java index f69a05da1..cda4983b7 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java @@ -2,18 +2,16 @@ package eu.dnetlib.doiboost.crossref; import java.io.ByteArrayOutputStream; +import java.util.Optional; import java.util.zip.Inflater; import org.apache.commons.codec.binary.Base64; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.IntWritable; import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; @@ -30,34 +28,45 @@ public class CrossrefImporter { parser.parseArgument(args); - final String hdfsuri = parser.get("namenode"); - System.out.println("HDFS URI" + hdfsuri); - Path hdfswritepath = new Path(parser.get("targetPath")); - System.out.println("TargetPath: " + hdfsuri); + final String namenode = parser.get("namenode"); + System.out.println("namenode: " + namenode); - final Long timestamp = StringUtils.isNotBlank(parser.get("timestamp")) - ? Long.parseLong(parser.get("timestamp")) - : -1; + Path targetPath = new Path(parser.get("targetPath")); + System.out.println("targetPath: " + targetPath); - if (timestamp > 0) - System.out.println("Timestamp added " + timestamp); + final Long timestamp = Optional + .ofNullable(parser.get("timestamp")) + .map(s -> { + try { + return Long.parseLong(s); + } catch (NumberFormatException e) { + return -1L; + } + }) + .orElse(-1L); + System.out.println("timestamp: " + timestamp); + + final String esServer = parser.get("esServer"); + System.out.println("esServer: " + esServer); + + final String esIndex = parser.get("esIndex"); + System.out.println("esIndex: " + esIndex); // ====== Init HDFS File System Object Configuration conf = new Configuration(); // Set FileSystem URI - conf.set("fs.defaultFS", hdfsuri); + conf.set("fs.defaultFS", namenode); // Because of Maven conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); - ESClient client = timestamp > 0 - ? new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref", timestamp) - : new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref"); + // "ip-90-147-167-25.ct1.garrservices.it", "crossref" + final ESClient client = new ESClient(esServer, esIndex, timestamp); try (SequenceFile.Writer writer = SequenceFile .createWriter( conf, - SequenceFile.Writer.file(hdfswritepath), + SequenceFile.Writer.file(targetPath), SequenceFile.Writer.keyClass(IntWritable.class), SequenceFile.Writer.valueClass(Text.class))) { @@ -74,8 +83,7 @@ public class CrossrefImporter { end = System.currentTimeMillis(); final float time = (end - start) / 1000.0F; System.out - .println( - String.format("Imported %d records last 100000 imported in %f seconds", i, time)); + .println(String.format("Imported %s records last 100000 imported in %s seconds", i, time)); start = System.currentTimeMillis(); } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java index e31ccf399..dcebbbcac 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java @@ -1,11 +1,11 @@ package eu.dnetlib.doiboost.crossref; -import java.io.IOException; import java.util.Iterator; import java.util.List; import org.apache.commons.io.IOUtils; +import org.apache.http.HttpHeaders; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpPost; import org.apache.http.entity.StringEntity; @@ -17,13 +17,17 @@ import org.slf4j.LoggerFactory; import com.jayway.jsonpath.JsonPath; public class ESClient implements Iterator { - private static final Logger logger = LoggerFactory.getLogger(ESClient.class); - static final String blobPath = "$.hits[*].hits[*]._source.blob"; - static final String scrollIdPath = "$._scroll_id"; - static final String JSON_NO_TS = "{\"size\":1000}"; - static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}"; - static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}"; + private static final String BLOB_PATH = "$.hits.hits[*]._source.blob"; + private static final String SCROLL_ID_PATH = "$._scroll_id"; + private static final String JSON_NO_TS = "{\"size\":1000}"; + private static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}"; + private static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}"; + + public static final String APPLICATION_JSON = "application/json"; + + public static final String ES_SEARCH_URL = "http://%s:9200/%s/_search?scroll=1m"; + public static final String ES_SCROLL_URL = "http://%s:9200/_search/scroll"; private final String scrollId; @@ -31,47 +35,30 @@ public class ESClient implements Iterator { private final String esHost; - public ESClient(final String esHost, final String esIndex) throws IOException { - + public ESClient(final String esHost, final String esIndex, final long timestamp) { this.esHost = esHost; - final String body = getResponse( - String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), JSON_NO_TS); - scrollId = getJPathString(scrollIdPath, body); - buffer = getBlobs(body); - } - public ESClient(final String esHost, final String esIndex, final long timestamp) - throws IOException { - this.esHost = esHost; - final String body = getResponse( - String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), - String.format(JSON_WITH_TS, timestamp)); - scrollId = getJPathString(scrollIdPath, body); + final String body = timestamp > 0 + ? getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), String.format(JSON_WITH_TS, timestamp)) + : getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), JSON_NO_TS); + scrollId = getJPathString(SCROLL_ID_PATH, body); buffer = getBlobs(body); } private String getResponse(final String url, final String json) { - CloseableHttpClient client = HttpClients.createDefault(); - try { - + try (CloseableHttpClient client = HttpClients.createDefault()) { HttpPost httpPost = new HttpPost(url); if (json != null) { StringEntity entity = new StringEntity(json); httpPost.setEntity(entity); - httpPost.setHeader("Accept", "application/json"); - httpPost.setHeader("Content-type", "application/json"); + httpPost.setHeader(HttpHeaders.ACCEPT, APPLICATION_JSON); + httpPost.setHeader(HttpHeaders.CONTENT_TYPE, APPLICATION_JSON); + } + try (CloseableHttpResponse response = client.execute(httpPost)) { + return IOUtils.toString(response.getEntity().getContent()); } - CloseableHttpResponse response = client.execute(httpPost); - - return IOUtils.toString(response.getEntity().getContent()); } catch (Throwable e) { throw new RuntimeException("Error on executing request ", e); - } finally { - try { - client.close(); - } catch (IOException e) { - throw new RuntimeException("Unable to close client ", e); - } } } @@ -87,7 +74,7 @@ public class ESClient implements Iterator { } private List getBlobs(final String body) { - final List res = JsonPath.read(body, "$.hits.hits[*]._source.blob"); + final List res = JsonPath.read(body, BLOB_PATH); return res; } @@ -102,11 +89,11 @@ public class ESClient implements Iterator { if (buffer.isEmpty()) { final String json_param = String.format(JSON_SCROLL, scrollId); - final String body = getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param); + final String body = getResponse(String.format(ES_SCROLL_URL, esHost), json_param); try { buffer = getBlobs(body); } catch (Throwable e) { - logger.error("Error on get next page: body:" + body); + System.out.println("Error on get next page: body:" + body); } } return nextItem; diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json index 87a138d52..0920d516a 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json @@ -1,5 +1,7 @@ [ - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the sequencial file to write", "paramRequired": true}, - {"paramName":"n", "paramLongName":"namenode", "paramDescription": "the hive metastore uris", "paramRequired": true}, - {"paramName":"ts", "paramLongName":"timestamp", "paramDescription": "timestamp", "paramRequired": false} + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the sequencial file to write", "paramRequired": true}, + {"paramName":"n", "paramLongName":"namenode", "paramDescription": "the hive metastore uris", "paramRequired": true}, + {"paramName":"ts", "paramLongName":"timestamp", "paramDescription": "timestamp", "paramRequired": false}, + {"paramName":"ess", "paramLongName":"esServer", "paramDescription": "elasticsearch server url", "paramRequired": true}, + {"paramName":"esi", "paramLongName":"esIndex", "paramDescription": "elasticsearch index name", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml index bc859d0e0..9464c1a61 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml @@ -36,7 +36,6 @@ - inputPathCrossref the Crossref input path @@ -45,6 +44,14 @@ crossrefTimestamp Timestamp for the Crossref incremental Harvesting + + esServer + elasticsearch server url for the Crossref Harvesting + + + esIndex + elasticsearch index name for the Crossref Harvesting + @@ -65,11 +72,19 @@ the ORCID working path - - - + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + @@ -85,20 +100,18 @@ - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - ${jobTracker} - ${nameNode} eu.dnetlib.doiboost.crossref.CrossrefImporter - -t${inputPathCrossref}/index_update - -n${nameNode} - -ts${timestamp} + --targetPath${inputPathCrossref}/index_update + --namenode${nameNode} + --esServer${esServer} + --esIndex${esIndex} + --timestamp${crossrefTimestamp} From 7c722f3fdc960c95c972451621031478ff3c949c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 5 Jan 2021 10:25:54 +0100 Subject: [PATCH 116/149] [DOIBoost] fixed typo --- .../eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json index 0cf9955c9..93d24a891 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json @@ -6,5 +6,5 @@ {"paramName": "da", "paramLongName":"dbaffiliationRelationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true}, {"paramName": "do", "paramLongName":"dbOrganizationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true}, {"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true}, - {"paramName": "sp", "paramLongName":"sFilePath", "paramDescription": "the Sequence file Path", "paramRequired": true}, + {"paramName": "sp", "paramLongName":"sFilePath", "paramDescription": "the Sequence file Path", "paramRequired": true} ] From ab2fe9266ab2fb99da3c2c71f4683927e2cf7973 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 5 Jan 2021 10:26:39 +0100 Subject: [PATCH 117/149] [DOIBoost] minor fixes in workflow definition --- .../dhp/doiboost/oozie_app/workflow.xml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml index 9464c1a61..3f5805b62 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml @@ -91,9 +91,9 @@ ${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'} ${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'} - ${wf:conf('resumeFrom') eq 'PreprocessMag'} - ${wf:conf('resumeFrom') eq 'PreprocessUW'} - ${wf:conf('resumeFrom') eq 'PreprocessORCID'} + ${wf:conf('resumeFrom') eq 'PreprocessMag'} + ${wf:conf('resumeFrom') eq 'PreprocessUW'} + ${wf:conf('resumeFrom') eq 'PreprocessORCID'} ${wf:conf('resumeFrom') eq 'CreateDOIBoost'} ${wf:conf('resumeFrom') eq 'GenerateActionSet'} @@ -227,13 +227,13 @@ --targetPath${workingPath} --masteryarn-cluster - + - + yarn-cluster cluster @@ -251,12 +251,12 @@ --targetPath${workingPath} --masteryarn-cluster - + - + yarn-cluster cluster @@ -287,7 +287,7 @@ eu.dnetlib.doiboost.SparkGenerateDoiBoost dhp-doiboost-${projectVersion}.jar - --executor-memory=${sparkExecutorMemory} + --executor-memory=${sparkExecutorIntersectionMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.sql.shuffle.partitions=3840 @@ -312,7 +312,7 @@ eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet dhp-doiboost-${projectVersion}.jar - --executor-memory=${sparkExecutorIntersectionMemory} + --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.sql.shuffle.partitions=3840 From 1361c9eb0c6c4f929eefaa071405d8e1d93ba202 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Jan 2021 10:07:30 +0100 Subject: [PATCH 118/149] [BIP! Scores integration] Create updates as Result rather than subclasses; Result considers also metrics in the mergeFrom operation --- dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java | 2 +- .../dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index 443c18230..0026ee9aa 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -243,7 +243,7 @@ public class Result extends OafEntity implements Serializable { Result r = (Result) e; - // TODO consider merging also Measures + measures = mergeLists(measures, r.getMeasures()); instance = mergeLists(instance, r.getInstance()); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 50bda898c..dfe48542c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -126,7 +126,7 @@ public class SparkAtomicActionScoreJob implements Serializable { }, Encoders.bean(BipScore.class)) .groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) .mapGroups((MapGroupsFunction) (k, it) -> { - Result ret = inputClazz.newInstance(); + Result ret = new Result(); BipScore first = it.next(); ret.setId(first.getId()); From 34229970e6df31c3d5520e6151b53e31943ad35c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 8 Jan 2021 16:29:17 +0100 Subject: [PATCH 119/149] [BIP! Scores integration] Create updates as Result rather than subclasses; Result considers also metrics in the mergeFrom operation --- .../actionmanager/bipfinder/SparkAtomicActionScoreJob.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index dfe48542c..2cd37d9ea 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -125,16 +125,17 @@ public class SparkAtomicActionScoreJob implements Serializable { return ret; }, Encoders.bean(BipScore.class)) .groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, it) -> { + .mapGroups((MapGroupsFunction) (k, it) -> { Result ret = new Result(); + ret.setDataInfo(getDataInfo()); BipScore first = it.next(); ret.setId(first.getId()); ret.setMeasures(getMeasure(first)); it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value))); - return (I) ret; - }, Encoders.bean(inputClazz)) + return ret; + }, Encoders.bean(Result.class)) .toJavaRDD() .map(p -> new AtomicAction(inputClazz, p)) .mapToPair( From 2a7a10809ed20ed94e2c3ebbaea157003d5946ed Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 11 Jan 2021 10:05:02 +0100 Subject: [PATCH 120/149] [BIP! Scores integration] merged missing classes from bipFinder branch --- .../bipfinder/BipDeserialize.java | 28 ++++++ .../bipfinder/CollectAndSave.java | 85 +++++++++++++++++++ .../dhp/actionmanager/bipfinder/KeyValue.java | 26 ++++++ .../bipfinder/PreparedResult.java | 28 ++++++ .../dhp/actionmanager/bipfinder/Score.java | 30 +++++++ 5 files changed, 197 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java new file mode 100644 index 000000000..d5b2ced7c --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java @@ -0,0 +1,28 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; + +/** + * Class that maps the model of the bipFinder! input data. + * Only needed for deserialization purposes + */ + +public class BipDeserialize extends HashMap> implements Serializable { + + public BipDeserialize() { + super(); + } + + public List get(String key) { + + if (super.get(key) == null) { + return new ArrayList<>(); + } + return super.get(key); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java new file mode 100644 index 000000000..0bebe2fb0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java @@ -0,0 +1,85 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.oaf.Result; + +/** + * Just collects all the atomic actions produced for the different results and saves them in + * outputpath for the ActionSet + */ +public class CollectAndSave implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + CollectAndSave.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("inputPath"); + log.info("inputPath {}: ", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + collectAndSave(spark, inputPath, outputPath); + }); + } + + private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + sc + .sequenceFile(inputPath + "/publication", Text.class, Text.class) + .union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)) + .union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)) + .union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class)) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + ; + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java new file mode 100644 index 000000000..6909a9634 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java @@ -0,0 +1,26 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; + +public class KeyValue implements Serializable { + + private String key; + private String value; + + public String getKey() { + return key; + } + + public void setKey(String key) { + this.key = key; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java new file mode 100644 index 000000000..493e94417 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java @@ -0,0 +1,28 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; + +/** + * Subset of the information of the generic results that are needed to create the atomic action + */ +public class PreparedResult implements Serializable { + private String id; // openaire id + private String value; // doi + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java new file mode 100644 index 000000000..7cc21b44d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.Serializable; +import java.util.List; + +/** + * represents the score in the input file + */ +public class Score implements Serializable { + + private String id; + private List unit; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getUnit() { + return unit; + } + + public void setUnit(List unit) { + this.unit = unit; + } +} From 41500669e221dd8ea1d5704b251770aea250e4a9 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 11 Jan 2021 14:39:47 +0100 Subject: [PATCH 121/149] [BIP! Scores integration] merged missing classes from bipFinder branch --- .../bipfinder/input_actionset_parameter.json | 20 + .../bipfinder/input_parameters.json | 32 + .../bipfinder/oozie_app/workflow.xml | 171 +++ .../SparkAtomicActionScoreJobTest.java | 323 +++++ .../actionmanager/bipfinder/bip_scores.json | 1101 +++++++++++++++++ .../actionmanager/bipfinder/publication.json | 18 + .../bipfinder/publication_2.json | 18 + .../bipfinder/publication_3.json | 18 + 8 files changed, 1701 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json new file mode 100644 index 000000000..7663a454b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "ip", + "paramLongName": "inputPath", + "paramDescription": "the URL from where to get the programme file", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json new file mode 100644 index 000000000..31771a40a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "ip", + "paramLongName": "inputPath", + "paramDescription": "the URL from where to get the programme file", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + }, + { + "paramName": "rtn", + "paramLongName": "resultTableName", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + }, + { + "paramName": "bsp", + "paramLongName": "bipScorePath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml new file mode 100644 index 000000000..5311a6614 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml @@ -0,0 +1,171 @@ + + + + inputPath + the input path of the resources to be extended + + + + bipScorePath + the path where to find the bipFinder scores + + + outputPath + the path where to store the actionset + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + + + + + + + yarn + cluster + Produces the atomic action with the bip finder scores for publications + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/publication + --bipScorePath${bipScorePath} + + + + + + + + yarn + cluster + Produces the atomic action with the bip finder scores for datasets + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dataset + --bipScorePath${bipScorePath} + + + + + + + + yarn + cluster + Produces the atomic action with the bip finder scores for orp + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/otherresearchproduct + --bipScorePath${bipScorePath} + + + + + + + + yarn + cluster + Produces the atomic action with the bip finder scores for software + eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/software + --bipScorePath${bipScorePath} + + + + + + + + + + yarn + cluster + saves all the aa produced for the several types of results in the as output path + eu.dnetlib.dhp.actionmanager.bipfinder.CollectAndSave + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${workingDir} + --outputPath${outputPath} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java new file mode 100644 index 000000000..7200d2896 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java @@ -0,0 +1,323 @@ + +package eu.dnetlib.dhp.actionmanager.bipfinder; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Publication; + +public class SparkAtomicActionScoreJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(SparkAtomicActionScoreJobTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SparkAtomicActionScoreJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SparkAtomicActionScoreJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void matchOne() throws Exception { + String bipScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") + .getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json") + .getPath(); + + SparkAtomicActionScoreJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); + + Assertions.assertTrue(tmp.count() == 1); + + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); + + Dataset execVerification = spark + .sql( + "Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); + + Assertions.assertEquals(2, execVerification.count()); + + Assertions + .assertEquals( + "50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", + execVerification.select("oaid").collectAsList().get(0).getString(0)); + + Assertions + .assertEquals( + "1.47565045883e-08", + execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0)); + + Assertions + .assertEquals( + "0.227515392", + execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0)); + + } + + @Test + public void matchOneWithTwo() throws Exception { + String bipScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") + .getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json") + .getPath(); + + SparkAtomicActionScoreJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); + + Assertions.assertTrue(tmp.count() == 1); + + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); + + Dataset execVerification = spark + .sql( + "Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); + + Assertions.assertEquals(4, execVerification.count()); + + Assertions + .assertEquals( + "50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", + execVerification.select("oaid").collectAsList().get(0).getString(0)); + + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'influence'").count()); + + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'popularity'").count()); + + List tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList(); + String tmp_influence = tmp_ds.get(0).getString(0); + Assertions + .assertTrue( + "1.47565045883e-08".equals(tmp_influence) || + "1.98956540239e-08".equals(tmp_influence)); + + tmp_influence = tmp_ds.get(1).getString(0); + Assertions + .assertTrue( + "1.47565045883e-08".equals(tmp_influence) || + "1.98956540239e-08".equals(tmp_influence)); + + Assertions.assertTrue(!tmp_ds.get(0).getString(0).equals(tmp_ds.get(1).getString(0))); + + } + + @Test + public void matchTwo() throws Exception { + String bipScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") + .getPath(); + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json") + .getPath(); + + SparkAtomicActionScoreJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-bipScorePath", + bipScoresPath, + "-resultTableName", + "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Publication) aa.getPayload())); + + Assertions.assertTrue(tmp.count() == 2); + + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + verificationDataset.createOrReplaceTempView("publication"); + + Dataset execVerification = spark + .sql( + "Select p.id oaid, mes.id, mUnit.value from publication p " + + "lateral view explode(measures) m as mes " + + "lateral view explode(mes.unit) u as mUnit "); + + Assertions.assertEquals(4, execVerification.count()); + + Assertions + .assertEquals( + 2, + execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count()); + + Assertions + .assertEquals( + 2, + execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count()); + + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'influence'").count()); + + Assertions + .assertEquals( + 2, + execVerification.filter("id = 'popularity'").count()); + + Assertions + .assertEquals( + "1.47565045883e-08", + execVerification + .filter( + "oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + + "and id = 'influence'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + + Assertions + .assertEquals( + "1.98956540239e-08", + execVerification + .filter( + "oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + + "and id = 'influence'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + + Assertions + .assertEquals( + "0.282046161584", + execVerification + .filter( + "oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + + "and id = 'popularity'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + + Assertions + .assertEquals( + "0.227515392", + execVerification + .filter( + "oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + + "and id = 'popularity'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json new file mode 100644 index 000000000..a4f3fa8b8 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json @@ -0,0 +1,1101 @@ +{"10.1001/10-v4n2-hsf10003": [{"id": "influence", "unit": [{"value": "1.62759106106e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.22519296", "key": "score"}]}]} +{"10.1001/2012.jama.10456": [{"id": "influence", "unit": [{"value": "1.66083991022e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.8690688", "key": "score"}]}]} +{"10.1001/2013.jamadermatol.729": [{"id": "influence", "unit": [{"value": "2.0769133069e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.0279936", "key": "score"}]}]} +{"10.1001/archderm.107.6.853": [{"id": "influence", "unit": [{"value": "1.95361113607e-08", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "0.600657255944", "key": "score"}]}]} +{"10.1001/archderm.1926.02370130020002": [{"id": "influence", "unit": [{"value": "1.48611319422e-08", "key": "score"}]}, {"id": 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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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travail de thèse est consacré à l'extension de l'Inversion Dynamique non-linéaire (NDI-Nonlinear Dynamic Inversion) pour un ensemble plus grand de systèmes non-linéaires, tout en garantissant des conditions de stabilité suffisantes. La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. However, this method is inherently non-robust to modelling errors and input saturations. Moreover, obtaining a quantifiable guarantee of the attained stability domain in a nonlinear control context is not a very straightforward task. Unlike standard NDI approaches, our methodology can be viewed as a generalized nonlinear compensation framework which allows to incorporate uncertainties and input saturations in the design process. Paralleling anti-windup strategies, the controller can be computed through a single multichannel optimization problem or through a simple two-step process. Within this framework, linear fractional transformations of the nonlinear closed-loop can be easily derived for robust stability analysis using standard tools for linear systems. The proposed method is tested for the flight control of a delta wing type reentry vehicle at hypersonic, transonic and subsonic phases of the atmospheric reentry. For this thesis work, a Flight Mechanics simulator including diverse external factors and modelling errors was developed in Simulink."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|artemis___fr::630e47d8b572e3df0e91327d6d8f036d","instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|driver______::66c20c26ac26136628f5207819ae1abc","value":"Archives des thèses et mémoires de l’ISAE (ArTeMIS)"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2012-09-21"},"distributionlocation":"","hostedby":{"key":"10|driver______::66c20c26ac26136628f5207819ae1abc","value":"Archives des thèses et mémoires de l’ISAE 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atmosphérique"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"A generalized framework for robust nonlinear compensation : application to an atmospheric reentry control problem"}]} \ No newline at end of file From 80cf55ef2e1e809f07670cfb4a2b52d651daa79e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 13 Jan 2021 16:24:30 +0100 Subject: [PATCH 122/149] [Broker] fixed partitionEventsByOpendoarIds workflow parameter names --- .../dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index 83fe47c75..7c5b722d2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -87,7 +87,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingDir${workingDir} + --outputDir${outputDir} --opendoarIds${opendoarIds} From ac91e495fc97cec1d5d98b67cda211b8ef9817d2 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 14 Jan 2021 13:20:35 +0100 Subject: [PATCH 123/149] Added eventId to ShortEventMessage --- .../eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java | 3 ++- .../dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml | 2 +- pom.xml | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index 08c74a291..e061c0d3b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -36,7 +36,7 @@ import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; public class PartitionEventsByDsIdJob { private static final Logger log = LoggerFactory.getLogger(PartitionEventsByDsIdJob.class); - private static final String OPENDOAR_NSPREFIX = "10|opendoar____::"; + private static final String OPENDOAR_NSPREFIX = "opendoar____::"; public static void main(final String[] args) throws Exception { @@ -123,6 +123,7 @@ public class PartitionEventsByDsIdJob { final ShortEventMessageWithGroupId res = new ShortEventMessageWithGroupId(); + res.setEventId(e.getEventId()); res.setOriginalId(payload.getResult().getOriginalId()); res.setTitle(payload.getResult().getTitles().stream().filter(StringUtils::isNotBlank).findFirst().orElse(null)); res.setTopic(e.getTopic()); diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index 83fe47c75..7c5b722d2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -87,7 +87,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingDir${workingDir} + --outputDir${outputDir} --opendoarIds${opendoarIds} diff --git a/pom.xml b/pom.xml index a2e2587b3..3e0626aed 100644 --- a/pom.xml +++ b/pom.xml @@ -704,7 +704,7 @@ 3.3.3 3.4.2 [2.12,3.0) - 3.1.1 + 3.1.6 7.5.0 4.7.2 1.20 From 223fa660cbcf464fc443d1ffe0a7eea5ad5b5ec8 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 14 Jan 2021 14:23:44 +0100 Subject: [PATCH 124/149] fixed conflict --- .../dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index 7c5b722d2..dba3c9f73 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the opendoar IDs whitelist (comma separated) - outputDir + workingPath the path where the the generated data will be stored @@ -87,7 +87,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --outputDir${outputDir} + --workingPath${workingPath} --opendoarIds${opendoarIds} From ff41a7b3a4f9bcf40dfee43ae4853270f575826c Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 10 Dec 2020 11:59:28 +0100 Subject: [PATCH 125/149] gzipped output --- .../dhp/broker/oa/CheckDuplictedIdsJob.java | 9 ++++---- .../broker/oa/PartitionEventsByDsIdJob.java | 23 ++++++++----------- .../dhp/broker/oa/util/ClusterUtils.java | 1 + 3 files changed, 15 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java index 5ca865e8f..951afb6c5 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java @@ -30,9 +30,8 @@ public class CheckDuplictedIdsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - CheckDuplictedIdsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); + .toString(CheckDuplictedIdsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); @@ -59,8 +58,8 @@ public class CheckDuplictedIdsJob { .map(o -> ClusterUtils.incrementAccumulator(o, total), Encoders.tuple(Encoders.STRING(), Encoders.LONG())) .write() .mode(SaveMode.Overwrite) - .json(countPath); - ; + .option("compression", "gzip") + .json(countPath);; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index e9644122f..1e060d824 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -42,9 +42,8 @@ public class PartitionEventsByDsIdJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - PartitionEventsByDsIdJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); + .toString(PartitionEventsByDsIdJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -67,13 +66,12 @@ public class PartitionEventsByDsIdJob { final Set validOpendoarIds = new HashSet<>(); if (!opendoarIds.trim().equals("-")) { validOpendoarIds - .addAll( - Arrays - .stream(opendoarIds.split(",")) - .map(String::trim) - .filter(StringUtils::isNotBlank) - .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) - .collect(Collectors.toSet())); + .addAll(Arrays + .stream(opendoarIds.split(",")) + .map(String::trim) + .filter(StringUtils::isNotBlank) + .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) + .collect(Collectors.toSet())); } log.info("validOpendoarIds: {}", validOpendoarIds); @@ -84,13 +82,12 @@ public class PartitionEventsByDsIdJob { .filter((FilterFunction) e -> StringUtils.isNotBlank(e.getMap().getTargetDatasourceId())) .filter((FilterFunction) e -> e.getMap().getTargetDatasourceId().startsWith(OPENDOAR_NSPREFIX)) .filter((FilterFunction) e -> validOpendoarIds.contains(e.getMap().getTargetDatasourceId())) - .map( - (MapFunction) e -> messageFromNotification(e), - Encoders.bean(ShortEventMessageWithGroupId.class)) + .map((MapFunction) e -> messageFromNotification(e), Encoders.bean(ShortEventMessageWithGroupId.class)) .coalesce(1) .write() .partitionBy("group") .mode(SaveMode.Overwrite) + .option("compression", "gzip") .json(partitionPath); }); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java index d8b8dd807..04985a6ab 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java @@ -67,6 +67,7 @@ public class ClusterUtils { .map(o -> ClusterUtils.incrementAccumulator(o, acc), Encoders.bean(clazz)) .write() .mode(SaveMode.Overwrite) + .option("compression", "gzip") .json(path); } From 10f3f7eca7c4339315b08458ccb195ed2992e019 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 10 Dec 2020 14:47:22 +0100 Subject: [PATCH 126/149] workingDir and outputDir --- .../dhp/broker/oa/CheckDuplictedIdsJob.java | 6 +-- .../dhp/broker/oa/GenerateEventsJob.java | 19 ++++------ .../dhp/broker/oa/GenerateStatsJob.java | 7 ++-- .../dhp/broker/oa/IndexEventSubsetJob.java | 7 ++-- .../dhp/broker/oa/IndexNotificationsJob.java | 19 ++++------ .../dnetlib/dhp/broker/oa/IndexOnESJob.java | 7 ++-- .../dnetlib/dhp/broker/oa/JoinStep0Job.java | 10 ++--- .../dnetlib/dhp/broker/oa/JoinStep1Job.java | 10 ++--- .../dnetlib/dhp/broker/oa/JoinStep2Job.java | 10 ++--- .../dnetlib/dhp/broker/oa/JoinStep3Job.java | 10 ++--- .../dnetlib/dhp/broker/oa/JoinStep4Job.java | 10 ++--- .../broker/oa/PartitionEventsByDsIdJob.java | 4 +- .../dhp/broker/oa/PrepareGroupsJob.java | 8 ++-- .../broker/oa/PrepareRelatedDatasetsJob.java | 6 +-- .../oa/PrepareRelatedDatasourcesJob.java | 6 +-- .../broker/oa/PrepareRelatedProjectsJob.java | 6 +-- .../oa/PrepareRelatedPublicationsJob.java | 6 +-- .../broker/oa/PrepareRelatedSoftwaresJob.java | 6 +-- .../broker/oa/PrepareSimpleEntititiesJob.java | 6 +-- .../dhp/broker/oa/check_duplicates.json | 9 +++++ .../dnetlib/dhp/broker/oa/common_params.json | 2 +- .../oa/generate_all/oozie_app/workflow.xml | 37 ++++++++++--------- .../dhp/broker/oa/generate_events.json | 8 +++- .../eu/dnetlib/dhp/broker/oa/index_es.json | 4 +- .../dhp/broker/oa/index_event_subset.json | 4 +- .../dhp/broker/oa/index_notifications.json | 4 +- .../notifications_only/oozie_app/workflow.xml | 6 +-- .../dhp/broker/oa/od_partitions_params.json | 4 +- .../opendoarPartition/oozie_app/workflow.xml | 4 +- .../dnetlib/dhp/broker/oa/stats_params.json | 6 +-- 30 files changed, 128 insertions(+), 123 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java index 951afb6c5..416ee5024 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java @@ -31,15 +31,15 @@ public class CheckDuplictedIdsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString(CheckDuplictedIdsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); - final String countPath = parser.get("workingPath") + "/counts"; + final String countPath = parser.get("outputDir") + "/counts"; log.info("countPath: {}", countPath); final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java index cfee360c5..9e128d49e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java @@ -33,9 +33,8 @@ public class GenerateEventsJob { public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - GenerateEventsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_events.json"))); + .toString(GenerateEventsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_events.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -44,10 +43,10 @@ public class GenerateEventsJob { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String eventsPath = workingPath + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final Set dsIdWhitelist = ClusterUtils.parseParamAsList(parser, "datasourceIdWhitelist"); @@ -70,13 +69,11 @@ public class GenerateEventsJob { final LongAccumulator total = spark.sparkContext().longAccumulator("total_events"); final Dataset groups = ClusterUtils - .readPath(spark, workingPath + "/duplicates", ResultGroup.class); + .readPath(spark, workingDir + "/duplicates", ResultGroup.class); final Dataset dataset = groups - .map( - g -> EventFinder - .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), - Encoders + .map(g -> EventFinder + .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), Encoders .bean(EventGroup.class)) .flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java index d5c53ea36..c44aead5e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java @@ -33,9 +33,8 @@ public class GenerateStatsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - GenerateStatsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/stats_params.json"))); + .toString(GenerateStatsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/stats_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -46,7 +45,7 @@ public class GenerateStatsJob { final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String dbUrl = parser.get("dbUrl"); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java index d3cbe0034..929c31600 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java @@ -39,14 +39,13 @@ public class IndexEventSubsetJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - IndexEventSubsetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_event_subset.json"))); + .toString(IndexEventSubsetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_event_subset.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String index = parser.get("index"); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index 792a2354a..e1d2e7d24 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -47,14 +47,13 @@ public class IndexNotificationsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - IndexNotificationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); + .toString(IndexNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String index = parser.get("index"); @@ -117,8 +116,7 @@ public class IndexNotificationsJob { final long date) { final List list = subscriptions .stream() - .filter( - s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) + .filter(s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) .filter(s -> verifyConditions(e.getMap(), s.conditionsAsMap())) .map(s -> generateNotification(s, e, date)) .collect(Collectors.toList()); @@ -149,18 +147,15 @@ public class IndexNotificationsJob { if (conditions.containsKey("trust") && !SubscriptionUtils - .verifyFloatRange( - map.getTrust(), conditions.get("trust").get(0).getValue(), - conditions.get("trust").get(0).getOtherValue())) { + .verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) { return false; } if (conditions.containsKey("targetDateofacceptance") && !conditions .get("targetDateofacceptance") .stream() - .anyMatch( - c -> SubscriptionUtils - .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { + .anyMatch(c -> SubscriptionUtils + .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { return false; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java index 762bfbb90..106528666 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java @@ -29,14 +29,13 @@ public class IndexOnESJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - IndexOnESJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_es.json"))); + .toString(IndexOnESJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_es.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); final String index = parser.get("index"); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java index 39fa76e43..01778ad74 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java @@ -42,10 +42,10 @@ public class JoinStep0Job { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step0"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step0"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -57,10 +57,10 @@ public class JoinStep0Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/simpleEntities", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/simpleEntities", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedDatasources", RelatedDatasource.class); + .readPath(spark, workingDir + "/relatedDatasources", RelatedDatasource.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedDatasourceAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java index 8e502f736..82c3619e1 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java @@ -40,10 +40,10 @@ public class JoinStep1Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step1"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step1"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -55,10 +55,10 @@ public class JoinStep1Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step0", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step0", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedProjects", RelatedProject.class); + .readPath(spark, workingDir + "/relatedProjects", RelatedProject.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedProjectAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java index 55ab497f0..bd6135d41 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java @@ -39,10 +39,10 @@ public class JoinStep2Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step2"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step2"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -54,10 +54,10 @@ public class JoinStep2Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step1", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step1", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedSoftwares", RelatedSoftware.class); + .readPath(spark, workingDir + "/relatedSoftwares", RelatedSoftware.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedSoftwareAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java index 4d06f6f13..18e8c00b2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java @@ -40,10 +40,10 @@ public class JoinStep3Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step3"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step3"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -55,10 +55,10 @@ public class JoinStep3Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step2", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step2", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedDatasets", RelatedDataset.class); + .readPath(spark, workingDir + "/relatedDatasets", RelatedDataset.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedDatasetAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java index b53d7e39b..965530362 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java @@ -40,10 +40,10 @@ public class JoinStep4Job { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String joinedEntitiesPath = workingPath + "/joinedEntities_step4"; + final String joinedEntitiesPath = workingDir + "/joinedEntities_step4"; log.info("joinedEntitiesPath: {}", joinedEntitiesPath); final SparkConf conf = new SparkConf(); @@ -55,10 +55,10 @@ public class JoinStep4Job { final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities"); final Dataset sources = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step3", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step3", OaBrokerMainEntity.class); final Dataset typedRels = ClusterUtils - .readPath(spark, workingPath + "/relatedPublications", RelatedPublication.class); + .readPath(spark, workingDir + "/relatedPublications", RelatedPublication.class); final TypedColumn, OaBrokerMainEntity> aggr = new RelatedPublicationAggregator() .toColumn(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index 1e060d824..ec694f5d3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -54,10 +54,10 @@ public class PartitionEventsByDsIdJob { final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("workingPath") + "/events"; + final String eventsPath = parser.get("outputDir") + "/events"; log.info("eventsPath: {}", eventsPath); - final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId"; + final String partitionPath = parser.get("outputDir") + "/eventsByOpendoarId"; log.info("partitionPath: {}", partitionPath); final String opendoarIds = parser.get("opendoarIds"); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java index eb9add00d..a575328e8 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java @@ -45,10 +45,10 @@ public class PrepareGroupsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String groupsPath = workingPath + "/duplicates"; + final String groupsPath = workingDir + "/duplicates"; log.info("groupsPath: {}", groupsPath); final SparkConf conf = new SparkConf(); @@ -60,7 +60,7 @@ public class PrepareGroupsJob { final LongAccumulator total = spark.sparkContext().longAccumulator("total_groups"); final Dataset results = ClusterUtils - .readPath(spark, workingPath + "/joinedEntities_step4", OaBrokerMainEntity.class); + .readPath(spark, workingDir + "/joinedEntities_step4", OaBrokerMainEntity.class); final Dataset mergedRels = ClusterUtils .readPath(spark, graphPath + "/relation", Relation.class) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java index 0cfc1adcb..8c2879b38 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java @@ -42,10 +42,10 @@ public class PrepareRelatedDatasetsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedDatasets"; + final String relsPath = workingDir + "/relatedDatasets"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java index 166372a7f..0c2318127 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasourcesJob.java @@ -48,10 +48,10 @@ public class PrepareRelatedDatasourcesJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedDatasources"; + final String relsPath = workingDir + "/relatedDatasources"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java index e988366c8..1952b5d9c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java @@ -44,10 +44,10 @@ public class PrepareRelatedProjectsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedProjects"; + final String relsPath = workingDir + "/relatedProjects"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java index 724acc4dc..d6ac27fc5 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java @@ -43,10 +43,10 @@ public class PrepareRelatedPublicationsJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedPublications"; + final String relsPath = workingDir + "/relatedPublications"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java index d15565d0d..c4ccf4af6 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java @@ -44,10 +44,10 @@ public class PrepareRelatedSoftwaresJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String relsPath = workingPath + "/relatedSoftwares"; + final String relsPath = workingDir + "/relatedSoftwares"; log.info("relsPath: {}", relsPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java index d3c7113ec..cf4450603 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java @@ -44,10 +44,10 @@ public class PrepareSimpleEntititiesJob { final String graphPath = parser.get("graphPath"); log.info("graphPath: {}", graphPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String simpleEntitiesPath = workingPath + "/simpleEntities"; + final String simpleEntitiesPath = workingDir + "/simpleEntities"; log.info("simpleEntitiesPath: {}", simpleEntitiesPath); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json new file mode 100644 index 000000000..2584b78fc --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json @@ -0,0 +1,9 @@ +[ + + { + "paramName": "o", + "paramLongName": "outputDir", + "paramDescription": "the path where the data are stored", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json index adee1888a..0d942cd59 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json @@ -7,7 +7,7 @@ }, { "paramName": "o", - "paramLongName": "workingPath", + "paramLongName": "workingDir", "paramDescription": "the path where the temporary data will be stored", "paramRequired": true } diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index 14e33b091..1a1df418b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the path where the graph is stored - workingPath + outputDir the path where the the generated data will be stored @@ -119,7 +119,7 @@ - + @@ -152,7 +152,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -176,7 +176,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -201,7 +201,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -225,7 +225,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -249,7 +249,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -273,7 +273,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -299,7 +299,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -323,7 +323,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -347,7 +347,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -371,7 +371,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -395,7 +395,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -419,7 +419,7 @@ --conf spark.sql.shuffle.partitions=3840 --graphPath${graphInputPath} - --workingPath${workingPath} + --workingDir${workingDir} @@ -442,7 +442,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --workingDir${workingDir} + --outputDir${outputDir} --datasourceIdWhitelist${datasourceIdWhitelist} --datasourceTypeWhitelist${datasourceTypeWhitelist} --datasourceIdBlacklist${datasourceIdBlacklist} @@ -468,7 +469,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --index${esEventIndexName} --esHost${esIndexHost} --maxEventsForTopic${maxIndexedEventsForDsAndTopic} @@ -495,7 +496,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --index${esNotificationsIndexName} --esHost${esIndexHost} --brokerApiBaseUrl${brokerApiBaseUrl} @@ -521,7 +522,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --dbUrl${brokerDbUrl} --dbUser${brokerDbUser} --dbPassword${brokerDbPassword} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json index bab808193..a482ee2dc 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json @@ -1,7 +1,13 @@ [ + { + "paramName": "wp", + "paramLongName": "workingDir", + "paramDescription": "the path where the temporary data are stored", + "paramRequired": true + }, { "paramName": "o", - "paramLongName": "workingPath", + "paramLongName": "outputDir", "paramDescription": "the path where the generated events will be stored", "paramRequired": true }, diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json index ac1dbf786..079709ad8 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the workinh path", + "paramLongName": "outputDir", + "paramDescription": "the data path", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json index 4921bc03e..441249661 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the workinh path", + "paramLongName": "outputDir", + "paramDescription": "the path where the generated data are stored", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json index 5eea894c8..63e9b1263 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the workinh path", + "paramLongName": "outputDir", + "paramDescription": "the dir that contains the events folder", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml index 879c0d349..c73b3fb52 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml @@ -6,8 +6,8 @@ the path where the graph is stored - workingPath - the path where the the generated data will be stored + outputDir + the path where the the generated data are stored datasourceIdWhitelist @@ -122,7 +122,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --outputDir${outputDir} --index${esNotificationsIndexName} --esHost${esIndexHost} --brokerApiBaseUrl${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json index 10ba926ab..12cd6a391 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the path where the temporary data will be stored", + "paramLongName": "outputDir", + "paramDescription": "the path where the data will be stored", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index dba3c9f73..83fe47c75 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the opendoar IDs whitelist (comma separated) - workingPath + outputDir the path where the the generated data will be stored @@ -87,7 +87,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingPath${workingPath} + --workingDir${workingDir} --opendoarIds${opendoarIds} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json index 15d7d251f..2388b1c1f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json @@ -1,8 +1,8 @@ [ { - "paramName": "wp", - "paramLongName": "workingPath", - "paramDescription": "the working path", + "paramName": "o", + "paramLongName": "outputDir", + "paramDescription": "the path where generated data are stored", "paramRequired": true }, { From 467aa77279f2ccd07dd0e976c7b6ec0b46a823a6 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 10 Dec 2020 14:47:51 +0100 Subject: [PATCH 127/149] workingDir and outputDir --- .../dhp/broker/oa/CheckDuplictedIdsJob.java | 8 ++++--- .../dhp/broker/oa/GenerateEventsJob.java | 11 ++++++---- .../dhp/broker/oa/GenerateStatsJob.java | 5 +++-- .../dhp/broker/oa/IndexEventSubsetJob.java | 5 +++-- .../dhp/broker/oa/IndexNotificationsJob.java | 17 +++++++++----- .../dnetlib/dhp/broker/oa/IndexOnESJob.java | 5 +++-- .../broker/oa/PartitionEventsByDsIdJob.java | 22 +++++++++++-------- 7 files changed, 45 insertions(+), 28 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java index 416ee5024..d42c692f7 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java @@ -30,8 +30,9 @@ public class CheckDuplictedIdsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(CheckDuplictedIdsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json"))); + .toString( + CheckDuplictedIdsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); @@ -59,7 +60,8 @@ public class CheckDuplictedIdsJob { .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(countPath);; + .json(countPath); + ; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java index 9e128d49e..457b82517 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java @@ -33,8 +33,9 @@ public class GenerateEventsJob { public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(GenerateEventsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_events.json"))); + .toString( + GenerateEventsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_events.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -72,8 +73,10 @@ public class GenerateEventsJob { .readPath(spark, workingDir + "/duplicates", ResultGroup.class); final Dataset dataset = groups - .map(g -> EventFinder - .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), Encoders + .map( + g -> EventFinder + .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), + Encoders .bean(EventGroup.class)) .flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java index c44aead5e..2772f8fd1 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java @@ -33,8 +33,9 @@ public class GenerateStatsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(GenerateStatsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/stats_params.json"))); + .toString( + GenerateStatsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/stats_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java index 929c31600..72efc9e6b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java @@ -39,8 +39,9 @@ public class IndexEventSubsetJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(IndexEventSubsetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_event_subset.json"))); + .toString( + IndexEventSubsetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_event_subset.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index e1d2e7d24..29fc72d04 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -47,8 +47,9 @@ public class IndexNotificationsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(IndexNotificationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); + .toString( + IndexNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); @@ -116,7 +117,8 @@ public class IndexNotificationsJob { final long date) { final List list = subscriptions .stream() - .filter(s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) + .filter( + s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) .filter(s -> verifyConditions(e.getMap(), s.conditionsAsMap())) .map(s -> generateNotification(s, e, date)) .collect(Collectors.toList()); @@ -147,15 +149,18 @@ public class IndexNotificationsJob { if (conditions.containsKey("trust") && !SubscriptionUtils - .verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) { + .verifyFloatRange( + map.getTrust(), conditions.get("trust").get(0).getValue(), + conditions.get("trust").get(0).getOtherValue())) { return false; } if (conditions.containsKey("targetDateofacceptance") && !conditions .get("targetDateofacceptance") .stream() - .anyMatch(c -> SubscriptionUtils - .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { + .anyMatch( + c -> SubscriptionUtils + .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { return false; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java index 106528666..006cde48c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java @@ -29,8 +29,9 @@ public class IndexOnESJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(IndexOnESJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_es.json"))); + .toString( + IndexOnESJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_es.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index ec694f5d3..08c74a291 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -42,8 +42,9 @@ public class PartitionEventsByDsIdJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(PartitionEventsByDsIdJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); + .toString( + PartitionEventsByDsIdJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -66,12 +67,13 @@ public class PartitionEventsByDsIdJob { final Set validOpendoarIds = new HashSet<>(); if (!opendoarIds.trim().equals("-")) { validOpendoarIds - .addAll(Arrays - .stream(opendoarIds.split(",")) - .map(String::trim) - .filter(StringUtils::isNotBlank) - .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) - .collect(Collectors.toSet())); + .addAll( + Arrays + .stream(opendoarIds.split(",")) + .map(String::trim) + .filter(StringUtils::isNotBlank) + .map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s)) + .collect(Collectors.toSet())); } log.info("validOpendoarIds: {}", validOpendoarIds); @@ -82,7 +84,9 @@ public class PartitionEventsByDsIdJob { .filter((FilterFunction) e -> StringUtils.isNotBlank(e.getMap().getTargetDatasourceId())) .filter((FilterFunction) e -> e.getMap().getTargetDatasourceId().startsWith(OPENDOAR_NSPREFIX)) .filter((FilterFunction) e -> validOpendoarIds.contains(e.getMap().getTargetDatasourceId())) - .map((MapFunction) e -> messageFromNotification(e), Encoders.bean(ShortEventMessageWithGroupId.class)) + .map( + (MapFunction) e -> messageFromNotification(e), + Encoders.bean(ShortEventMessageWithGroupId.class)) .coalesce(1) .write() .partitionBy("group") From 3c9cbd19f3fdada0285fd709daae5fe6dd4c0dc7 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 14 Dec 2020 11:03:55 +0100 Subject: [PATCH 128/149] whitelist of topics --- .../dhp/broker/oa/GenerateEventsJob.java | 5 +- .../dhp/broker/oa/util/EventFinder.java | 9 +- .../oa/generate_all/oozie_app/workflow.xml | 6 + .../dhp/broker/oa/generate_events.json | 6 + .../oa/reindex/oozie_app/config-default.xml | 18 +++ .../broker/oa/reindex/oozie_app/workflow.xml | 116 ++++++++++++++++++ 6 files changed, 158 insertions(+), 2 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java index 457b82517..1ae241e34 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java @@ -59,6 +59,9 @@ public class GenerateEventsJob { final Set dsIdBlacklist = ClusterUtils.parseParamAsList(parser, "datasourceIdBlacklist"); log.info("datasourceIdBlacklist: {}", StringUtils.join(dsIdBlacklist, ",")); + final Set topicWhitelist = ClusterUtils.parseParamAsList(parser, "topicWhitelist"); + log.info("topicWhitelist: {}", StringUtils.join(topicWhitelist, ",")); + final SparkConf conf = new SparkConf(); runWithSparkSession(conf, isSparkSessionManaged, spark -> { @@ -75,7 +78,7 @@ public class GenerateEventsJob { final Dataset dataset = groups .map( g -> EventFinder - .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators), + .generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, topicWhitelist, accumulators), Encoders .bean(EventGroup.class)) .flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java index 1ab56cc34..103751f95 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java @@ -76,6 +76,7 @@ public class EventFinder { final Set dsIdWhitelist, final Set dsIdBlacklist, final Set dsTypeWhitelist, + final Set topicWhitelist, final Map accumulators) { final List> list = new ArrayList<>(); @@ -84,7 +85,13 @@ public class EventFinder { for (final OaBrokerRelatedDatasource targetDs : target.getDatasources()) { if (verifyTarget(targetDs, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) { for (final UpdateMatcher matcher : matchers) { - list.addAll(matcher.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators)); + for (final UpdateInfo info : matcher + .searchUpdatesForRecord(target, targetDs, results.getData(), accumulators)) { + if (topicWhitelist == null || topicWhitelist.isEmpty() + || topicWhitelist.contains(info.getTopic().getPath())) { + list.add(info); + } + } } } } diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index 1a1df418b..ea81c90d0 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -24,6 +24,11 @@ - a black list (comma separeted, - for empty list) of datasource ids + + topicWhitelist + * + a white list (comma separeted, * for all) of topics + esEventIndexName the elasticsearch index name for events @@ -447,6 +452,7 @@ --datasourceIdWhitelist${datasourceIdWhitelist} --datasourceTypeWhitelist${datasourceTypeWhitelist} --datasourceIdBlacklist${datasourceIdBlacklist} + --topicWhitelist${topicWhitelist} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json index a482ee2dc..e803bb5b9 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json @@ -28,5 +28,11 @@ "paramLongName": "datasourceIdBlacklist", "paramDescription": "a black list (comma separeted, - for empty list) of datasource ids", "paramRequired": true + }, + { + "paramName": "topicWhitelist", + "paramLongName": "topicWhitelist", + "paramDescription": "a white list (comma separeted, * for all) of topics", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml new file mode 100644 index 000000000..2e0ed9aee --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/config-default.xml @@ -0,0 +1,18 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml new file mode 100644 index 000000000..43c26f3a3 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml @@ -0,0 +1,116 @@ + + + + + outputDir + the path where the the generated data will be stored + + + esEventIndexName + the elasticsearch index name for events + + + esIndexHost + the elasticsearch host + + + maxIndexedEventsForDsAndTopic + the max number of events for each couple (ds/topic) + + + brokerApiBaseUrl + the url of the broker service api + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + IndexEventSubsetOnESJob + eu.dnetlib.dhp.broker.oa.IndexEventSubsetJob + dhp-broker-events-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.dynamicAllocation.maxExecutors="8" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --outputDir${outputDir} + --index${esEventIndexName} + --esHost${esIndexHost} + --maxEventsForTopic${maxIndexedEventsForDsAndTopic} + --brokerApiBaseUrl${brokerApiBaseUrl} + + + + + + + + + + \ No newline at end of file From 1391341d0690ed978da64a1d7c232f84cea89166 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 14 Dec 2020 11:11:41 +0100 Subject: [PATCH 129/149] mkdir of output dir --- .../dhp/broker/oa/generate_all/oozie_app/workflow.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index ea81c90d0..250f928f8 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -116,15 +116,15 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + - + From 6f4d1a37f0810cf197047190aebf16293bd38c42 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 14 Dec 2020 12:02:33 +0100 Subject: [PATCH 130/149] ES wf properties --- .../dhp/broker/oa/IndexEventSubsetJob.java | 20 ++++++++++--- .../dhp/broker/oa/IndexNotificationsJob.java | 20 ++++++++++--- .../dnetlib/dhp/broker/oa/IndexOnESJob.java | 22 +++++++++++---- .../oa/generate_all/oozie_app/workflow.xml | 28 +++++++++++++++++++ .../eu/dnetlib/dhp/broker/oa/index_es.json | 24 ++++++++++++++++ .../dhp/broker/oa/index_event_subset.json | 24 ++++++++++++++++ .../dhp/broker/oa/index_notifications.json | 24 ++++++++++++++++ .../notifications_only/oozie_app/workflow.xml | 24 ++++++++++++++++ .../broker/oa/reindex/oozie_app/workflow.xml | 24 ++++++++++++++++ 9 files changed, 196 insertions(+), 14 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java index 72efc9e6b..e18a7ef56 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java @@ -55,6 +55,18 @@ public class IndexEventSubsetJob { final String indexHost = parser.get("esHost"); log.info("indexHost: {}", indexHost); + final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount"); + log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount); + + final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait"); + log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait); + + final String esBatchSizeEntries = parser.get("esBatchSizeEntries"); + log.info("esBatchSizeEntries: {}", esBatchSizeEntries); + + final String esNodesWanOnly = parser.get("esNodesWanOnly"); + log.info("esNodesWanOnly: {}", esNodesWanOnly); + final int maxEventsForTopic = NumberUtils.toInt(parser.get("maxEventsForTopic")); log.info("maxEventsForTopic: {}", maxEventsForTopic); @@ -86,10 +98,10 @@ public class IndexEventSubsetJob { esCfg.put("es.index.auto.create", "false"); esCfg.put("es.nodes", indexHost); esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY - esCfg.put("es.batch.write.retry.count", "8"); - esCfg.put("es.batch.write.retry.wait", "60s"); - esCfg.put("es.batch.size.entries", "200"); - esCfg.put("es.nodes.wan.only", "true"); + esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); + esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); + esCfg.put("es.batch.size.entries", esBatchSizeEntries); + esCfg.put("es.nodes.wan.only", esNodesWanOnly); log.info("*** Start indexing"); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index 29fc72d04..75f4eb066 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -63,6 +63,18 @@ public class IndexNotificationsJob { final String indexHost = parser.get("esHost"); log.info("indexHost: {}", indexHost); + final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount"); + log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount); + + final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait"); + log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait); + + final String esBatchSizeEntries = parser.get("esBatchSizeEntries"); + log.info("esBatchSizeEntries: {}", esBatchSizeEntries); + + final String esNodesWanOnly = parser.get("esNodesWanOnly"); + log.info("esNodesWanOnly: {}", esNodesWanOnly); + final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl"); log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl); @@ -92,10 +104,10 @@ public class IndexNotificationsJob { esCfg.put("es.index.auto.create", "false"); esCfg.put("es.nodes", indexHost); esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY - esCfg.put("es.batch.write.retry.count", "8"); - esCfg.put("es.batch.write.retry.wait", "60s"); - esCfg.put("es.batch.size.entries", "200"); - esCfg.put("es.nodes.wan.only", "true"); + esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); + esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); + esCfg.put("es.batch.size.entries", esBatchSizeEntries); + esCfg.put("es.nodes.wan.only", esNodesWanOnly); log.info("*** Start indexing"); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java index 006cde48c..380a689e4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java @@ -45,6 +45,18 @@ public class IndexOnESJob { final String indexHost = parser.get("esHost"); log.info("indexHost: {}", indexHost); + final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount"); + log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount); + + final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait"); + log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait); + + final String esBatchSizeEntries = parser.get("esBatchSizeEntries"); + log.info("esBatchSizeEntries: {}", esBatchSizeEntries); + + final String esNodesWanOnly = parser.get("esNodesWanOnly"); + log.info("esNodesWanOnly: {}", esNodesWanOnly); + final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); final JavaRDD inputRdd = ClusterUtils @@ -53,15 +65,13 @@ public class IndexOnESJob { .javaRDD(); final Map esCfg = new HashMap<>(); - // esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54"); - esCfg.put("es.index.auto.create", "false"); esCfg.put("es.nodes", indexHost); esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY - esCfg.put("es.batch.write.retry.count", "8"); - esCfg.put("es.batch.write.retry.wait", "60s"); - esCfg.put("es.batch.size.entries", "200"); - esCfg.put("es.nodes.wan.only", "true"); + esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); + esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); + esCfg.put("es.batch.size.entries", esBatchSizeEntries); + esCfg.put("es.nodes.wan.only", esNodesWanOnly); JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); } diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index 250f928f8..d06eec87e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -41,6 +41,26 @@ esIndexHost the elasticsearch host + + esBatchWriteRetryCount + 8 + an ES configuration property + + + esBatchWriteRetryWait + 60s + an ES configuration property + + + esBatchSizeEntries + 200 + an ES configuration property + + + esNodesWanOnly + true + an ES configuration property + maxIndexedEventsForDsAndTopic the max number of events for each couple (ds/topic) @@ -478,6 +498,10 @@ --outputDir${outputDir} --index${esEventIndexName} --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} --maxEventsForTopic${maxIndexedEventsForDsAndTopic} --brokerApiBaseUrl${brokerApiBaseUrl} @@ -505,6 +529,10 @@ --outputDir${outputDir} --index${esNotificationsIndexName} --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} --brokerApiBaseUrl${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json index 079709ad8..f7e072d0f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_es.json @@ -16,5 +16,29 @@ "paramLongName": "esHost", "paramDescription": "the ES host", "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryCount", + "paramLongName": "esBatchWriteRetryCount", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryWait", + "paramLongName": "esBatchWriteRetryWait", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchSizeEntries", + "paramLongName": "esBatchSizeEntries", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esNodesWanOnly", + "paramLongName": "esNodesWanOnly", + "paramDescription": "an ES configuration property", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json index 441249661..0046490bb 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json @@ -16,7 +16,31 @@ "paramLongName": "esHost", "paramDescription": "the ES host", "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryCount", + "paramLongName": "esBatchWriteRetryCount", + "paramDescription": "an ES configuration property", + "paramRequired": true }, + { + "paramName": "esBatchWriteRetryWait", + "paramLongName": "esBatchWriteRetryWait", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchSizeEntries", + "paramLongName": "esBatchSizeEntries", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esNodesWanOnly", + "paramLongName": "esNodesWanOnly", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, { "paramName": "n", "paramLongName": "maxEventsForTopic", diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json index 63e9b1263..370b48411 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json @@ -17,6 +17,30 @@ "paramDescription": "the ES host", "paramRequired": true }, + { + "paramName": "esBatchWriteRetryCount", + "paramLongName": "esBatchWriteRetryCount", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchWriteRetryWait", + "paramLongName": "esBatchWriteRetryWait", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esBatchSizeEntries", + "paramLongName": "esBatchSizeEntries", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, + { + "paramName": "esNodesWanOnly", + "paramLongName": "esNodesWanOnly", + "paramDescription": "an ES configuration property", + "paramRequired": true + }, { "paramName": "broker", "paramLongName": "brokerApiBaseUrl", diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml index c73b3fb52..248326d57 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml @@ -36,6 +36,26 @@ esIndexHost the elasticsearch host + + esBatchWriteRetryCount + 8 + an ES configuration property + + + esBatchWriteRetryWait + 60s + an ES configuration property + + + esBatchSizeEntries + 200 + an ES configuration property + + + esNodesWanOnly + true + an ES configuration property + maxIndexedEventsForDsAndTopic the max number of events for each couple (ds/topic) @@ -125,6 +145,10 @@ --outputDir${outputDir} --index${esNotificationsIndexName} --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} --brokerApiBaseUrl${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml index 43c26f3a3..9095004ad 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml @@ -13,6 +13,26 @@ esIndexHost the elasticsearch host + + esBatchWriteRetryCount + 8 + an ES configuration property + + + esBatchWriteRetryWait + 60s + an ES configuration property + + + esBatchSizeEntries + 200 + an ES configuration property + + + esNodesWanOnly + true + an ES configuration property + maxIndexedEventsForDsAndTopic the max number of events for each couple (ds/topic) @@ -102,6 +122,10 @@ --outputDir${outputDir} --index${esEventIndexName} --esHost${esIndexHost} + --esBatchWriteRetryCount${esBatchWriteRetryCount} + --esBatchWriteRetryWait${esBatchWriteRetryWait} + --esBatchSizeEntries${esBatchSizeEntries} + --esNodesWanOnly${esNodesWanOnly} --maxEventsForTopic${maxIndexedEventsForDsAndTopic} --brokerApiBaseUrl${brokerApiBaseUrl} From 26a941315a79efd07599fa82c02027d956a89e16 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 14 Dec 2020 15:24:33 +0100 Subject: [PATCH 131/149] openaireId --- .../dhp/broker/oa/util/ConversionUtils.java | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index 053627a5f..085681488 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -74,7 +74,7 @@ public class ConversionUtils { } final OaBrokerRelatedDataset res = new OaBrokerRelatedDataset(); - res.setOpenaireId(d.getId()); + res.setOpenaireId(cleanOpenaireId(d.getId())); res.setOriginalId(first(d.getOriginalId())); res.setTitle(structPropValue(d.getTitle())); res.setPids(mappedList(d.getPid(), ConversionUtils::oafPidToBrokerPid)); @@ -89,7 +89,7 @@ public class ConversionUtils { } final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication(); - res.setOpenaireId(p.getId()); + res.setOpenaireId(cleanOpenaireId(p.getId())); res.setOriginalId(first(p.getOriginalId())); res.setTitle(structPropValue(p.getTitle())); res.setPids(mappedList(p.getPid(), ConversionUtils::oafPidToBrokerPid)); @@ -106,7 +106,7 @@ public class ConversionUtils { final OaBrokerMainEntity res = new OaBrokerMainEntity(); - res.setOpenaireId(result.getId()); + res.setOpenaireId(cleanOpenaireId(result.getId())); res.setOriginalId(first(result.getOriginalId())); res.setTypology(classId(result.getResulttype())); res.setTitles(structPropList(result.getTitle())); @@ -129,6 +129,10 @@ public class ConversionUtils { return res; } + private static String cleanOpenaireId(final String id) { + return id.contains("|") ? StringUtils.substringAfter(id, "|") : id; + } + private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) { if (author == null) { return null; @@ -188,7 +192,7 @@ public class ConversionUtils { } final OaBrokerProject res = new OaBrokerProject(); - res.setOpenaireId(p.getId()); + res.setOpenaireId(cleanOpenaireId(p.getId())); res.setTitle(fieldValue(p.getTitle())); res.setAcronym(fieldValue(p.getAcronym())); res.setCode(fieldValue(p.getCode())); @@ -214,7 +218,7 @@ public class ConversionUtils { } final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware(); - res.setOpenaireId(sw.getId()); + res.setOpenaireId(cleanOpenaireId(sw.getId())); res.setName(structPropValue(sw.getTitle())); res.setDescription(fieldValue(sw.getDescription())); res.setRepository(fieldValue(sw.getCodeRepositoryUrl())); @@ -230,7 +234,7 @@ public class ConversionUtils { final OaBrokerRelatedDatasource res = new OaBrokerRelatedDatasource(); res.setName(StringUtils.defaultIfBlank(fieldValue(ds.getOfficialname()), fieldValue(ds.getEnglishname()))); - res.setOpenaireId(ds.getId()); + res.setOpenaireId(cleanOpenaireId(ds.getId())); res.setType(classId(ds.getDatasourcetype())); return res; } From e3e0ab1de1c009d2da59ca717f09bf43411fe5b8 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 15 Dec 2020 08:30:26 +0100 Subject: [PATCH 132/149] fixed a problem with join --- .../eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java | 2 +- .../dhp/broker/oa/PrepareRelatedDatasetsJob.java | 5 +++-- .../dhp/broker/oa/PrepareRelatedProjectsJob.java | 2 +- .../broker/oa/PrepareRelatedPublicationsJob.java | 5 +++-- .../dhp/broker/oa/PrepareRelatedSoftwaresJob.java | 2 +- .../eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java | 11 +++++++++++ .../dnetlib/dhp/broker/oa/util/ConversionUtils.java | 2 +- .../oa/util/DatasourceRelationsAccumulator.java | 13 +++++++++++-- 8 files changed, 32 insertions(+), 10 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java index a575328e8..dc156cbcf 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java @@ -63,7 +63,7 @@ public class PrepareGroupsJob { .readPath(spark, workingDir + "/joinedEntities_step4", OaBrokerMainEntity.class); final Dataset mergedRels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); final TypedColumn, ResultGroup> aggr = new ResultAggregator() diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java index 8c2879b38..9bdf32a64 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java @@ -62,7 +62,7 @@ public class PrepareRelatedDatasetsJob { .map(ConversionUtils::oafDatasetToBrokerDataset, Encoders.bean(OaBrokerRelatedDataset.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass())) @@ -72,7 +72,8 @@ public class PrepareRelatedDatasetsJob { final Dataset dataset = rels .joinWith(datasets, datasets.col("openaireId").equalTo(rels.col("target")), "inner") .map(t -> { - final RelatedDataset rel = new RelatedDataset(t._1.getSource(), t._2); + final RelatedDataset rel = new RelatedDataset(t._1.getSource(), + t._2); rel.getRelDataset().setRelType(t._1.getRelClass()); return rel; }, Encoders.bean(RelatedDataset.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java index 1952b5d9c..9498c0f33 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java @@ -64,7 +64,7 @@ public class PrepareRelatedProjectsJob { .map(ConversionUtils::oafProjectToBrokerProject, Encoders.bean(OaBrokerProject.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT)) .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java index d6ac27fc5..8270500fd 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java @@ -65,7 +65,7 @@ public class PrepareRelatedPublicationsJob { Encoders.bean(OaBrokerRelatedPublication.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass())) @@ -75,7 +75,8 @@ public class PrepareRelatedPublicationsJob { final Dataset dataset = rels .joinWith(pubs, pubs.col("openaireId").equalTo(rels.col("target")), "inner") .map(t -> { - final RelatedPublication rel = new RelatedPublication(t._1.getSource(), t._2); + final RelatedPublication rel = new RelatedPublication( + t._1.getSource(), t._2); rel.getRelPublication().setRelType(t._1.getRelClass()); return rel; }, Encoders.bean(RelatedPublication.class)); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java index c4ccf4af6..16b450733 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java @@ -64,7 +64,7 @@ public class PrepareRelatedSoftwaresJob { .map(ConversionUtils::oafSoftwareToBrokerSoftware, Encoders.bean(OaBrokerRelatedSoftware.class)); final Dataset rels = ClusterUtils - .readPath(spark, graphPath + "/relation", Relation.class) + .loadRelations(graphPath, spark) .filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT)) .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java index 04985a6ab..9ce64f6bd 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java @@ -17,6 +17,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.oaf.Relation; public class ClusterUtils { @@ -30,6 +31,16 @@ public class ClusterUtils { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } + public static Dataset loadRelations(final String graphPath, final SparkSession spark) { + return ClusterUtils + .readPath(spark, graphPath + "/relation", Relation.class) + .map(r -> { + r.setSource(ConversionUtils.cleanOpenaireId(r.getSource())); + r.setTarget(ConversionUtils.cleanOpenaireId(r.getTarget())); + return r; + }, Encoders.bean(Relation.class)); + } + public static Dataset readPath( final SparkSession spark, final String inputPath, diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index 085681488..ecbfd821e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -129,7 +129,7 @@ public class ConversionUtils { return res; } - private static String cleanOpenaireId(final String id) { + public static String cleanOpenaireId(final String id) { return id.contains("|") ? StringUtils.substringAfter(id, "|") : id; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java index 75c4625ce..c693be93c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java @@ -59,9 +59,18 @@ public class DatasourceRelationsAccumulator implements Serializable { final DatasourceRelationsAccumulator res = new DatasourceRelationsAccumulator(); collectedFromSet .stream() - .map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.COLLECTED_FROM_REL)) + .map( + s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s), + BrokerConstants.COLLECTED_FROM_REL)) .forEach(res::addTuple); - hostedBySet.stream().map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.HOSTED_BY_REL)).forEach(res::addTuple); + + hostedBySet + .stream() + .map( + s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s), + BrokerConstants.HOSTED_BY_REL)) + .forEach(res::addTuple); + return res; } From 64b0b0bfb309c96ec41e3a2973d180c133398531 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 15 Dec 2020 14:54:11 +0100 Subject: [PATCH 133/149] fixed a bug with invalid subject topic --- .../matchers/simple/EnrichMissingSubject.java | 19 ++++++++++++++++++- .../oa/matchers/simple/EnrichMoreSubject.java | 19 ++++++++++++++++++- 2 files changed, 36 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java index 26ebbb7c0..cb3ea5464 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java @@ -16,7 +16,24 @@ public class EnrichMissingSubject extends UpdateMatcher { public EnrichMissingSubject() { super(20, - s -> Topic.fromPath("ENRICH/MISSING/SUBJECT/" + s.getType()), + s -> { + switch (s.getType().toLowerCase()) { + case "acm": + return Topic.ENRICH_MISSING_SUBJECT_ACM; + case "arxiv": + return Topic.ENRICH_MISSING_SUBJECT_ARXIV; + case "ddc": + return Topic.ENRICH_MISSING_SUBJECT_DDC; + case "jel": + return Topic.ENRICH_MISSING_SUBJECT_JEL; + case "mesh": + return Topic.ENRICH_MISSING_SUBJECT_MESHEUROPMC; + case "rvk": + return Topic.ENRICH_MISSING_SUBJECT_RVK; + default: + return null; + } + }, (p, s) -> p.getSubjects().add(s), s -> subjectAsString(s)); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java index bbe6609d7..1f6edf96e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java @@ -16,7 +16,24 @@ public class EnrichMoreSubject extends UpdateMatcher { public EnrichMoreSubject() { super(20, - s -> Topic.fromPath("ENRICH/MORE/SUBJECT/" + s.getType()), + s -> { + switch (s.getType().toLowerCase()) { + case "acm": + return Topic.ENRICH_MORE_SUBJECT_ACM; + case "arxiv": + return Topic.ENRICH_MORE_SUBJECT_ARXIV; + case "ddc": + return Topic.ENRICH_MORE_SUBJECT_DDC; + case "jel": + return Topic.ENRICH_MORE_SUBJECT_JEL; + case "mesh": + return Topic.ENRICH_MORE_SUBJECT_MESHEUROPMC; + case "rvk": + return Topic.ENRICH_MORE_SUBJECT_RVK; + default: + return null; + } + }, (p, s) -> p.getSubjects().add(s), s -> subjectAsString(s)); } From b9d90e95b802da19854d4938e7554fe60c15d4a4 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 14 Jan 2021 13:20:35 +0100 Subject: [PATCH 134/149] Added eventId to ShortEventMessage --- .../eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java | 3 ++- .../dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml | 2 +- pom.xml | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java index 08c74a291..e061c0d3b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java @@ -36,7 +36,7 @@ import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; public class PartitionEventsByDsIdJob { private static final Logger log = LoggerFactory.getLogger(PartitionEventsByDsIdJob.class); - private static final String OPENDOAR_NSPREFIX = "10|opendoar____::"; + private static final String OPENDOAR_NSPREFIX = "opendoar____::"; public static void main(final String[] args) throws Exception { @@ -123,6 +123,7 @@ public class PartitionEventsByDsIdJob { final ShortEventMessageWithGroupId res = new ShortEventMessageWithGroupId(); + res.setEventId(e.getEventId()); res.setOriginalId(payload.getResult().getOriginalId()); res.setTitle(payload.getResult().getTitles().stream().filter(StringUtils::isNotBlank).findFirst().orElse(null)); res.setTopic(e.getTopic()); diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index 83fe47c75..7c5b722d2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -87,7 +87,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --workingDir${workingDir} + --outputDir${outputDir} --opendoarIds${opendoarIds} diff --git a/pom.xml b/pom.xml index a2e2587b3..3e0626aed 100644 --- a/pom.xml +++ b/pom.xml @@ -704,7 +704,7 @@ 3.3.3 3.4.2 [2.12,3.0) - 3.1.1 + 3.1.6 7.5.0 4.7.2 1.20 From b230d4441192fbb7dde49fe484fe9580d0afd382 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 14 Jan 2021 14:23:44 +0100 Subject: [PATCH 135/149] fixed conflict --- .../dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index 7c5b722d2..dba3c9f73 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the opendoar IDs whitelist (comma separated) - outputDir + workingPath the path where the the generated data will be stored @@ -87,7 +87,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=3840 - --outputDir${outputDir} + --workingPath${workingPath} --opendoarIds${opendoarIds} From cfbcdc95bc5d90f7e08f6a20d4ff449da4b57fc2 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 14 Jan 2021 14:45:23 +0100 Subject: [PATCH 136/149] fixed a wf param --- .../dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index 3b575a5b7..7c5b722d2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the opendoar IDs whitelist (comma separated) - workingPath + outputDir the path where the the generated data will be stored From 3e8d2a6b2d34691358a5e5f87dc072f195a0a5aa Mon Sep 17 00:00:00 2001 From: Dimitris Date: Fri, 15 Jan 2021 16:19:12 +0200 Subject: [PATCH 137/149] Clean workflows --- .../nb-configuration.xml | 18 - .../dhp-usage-datasets-stats-update/pom.xml | 112 -- .../runworkflow.sh | 1 - .../datasetsusagestats/export/ConnectDB.java | 131 -- .../export/DatasetsStatsDB.java | 168 --- .../DownloadReportsListFromDatacite.java | 102 -- .../export/ExecuteWorkflow.java | 69 - .../export/ReadReportsListFromDatacite.java | 408 ------ .../export/UsageStatsExporter.java | 111 -- .../datasets_usagestats_parameters.json | 56 - .../oozie_app/config-default.xml | 38 - .../datasetsusagestats/oozie_app/workflow.xml | 70 - dhp-workflows/dhp-usage-stats-update/pom.xml | 78 - .../oa/graph/usagestats/export/ConnectDB.java | 125 -- .../usagestats/export/ExecuteWorkflow.java | 197 --- .../oa/graph/usagestats/export/IrusStats.java | 419 ------ .../export/LaReferenciaDownloadLogs.java | 265 ---- .../usagestats/export/LaReferenciaStats.java | 436 ------ .../usagestats/export/PiwikDownloadLogs.java | 325 ----- .../graph/usagestats/export/PiwikStatsDB.java | 1262 ----------------- .../export/ReadCounterRobotsList.java | 54 - .../oa/graph/usagestats/export/SarcStats.java | 575 -------- .../usagestats/export/UsageStatsExporter.java | 179 --- .../export/usagestats_parameters.json | 231 --- .../usagestats/oozie_app/config-default.xml | 38 - .../graph/usagestats/oozie_app/workflow.xml | 90 -- 26 files changed, 5558 deletions(-) delete mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/nb-configuration.xml delete mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/pom.xml delete mode 100755 dhp-workflows/dhp-usage-datasets-stats-update/runworkflow.sh delete mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java delete mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DatasetsStatsDB.java delete mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java delete mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java delete mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ReadReportsListFromDatacite.java delete mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java delete mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/export/datasets_usagestats_parameters.json delete mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-usage-stats-update/pom.xml delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ExecuteWorkflow.java delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ReadCounterRobotsList.java delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/export/usagestats_parameters.json delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/nb-configuration.xml b/dhp-workflows/dhp-usage-datasets-stats-update/nb-configuration.xml deleted file mode 100644 index a65c4514a..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/nb-configuration.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - - - - JDK_1.8 - - diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/pom.xml b/dhp-workflows/dhp-usage-datasets-stats-update/pom.xml deleted file mode 100644 index 5593d4d87..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/pom.xml +++ /dev/null @@ -1,112 +0,0 @@ - - - - - - - - - dhp-workflows - eu.dnetlib.dhp - 1.1.7-SNAPSHOT - - 4.0.0 - dhp-usage-datasets-stats-update - - - - pl.project13.maven - git-commit-id-plugin - 2.1.15 - - - - revision - - - - - ${project.basedir}/../.git - - - - - org.apache.maven.plugins - maven-compiler-plugin - 3.6.1 - - 1.8 - 1.8 - - - - - - UTF-8 - UTF-8 - 0.13.1-cdh5.2.1 - 2.5.0-cdh5.2.1 - - - - - org.apache.spark - spark-core_2.11 - 2.2.0 - - - org.apache.spark - spark-sql_2.11 - 2.4.5 - - - com.googlecode.json-simple - json-simple - 1.1.1 - - - org.json - json - 20180130 - jar - - - org.apache.hive - hive-jdbc - ${cdh.hive.version} - - - org.apache.hadoop - hadoop-common - ${cdh.hadoop.version} - - - eu.dnetlib.dhp - dhp-common - ${project.version} - - - com.mchange - c3p0 - 0.9.5.2 - - - c3p0 - c3p0 - 0.9.1.2 - jar - - - dhp-usage-datasets-stats-update - diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/runworkflow.sh b/dhp-workflows/dhp-usage-datasets-stats-update/runworkflow.sh deleted file mode 100755 index 9b4325508..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/runworkflow.sh +++ /dev/null @@ -1 +0,0 @@ -mvn clean package -Poozie-package,deploy,run -Dworkflow.source.dir=eu/dnetlib/dhp/oa/graph/datasetsusagestats \ No newline at end of file diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java deleted file mode 100644 index 25b30e8ad..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java +++ /dev/null @@ -1,131 +0,0 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ - -package eu.dnetlib.oa.graph.datasetsusagestats.export; - -import java.sql.Connection; -import java.sql.DriverManager; -import java.sql.SQLException; -import java.sql.Statement; -import java.util.Properties; - -import org.apache.log4j.Logger; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -/** - * @author D. Pierrakos, S. Zoupanos - */ -import com.mchange.v2.c3p0.ComboPooledDataSource; - -public abstract class ConnectDB { - - public static Connection DB_HIVE_CONNECTION; - public static Connection DB_IMPALA_CONNECTION; - - private static String dbHiveUrl; - private static String dbImpalaUrl; - private static String datasetUsageStatsDBSchema; - private static String statsDBSchema; - private final static Logger logger = Logger.getLogger(ConnectDB.class); - private Statement stmt = null; - - static void init() throws ClassNotFoundException { - - dbHiveUrl = ExecuteWorkflow.dbHiveUrl; - dbImpalaUrl = ExecuteWorkflow.dbImpalaUrl; - datasetUsageStatsDBSchema = ExecuteWorkflow.datasetUsageStatsDBSchema; - statsDBSchema = ExecuteWorkflow.statsDBSchema; - - Class.forName("org.apache.hive.jdbc.HiveDriver"); - } - - public static Connection getHiveConnection() throws SQLException { - if (DB_HIVE_CONNECTION != null && !DB_HIVE_CONNECTION.isClosed()) { - return DB_HIVE_CONNECTION; - } else { - DB_HIVE_CONNECTION = connectHive(); - - return DB_HIVE_CONNECTION; - } - } - - public static Connection getImpalaConnection() throws SQLException { - if (DB_IMPALA_CONNECTION != null && !DB_IMPALA_CONNECTION.isClosed()) { - return DB_IMPALA_CONNECTION; - } else { - DB_IMPALA_CONNECTION = connectImpala(); - - return DB_IMPALA_CONNECTION; - } - } - - public static String getDataSetUsageStatsDBSchema() { - return ConnectDB.datasetUsageStatsDBSchema; - } - - public static String getStatsDBSchema() { - return ConnectDB.statsDBSchema; - } - - private static Connection connectHive() throws SQLException { - /* - * Connection connection = DriverManager.getConnection(dbHiveUrl); Statement stmt = - * connection.createStatement(); log.debug("Opened database successfully"); return connection; - */ - ComboPooledDataSource cpds = new ComboPooledDataSource(); - cpds.setJdbcUrl(dbHiveUrl); - cpds.setUser("dimitris.pierrakos"); - cpds.setAcquireIncrement(1); - cpds.setMaxPoolSize(100); - cpds.setMinPoolSize(1); - cpds.setInitialPoolSize(1); - cpds.setMaxIdleTime(300); - cpds.setMaxConnectionAge(36000); - - cpds.setAcquireRetryAttempts(5); - cpds.setAcquireRetryDelay(2000); - cpds.setBreakAfterAcquireFailure(false); - - cpds.setCheckoutTimeout(0); - cpds.setPreferredTestQuery("SELECT 1"); - cpds.setIdleConnectionTestPeriod(60); - - logger.info("Opened database successfully"); - - return cpds.getConnection(); - - } - - private static Connection connectImpala() throws SQLException { - /* - * Connection connection = DriverManager.getConnection(dbImpalaUrl); Statement stmt = - * connection.createStatement(); log.debug("Opened database successfully"); return connection; - */ - ComboPooledDataSource cpds = new ComboPooledDataSource(); - cpds.setJdbcUrl(dbImpalaUrl); - cpds.setUser("dimitris.pierrakos"); - cpds.setAcquireIncrement(1); - cpds.setMaxPoolSize(100); - cpds.setMinPoolSize(1); - cpds.setInitialPoolSize(1); - cpds.setMaxIdleTime(300); - cpds.setMaxConnectionAge(36000); - - cpds.setAcquireRetryAttempts(5); - cpds.setAcquireRetryDelay(2000); - cpds.setBreakAfterAcquireFailure(false); - - cpds.setCheckoutTimeout(0); - cpds.setPreferredTestQuery("SELECT 1"); - cpds.setIdleConnectionTestPeriod(60); - - logger.info("Opened database successfully"); - return cpds.getConnection(); - - } -} diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DatasetsStatsDB.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DatasetsStatsDB.java deleted file mode 100644 index 88db1f819..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DatasetsStatsDB.java +++ /dev/null @@ -1,168 +0,0 @@ - -package eu.dnetlib.oa.graph.datasetsusagestats.export; - -import java.sql.Connection; -import java.sql.SQLException; -import java.sql.Statement; -import java.util.*; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -public class DatasetsStatsDB { - - private String logPath; - private String logRepoPath; - private String logPortalPath; - - private Statement stmt = null; - - private static final Logger logger = LoggerFactory.getLogger(DatasetsStatsDB.class); - - private String CounterRobotsURL; - private ArrayList robotsList; - - public DatasetsStatsDB(String logRepoPath, String logPortalPath) throws Exception { - this.logRepoPath = logRepoPath; - this.logPortalPath = logPortalPath; - - } - - public void recreateDBAndTables() throws Exception { - this.createDatabase(); - this.createTables(); - } - -// public void reCreateLogDirs() throws IllegalArgumentException, IOException { -// FileSystem dfs = FileSystem.get(new Configuration()); -// -// logger.info("Deleting repoLog directory: " + ExecuteWorkflow.repoLogPath); -// dfs.delete(new Path(ExecuteWorkflow.repoLogPath), true); -// -// logger.info("Deleting portalLog directory: " + ExecuteWorkflow.portalLogPath); -// dfs.delete(new Path(ExecuteWorkflow.portalLogPath), true); -// -// logger.info("Creating repoLog directory: " + ExecuteWorkflow.repoLogPath); -// dfs.mkdirs(new Path(ExecuteWorkflow.repoLogPath)); -// -// logger.info("Creating portalLog directory: " + ExecuteWorkflow.portalLogPath); -// dfs.mkdirs(new Path(ExecuteWorkflow.portalLogPath)); -// } - public ArrayList getRobotsList() { - return robotsList; - } - - public void setRobotsList(ArrayList robotsList) { - this.robotsList = robotsList; - } - - public String getCounterRobotsURL() { - return CounterRobotsURL; - } - - public void setCounterRobotsURL(String CounterRobotsURL) { - this.CounterRobotsURL = CounterRobotsURL; - } - - private void createDatabase() throws Exception { - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - logger.info("Dropping datasets DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); - String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema() + " CASCADE"; - stmt.executeUpdate(dropDatabase); - } catch (Exception e) { - logger.error("Failed to drop database: " + e); - throw new Exception("Failed to drop database: " + e.toString(), e); - } - - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - logger.info("Creating usagestats DB: " + ConnectDB.getDataSetUsageStatsDBSchema()); - String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema(); - stmt.executeUpdate(createDatabase); - - } catch (Exception e) { - logger.error("Failed to create database: " + e); - throw new Exception("Failed to create database: " + e.toString(), e); - } - } - - private void createTables() throws Exception { - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - // Create Reports table - This table should exist - logger.info("Creating Reports Table"); - String sqlCreateTableDataciteReports = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getDataSetUsageStatsDBSchema() - + ".datacitereports(reportid STRING, \n" - + " name STRING, \n" - + " source STRING,\n" - + " release STRING,\n" - + " createdby STRING,\n" - + " report_start_date STRING,\n" - + " report_end_date STRING)\n" - + " CLUSTERED BY (reportid)\n" - + " into 100 buckets stored as orc tblproperties('transactional'='true')"; - - stmt.executeUpdate(sqlCreateTableDataciteReports); - logger.info("Reports Table Created"); - - // Create Datasets Table - logger.info("Creating DataSets Table"); - String sqlCreateTableDataSets = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getDataSetUsageStatsDBSchema() - + ".datasets(ds_type STRING,\n" - + " ds_title STRING,\n" - + " yop STRING,\n" - + " uri STRING,\n" - + " platform STRING,\n" - + " data_type STRING,\n" - + " publisher STRING,\n" - + " publisher_id_type STRING,\n" - + " publisher_id_value STRING,\n" - + " ds_dates_type STRING,\n" - + " ds_pub_date STRING,\n" - + " ds_contributors STRING,\n" - // + " ds_contributor_value array ,\n" - + " reportid STRING)\n" - + " CLUSTERED BY (ds_type)\n" - + " into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTableDataSets); - logger.info("DataSets Table Created"); - - // Create Datasets Performance Table - logger.info("Creating DataSetsPerformance Table"); - String sqlCreateTableDataSetsPerformance = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getDataSetUsageStatsDBSchema() - + ".datasetsperformance(ds_type STRING,\n" - + " period_end STRING,\n" - + " period_from STRING,\n" - + " access_method STRING,\n" - + " metric_type STRING,\n" - + " count INT,\n" - + " country_counts STRING,\n" - + " reportid STRING)\n" - + " CLUSTERED BY (ds_type)\n" - + " into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTableDataSetsPerformance); - logger.info("DataSetsPerformance Table Created"); - - stmt.close(); - ConnectDB.getHiveConnection().close(); - - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - } - } - - private Connection getConnection() throws SQLException { - return ConnectDB.getHiveConnection(); - } -} diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java deleted file mode 100644 index a73b299ec..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java +++ /dev/null @@ -1,102 +0,0 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ - -package eu.dnetlib.oa.graph.datasetsusagestats.export; - -import java.io.BufferedInputStream; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; -import java.net.MalformedURLException; -import java.net.URL; -import java.util.ArrayList; -import java.util.Iterator; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.json.simple.parser.ParseException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.google.gson.Gson; -import com.google.gson.JsonArray; -import com.google.gson.JsonElement; -import com.google.gson.JsonObject; - -/** - * @author dpie - */ -public class DownloadReportsListFromDatacite { - - private String dataciteBaseURL; - private String dataciteReportPath; - private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); - - public DownloadReportsListFromDatacite(String dataciteBaseURL, String dataciteReportPath) - throws MalformedURLException, Exception { - - this.dataciteBaseURL = dataciteBaseURL; - this.dataciteReportPath = dataciteReportPath; - } - - public void downloadReportsList() throws ParseException { - StringBuilder responseStrBuilder = new StringBuilder(); - - Gson gson = new Gson(); - - try { - BufferedInputStream in = new BufferedInputStream(new URL(dataciteBaseURL).openStream()); - logger.info("Downloading from " + dataciteBaseURL); - - BufferedReader streamReader = new BufferedReader(new InputStreamReader(in, "UTF-8")); - String inputStr; - - while ((inputStr = streamReader.readLine()) != null) { - responseStrBuilder.append(inputStr); - } - } catch (IOException e) { - logger.info(e.getMessage()); - } - JsonObject jsonObject = gson.fromJson(responseStrBuilder.toString(), JsonObject.class); - JsonArray dataArray = jsonObject.getAsJsonArray("reports"); - ArrayList reportsList = new ArrayList(); - for (JsonElement element : dataArray) { - reportsList.add(element.getAsJsonObject().get("id").getAsString()); - } - - Iterator it = reportsList.iterator(); - while (it.hasNext()) { - String reportId = it.next().toString(); - String url = dataciteBaseURL + reportId; - - try { - BufferedInputStream in = new BufferedInputStream(new URL(url).openStream()); - BufferedReader streamReader = new BufferedReader(new InputStreamReader(in, "UTF-8")); - String inputStr; - StringBuilder responseStrBuilder2 = new StringBuilder(); - while ((inputStr = streamReader.readLine()) != null) { - responseStrBuilder2.append(inputStr); - } - FileSystem fs = FileSystem.get(new Configuration()); - FSDataOutputStream fin = fs - .create( - new Path(dataciteReportPath + "/" + reportId + ".json"), - true); - byte[] jsonObjectRawBytes = responseStrBuilder2.toString().getBytes(); - fin.write(jsonObjectRawBytes); - fin.writeChar('\n'); - - fin.close(); - - fin.close(); - } catch (IOException e) { - System.out.println(e); - } - } - } -} diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java deleted file mode 100644 index b28578e4b..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java +++ /dev/null @@ -1,69 +0,0 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ - -package eu.dnetlib.oa.graph.datasetsusagestats.export; - -import org.apache.commons.io.IOUtils; -import org.apache.log4j.BasicConfigurator; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -public class ExecuteWorkflow { - - static String dataciteBaseURL; - static String dataciteReportPath; - static String dbHiveUrl; - static String dbImpalaUrl; - static String datasetUsageStatsDBSchema; - static String statsDBSchema; - static boolean recreateDbAndTables; - static boolean datasetsEmptyDirs; - static boolean finalTablesVisibleToImpala; - - public static void main(String args[]) throws Exception { - - // Sending the logs to the console - BasicConfigurator.configure(); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - UsageStatsExporter.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/datasetsusagestats/export/datasets_usagestats_parameters.json"))); - parser.parseArgument(args); - - // Setting up the initial parameters - dataciteBaseURL = parser.get("dataciteBaseURL"); - dataciteReportPath = parser.get("dataciteReportPath"); - dbHiveUrl = parser.get("dbHiveUrl"); - dbImpalaUrl = parser.get("dbImpalaUrl"); - datasetUsageStatsDBSchema = parser.get("datasetUsageStatsDBSchema"); - statsDBSchema = parser.get("statsDBSchema"); - - if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) - recreateDbAndTables = true; - else - recreateDbAndTables = false; - - if (parser.get("datasetsEmptyDirs").toLowerCase().equals("true")) - datasetsEmptyDirs = true; - else - datasetsEmptyDirs = false; - -// if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) -// finalTablesVisibleToImpala = true; -// else -// finalTablesVisibleToImpala = false; -// - UsageStatsExporter usagestatsExport = new UsageStatsExporter(); - usagestatsExport.export(); - } - -} diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ReadReportsListFromDatacite.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ReadReportsListFromDatacite.java deleted file mode 100644 index ccb3eebd3..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ReadReportsListFromDatacite.java +++ /dev/null @@ -1,408 +0,0 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ - -package eu.dnetlib.oa.graph.datasetsusagestats.export; - -import java.io.*; -import java.io.ByteArrayInputStream; -import java.io.File; -import java.io.IOException; -import java.io.InputStreamReader; -import java.net.MalformedURLException; -import java.sql.Array; -import java.sql.PreparedStatement; -import java.sql.ResultSet; -import java.sql.SQLException; -import java.sql.Statement; -import java.util.ArrayList; -import java.util.Base64; -import java.util.Iterator; -import java.util.Set; -import java.util.zip.GZIPInputStream; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.LocatedFileStatus; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.fs.RemoteIterator; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.google.gson.Gson; -import com.google.gson.JsonArray; -import com.google.gson.JsonElement; -import com.google.gson.JsonObject; - -/** - * @author dpie - */ -public class ReadReportsListFromDatacite { - - private String dataciteReportPath; - private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); - - public ReadReportsListFromDatacite(String dataciteReportPath) throws MalformedURLException, Exception { - - this.dataciteReportPath = dataciteReportPath; - } - - public void readReports() throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - File folder = new File(dataciteReportPath); - ArrayList jsonFiles = listHdfsDir(dataciteReportPath); - for (String jsonFile : jsonFiles) { - logger.info("Reading report file " + jsonFile); - this.createTmpReportsTable(jsonFile); - - String sqlSelectReportID = "SELECT get_json_object(json, '$.report.id') FROM " - + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; - stmt.execute(sqlSelectReportID); - ResultSet rstmpReportID = stmt.getResultSet(); - - String reportID = null; - while (rstmpReportID.next()) { - reportID = rstmpReportID.getString(1); - } - - logger.info("Checking report with id " + reportID); - String sqlCheckIfReportExists = "SELECT source FROM " + ConnectDB.getDataSetUsageStatsDBSchema() - + ".datacitereports where reportid=?"; - PreparedStatement stGetReportID = ConnectDB.getHiveConnection().prepareStatement(sqlCheckIfReportExists); - stGetReportID.setString(1, reportID); - - ResultSet rsCheckIfReportExist = stGetReportID.executeQuery(); - - if (rsCheckIfReportExist.next()) { - logger.info("Report found with ID " + reportID); - dropTmpReportsTable(); - } else { - String sqlInsertReport = "INSERT INTO " + ConnectDB.getDataSetUsageStatsDBSchema() - + " .datacitereports " - + "SELECT\n" - + " get_json_object(json, '$.report.id') AS reportid,\n" - + " get_json_object(json, '$.report.report-header.report-name') AS name,\n" - + " get_json_object(json, '$.report.report-header.report-id') AS source,\n" - + " get_json_object(json, '$.report.report-header.release') AS release,\n" - + " get_json_object(json, '$.report.report-header.created-by\') AS createdby,\n" - + " get_json_object(json, '$.report.report-header.reporting-period.begin-date') AS fromdate,\n" - + " get_json_object(json, '$.report.report-header.reporting-period.end-date') AS todate \n" - + "FROM " + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; - stmt.execute(sqlInsertReport); - - logger.info("Report added"); - - logger.info("Adding datasets"); - String sqlSelecteDatasetsArray = "SELECT get_json_object(json, '$.report.report-datasets') FROM " - + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; - stmt.execute(sqlSelecteDatasetsArray); - ResultSet rstmpReportDatasets = stmt.getResultSet(); - - if (rstmpReportDatasets.next() && rstmpReportDatasets.getString(1).indexOf(',') > 0) { - String[] listDatasets = rstmpReportDatasets.getString(1).split(","); - logger.info("Datasets found " + listDatasets.length); - - for (int i = 0; i < listDatasets.length; i++) { - - String sqlInsertDataSets = "INSERT INTO " + ConnectDB.getDataSetUsageStatsDBSchema() - + " .datasets " - + "SELECT\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].dataset-id[0].value') AS ds_type,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].dataset-title') AS ds_title,\n" - + " get_json_object(json, '$.report.report-datasets[" + i + "].yop') AS yop,\n" - + " get_json_object(json, '$.report.report-datasets[" + i + "].uri') AS uri,\n" - + " get_json_object(json, '$.report.report-datasets[" + i + "].platform') AS platform,\n" - + " get_json_object(json, '$.report.report-datasets[" + i + "].data-type') AS data_type,\n" - + " get_json_object(json, '$.report.report-datasets[" + i + "].publisher') AS publisher,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].publisher-id.type[0]') AS publisher_id_type,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].publisher-id.value[0]') AS publisher_id_value,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].dataset-dates.type[0]') AS ds_dates_type,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].dataset-dates.value[0]') AS ds_dates_value,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].dataset-contributors') AS ds_contributors,\n" - + " get_json_object(json, '$.report.id') AS reportid \n" - + "FROM " + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; - stmt.execute(sqlInsertDataSets); - - logger.info("Dataset added " + i); - - logger.info("Adding Dataset Performance"); - String sqlSelecteDatasetsPerformance = "SELECT get_json_object(json, '$.report.report-datasets[" - + i + "].performance') FROM " + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; - stmt.execute(sqlSelecteDatasetsPerformance); - ResultSet rstmpReportDatasetsPerformance = stmt.getResultSet(); - if (rstmpReportDatasetsPerformance.next() - && rstmpReportDatasetsPerformance.getString(1).indexOf(',') > 0) { - String[] listDatasetsPerformance = rstmpReportDatasetsPerformance.getString(1).split(","); - logger.info("Datasets Performance found " + listDatasetsPerformance.length); - for (int j = 0; j < listDatasetsPerformance.length; j++) { - String sqlSelecteDatasetsPerformanceInstance = "SELECT get_json_object(json, '$.report.report-datasets[" - + i + "].performance') FROM " + ConnectDB.getDataSetUsageStatsDBSchema() - + ".tmpjson"; - stmt.execute(sqlSelecteDatasetsPerformanceInstance); - ResultSet rstmpReportDatasetsPerformanceInstance = stmt.getResultSet(); - if (rstmpReportDatasetsPerformanceInstance.next() - && rstmpReportDatasetsPerformanceInstance.getString(1).indexOf(',') > 0) { - String[] listDatasetsPerformanceInstance = rstmpReportDatasetsPerformanceInstance - .getString(1) - .split(","); - logger.info("Datasets Performance found " + listDatasetsPerformanceInstance.length); - for (int k = 0; k < listDatasetsPerformanceInstance.length; k++) { - String sqlInsertDataSetsPerformance = "INSERT INTO " - + ConnectDB.getDataSetUsageStatsDBSchema() + " .datasetsperformance " - + "SELECT\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].dataset-id[0].value') AS ds_type,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].performance[" + j + "].period.end-date') AS period_end,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].performance[" + j + "].period.begin-date') AS period_from,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].performance[" + j + "].instance[" + k - + "].access-method') AS access_method,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].performance[" + j + "].instance[" + k - + "].metric-type') AS metric_type,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].performance[" + j + "].instance[" + k + "].count') AS count,\n" - + " get_json_object(json, '$.report.report-datasets[" + i - + "].performance[" + j + "].instance[" + k - + "].country-counts') AS country_counts,\n" - + " get_json_object(json, '$.report.id') AS reportid \n" - + "FROM " + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; - stmt.execute(sqlInsertDataSetsPerformance); - } - } - } - } - logger.info("DatasetPerformance added for dataset" + i); - } - } - logger.info("Adding gzip performance"); - String sqlSelecteReportSubsets = "SELECT get_json_object(json, '$.report.report-subsets.gzip[0]') FROM " - + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; - stmt.execute(sqlSelecteReportSubsets); - ResultSet rstmpReportSubsets = stmt.getResultSet(); - if (rstmpReportSubsets.next()) { - String unCompressedReport = uncompressString(rstmpReportSubsets.getString(1)); - this.readCompressedReport(unCompressedReport, reportID); - } - } - } - this.dropTmpReportsTable(); - } - - public void readCompressedReport(String report, String reportId) throws Exception { - Gson gson = new Gson(); - JsonObject jsonObject = gson.fromJson(report, JsonObject.class); - - JsonArray jsonReportDatasets; - if (jsonObject.getAsJsonArray("report_datasets") != null) { - jsonReportDatasets = jsonObject.getAsJsonArray("report_datasets"); - } else { - jsonReportDatasets = jsonObject.getAsJsonArray("report-datasets"); - } - - for (JsonElement datasetElement : jsonReportDatasets) { - // JsonElement dataset_title = datasetElement.getAsJsonObject().get("dataset-title"); - String dataset_title = datasetElement.getAsJsonObject().get("dataset-title").getAsString(); - String yop = datasetElement.getAsJsonObject().get("yop").getAsString(); - String uri = datasetElement.getAsJsonObject().get("uri").getAsString(); - String platform = datasetElement.getAsJsonObject().get("platform").getAsString(); - String data_type = datasetElement.getAsJsonObject().get("data-type").getAsString(); - String publisher = datasetElement.getAsJsonObject().get("publisher").getAsString(); - - JsonArray publisher_id = datasetElement.getAsJsonObject().getAsJsonArray("publisher-id"); - String publisher_id_type = ""; - String publisher_id_value = ""; - for (JsonElement publisher_id_Element : publisher_id) { - publisher_id_type = publisher_id_Element.getAsJsonObject().get("type").getAsString(); - publisher_id_value = publisher_id_Element.getAsJsonObject().get("value").getAsString(); - } - JsonArray dataset_days = datasetElement.getAsJsonObject().getAsJsonArray("dataset-dates"); - String ds_dates_type = ""; - String ds_dates_value = ""; - for (JsonElement datasetDaysElement : dataset_days) { - ds_dates_type = datasetDaysElement.getAsJsonObject().get("type").getAsString(); - ds_dates_value = datasetDaysElement.getAsJsonObject().get("value").getAsString(); - } - - JsonArray datasetContributors = null; - String ds_contributor_type = ""; - String[] ds_contributor_values = null; - Array ds_contributor_valuesArr = null; - - if (datasetElement.getAsJsonObject().getAsJsonArray("dataset-contributors") != null) { - datasetContributors = datasetElement.getAsJsonObject().getAsJsonArray("dataset-contributors"); - - JsonArray datasetid = datasetElement.getAsJsonObject().getAsJsonArray("dataset-id"); - String doi = ""; - for (JsonElement datasetIDElement : datasetid) -//System.out.println(datasetIDElement.getAsJsonObject().get("value").getAsString()); - { - doi = datasetIDElement.getAsJsonObject().get("value").getAsString(); - } - - String sqlInsertDataset = "INSERT INTO " + ConnectDB.getDataSetUsageStatsDBSchema() - + " .datasets(ds_type," - + "ds_title,yop,uri,platform,data_type,publisher,publisher_id_type,publisher_id_value," - + "ds_dates_type, ds_dates_value, ds_contributors,reportid) VALUES(?,?,?,?,?,?,?,?,?,?,?,?,?) "; - - PreparedStatement pstmtDataset = ConnectDB.DB_HIVE_CONNECTION.prepareStatement(sqlInsertDataset); - - pstmtDataset.setString(1, doi); - pstmtDataset.setString(2, dataset_title); - pstmtDataset.setString(3, yop); - pstmtDataset.setString(4, uri); - pstmtDataset.setString(5, platform); - pstmtDataset.setString(6, data_type); - pstmtDataset.setString(7, publisher); - pstmtDataset.setString(8, publisher_id_type); - pstmtDataset.setString(9, publisher_id_value); - pstmtDataset.setString(10, ds_dates_type); - pstmtDataset.setString(11, ds_dates_value); - pstmtDataset.setString(13, datasetContributors.getAsString()); - pstmtDataset.setString(14, reportId); - - pstmtDataset.execute(); - logger.info("Dataset from compressed report addded " + doi); - /* - * JsonArray performance = datasetElement.getAsJsonObject().getAsJsonArray("performance"); for - * (JsonElement performanceElement : performance) { JsonObject period = - * performanceElement.getAsJsonObject().getAsJsonObject("period"); String end_date = - * period.getAsJsonObject().get("end-date").getAsString(); String begin_date = - * period.getAsJsonObject().get("begin-date").getAsString(); JsonArray instance = - * performanceElement.getAsJsonObject().getAsJsonArray("instance"); for (JsonElement instanceElement : - * instance) { int count = instanceElement.getAsJsonObject().get("count").getAsInt(); JsonObject - * country_counts = instanceElement.getAsJsonObject().getAsJsonObject("country-counts"); Set - * keys = country_counts.keySet(); String[] country = new String[country_counts.size()]; String[] - * country_counts_val = new String[country_counts.size()]; Iterator it2 = keys.iterator(); int j = 0; - * while (it2.hasNext()) { country[j] = it2.next().toString(); country_counts_val[j] = - * country_counts.get(country[j]).getAsString(); } Array countryArr = conn.createArrayOf("text", - * country); Array countrycountsArr = conn.createArrayOf("text", country_counts_val); String metrictype - * = instanceElement.getAsJsonObject().get("metric-type").getAsString(); String accessMethod = - * instanceElement.getAsJsonObject().get("access-method").getAsString(); String - * sqlInsertDatasetPerformance = - * "INSERT INTO datasetperformance(ds_type,period_end,period_from,access_method,metric_type,count,country,country_count, reportid) VALUES(?,?,?,?,?,?,?,?,?)" - * ; PreparedStatement pstmtDatasetPerformance = conn.prepareStatement(sqlInsertDatasetPerformance); - * //System.out.println(begin_date + " " + end_date + " " + doi + " " + metrictype + " " + count); - * pstmtDatasetPerformance.setString(1, doi); pstmtDatasetPerformance.setString(2, end_date); - * pstmtDatasetPerformance.setString(3, begin_date); pstmtDatasetPerformance.setString(4, accessMethod); - * pstmtDatasetPerformance.setString(5, metrictype); pstmtDatasetPerformance.setInt(6, count); - * pstmtDatasetPerformance.setArray(7, countryArr); pstmtDatasetPerformance.setArray(8, - * countrycountsArr); pstmtDatasetPerformance.setString(9, reportId); pstmtDatasetPerformance.execute(); - * } } - */ - } - } - - } - - private ArrayList listHdfsDir(String dir) throws Exception { - - FileSystem hdfs = FileSystem.get(new Configuration()); - RemoteIterator Files; - ArrayList fileNames = new ArrayList<>(); - - try { - Path exportPath = new Path(hdfs.getUri() + dir); - Files = hdfs.listFiles(exportPath, false); - while (Files.hasNext()) { - String fileName = Files.next().getPath().toString(); - fileNames.add(fileName); - } - - hdfs.close(); - } catch (Exception e) { - logger.error("HDFS file path with exported data does not exist : " + new Path(hdfs.getUri() + dir)); - throw new Exception("HDFS file path with exported data does not exist : " + dir, e); - } - - return fileNames; - } - - private String readHDFSFile(String filename) throws Exception { - String result; - try { - - FileSystem fs = FileSystem.get(new Configuration()); - // log.info("reading file : " + filename); - - BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(new Path(filename)))); - - StringBuilder sb = new StringBuilder(); - String line = br.readLine(); - - while (line != null) { - sb.append(line); - // sb.append(line); - line = br.readLine(); - } - // result = sb.toString().replace("][{\"idSite\"", ",{\"idSite\""); - result = sb.toString().trim(); - // fs.close(); - } catch (Exception e) { - throw new Exception(e); - } - - return result; - } - - public static String uncompressString(String zippedBase64Str) - throws IOException { - String result = null; - - // In my solr project, I use org.apache.solr.common.util.Base64. - // byte[] bytes = - // org.apache.solr.common.util.Base64.base64ToByteArray(zippedBase64Str); - byte[] bytes = Base64.getDecoder().decode(zippedBase64Str); - GZIPInputStream zi = null; - try { - zi = new GZIPInputStream(new ByteArrayInputStream(bytes)); - result = IOUtils.toString(zi); - } finally { - IOUtils.closeQuietly(zi); - } - return result; - } - - private void createTmpReportsTable(String jsonFile) throws SQLException { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - dropTmpReportsTable(); - String createTmpTable = "CREATE TEMPORARY TABLE " + ConnectDB.getDataSetUsageStatsDBSchema() - + ".tmpjson (json STRING)"; - stmt.executeUpdate(createTmpTable); - logger.info("Tmp Table Created"); - - String insertJsonReport = "LOAD DATA INPATH '" + jsonFile + "' INTO TABLE " - + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; - stmt.execute(insertJsonReport); - logger.info("JSON Report File inserted to tmpjson Table"); - } - - private void dropTmpReportsTable() throws SQLException { - logger.info("Dropping tmpjson Table"); - String dropTmpTable = "DROP TABLE IF EXISTS " + ConnectDB.getDataSetUsageStatsDBSchema() + ".tmpjson"; - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - stmt.executeUpdate(dropTmpTable); - logger.info("Dropped tmpjson Table"); - - } - -} - -/* - * PreparedStatement prepStatem = conn. - * prepareStatement("insert into usageStats (source, entityID,sourceItemType,entityType, counter,action,timestamp_month,referrer) values (?,?,?,?,?,?,?,?)" - * ); - */ diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java deleted file mode 100644 index 7b07fbc25..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java +++ /dev/null @@ -1,111 +0,0 @@ - -package eu.dnetlib.oa.graph.datasetsusagestats.export; - -import java.io.IOException; -import java.sql.SQLException; -import java.sql.Statement; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * Main class for downloading and processing Usage statistics - * - * @author D. Pierrakos, S. Zoupanos - */ -public class UsageStatsExporter { - - private Statement stmt = null; - - public UsageStatsExporter() { - - } - - private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); - - private void reCreateLogDirs() throws IllegalArgumentException, IOException { - FileSystem dfs = FileSystem.get(new Configuration()); - - logger.info("Deleting Log directory: " + ExecuteWorkflow.dataciteReportPath); - dfs.delete(new Path(ExecuteWorkflow.dataciteReportPath), true); - - logger.info("Creating Log directory: " + ExecuteWorkflow.dataciteReportPath); - dfs.mkdirs(new Path(ExecuteWorkflow.dataciteReportPath)); - - } - - public void export() throws Exception { - - logger.info("Initialising DB properties"); - ConnectDB.init(); - ConnectDB.getHiveConnection(); - - if (ExecuteWorkflow.recreateDbAndTables) { - DatasetsStatsDB datasetsDB = new DatasetsStatsDB("", ""); - datasetsDB.recreateDBAndTables(); - } - logger.info("Initializing the download logs module"); - DownloadReportsListFromDatacite drfd = new DownloadReportsListFromDatacite(ExecuteWorkflow.dataciteBaseURL, - ExecuteWorkflow.dataciteReportPath); - - if (ExecuteWorkflow.datasetsEmptyDirs) { - logger.info("Downloading Reports List From Datacite"); - drfd.downloadReportsList(); - logger.info("Reports List has been downloaded"); - } - - ReadReportsListFromDatacite readReportsListFromDatacite = new ReadReportsListFromDatacite( - ExecuteWorkflow.dataciteReportPath); - logger.info("Store Reports To DB"); - readReportsListFromDatacite.readReports(); - logger.info("Reports Stored To DB"); - } - -// runImpalaQuery(); - /* - * PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); - * logger.info("Re-creating database and tables"); logger.info("Initializing the download logs module"); - * PiwikDownloadLogs piwd = new PiwikDownloadLogs(ExecuteWorkflow.matomoBaseURL, ExecuteWorkflow.matomoAuthToken); - * if (ExecuteWorkflow.piwikEmptyDirs) { logger.info("Recreating Piwik log directories"); - * piwikstatsdb.reCreateLogDirs(); } // Downloading piwik logs (also managing directory creation) if - * (ExecuteWorkflow.downloadPiwikLogs) { logger.info("Downloading piwik logs"); piwd .GetOpenAIRELogs( - * ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath, ExecuteWorkflow.portalMatomoID); } - * logger.info("Downloaded piwik logs"); // Create DB tables, insert/update statistics String cRobotsUrl = - * "https://raw.githubusercontent.com/atmire/COUNTER-Robots/master/COUNTER_Robots_list.json"; - * piwikstatsdb.setCounterRobotsURL(cRobotsUrl); if (ExecuteWorkflow.processPiwikLogs) { - * logger.info("Processing logs"); piwikstatsdb.processLogs(); } logger.info("Creating LaReferencia tables"); - * LaReferenciaDownloadLogs lrf = new LaReferenciaDownloadLogs(ExecuteWorkflow.lareferenciaBaseURL, - * ExecuteWorkflow.lareferenciaAuthToken); if (ExecuteWorkflow.laReferenciaEmptyDirs) { - * logger.info("Recreating LaReferencia log directories"); lrf.reCreateLogDirs(); } if - * (ExecuteWorkflow.downloadLaReferenciaLogs) { logger.info("Downloading LaReferencia logs"); - * lrf.GetLaReferenciaRepos(ExecuteWorkflow.lareferenciaLogPath); logger.info("Downloaded LaReferencia logs"); } - * LaReferenciaStats lastats = new LaReferenciaStats(ExecuteWorkflow.lareferenciaLogPath); if - * (ExecuteWorkflow.processLaReferenciaLogs) { logger.info("Processing LaReferencia logs"); lastats.processLogs(); - * logger.info("LaReferencia logs done"); } IrusStats irusstats = new IrusStats(ExecuteWorkflow.irusUKBaseURL); if - * (ExecuteWorkflow.irusCreateTablesEmptyDirs) { logger.info("Creating Irus Stats tables"); - * irusstats.createTables(); logger.info("Created Irus Stats tables"); logger.info("Re-create log dirs"); - * irusstats.reCreateLogDirs(); logger.info("Re-created log dirs"); } if (ExecuteWorkflow.irusDownloadReports) { - * irusstats.getIrusRRReport(ExecuteWorkflow.irusUKReportPath); } if (ExecuteWorkflow.irusProcessStats) { - * irusstats.processIrusStats(); logger.info("Irus done"); } SarcStats sarcStats = new SarcStats(); if - * (ExecuteWorkflow.sarcCreateTablesEmptyDirs) { sarcStats.reCreateLogDirs(); } if - * (ExecuteWorkflow.sarcDownloadReports) { sarcStats.getAndProcessSarc(ExecuteWorkflow.sarcsReportPathArray, - * ExecuteWorkflow.sarcsReportPathNonArray); } if (ExecuteWorkflow.sarcProcessStats) { - * sarcStats.processSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); - * sarcStats.finalizeSarcStats(); } logger.info("Sarc done"); // finalize usagestats if - * (ExecuteWorkflow.finalizeStats) { piwikstatsdb.finalizeStats(); logger.info("Finalized stats"); } // Make the - * tables available to Impala if (ExecuteWorkflow.finalTablesVisibleToImpala) { - * logger.info("Making tables visible to Impala"); invalidateMetadata(); } logger.info("End"); - */ -} -/* - * private void invalidateMetadata() throws SQLException { Statement stmt = null; stmt = - * ConnectDB.getImpalaConnection().createStatement(); String sql = "INVALIDATE METADATA " + - * ConnectDB.getDataSetUsageStatsDBSchema() + ".downloads_stats"; stmt.executeUpdate(sql); sql = "INVALIDATE METADATA " - * + ConnectDB.getDataSetUsageStatsDBSchema() + ".views_stats"; stmt.executeUpdate(sql); sql = "INVALIDATE METADATA " + - * ConnectDB.getDataSetUsageStatsDBSchema() + ".usage_stats"; stmt.executeUpdate(sql); sql = "INVALIDATE METADATA " + - * ConnectDB.getDataSetUsageStatsDBSchema() + ".pageviews_stats"; stmt.executeUpdate(sql); stmt.close(); - * ConnectDB.getHiveConnection().close(); } - */ diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/export/datasets_usagestats_parameters.json b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/export/datasets_usagestats_parameters.json deleted file mode 100644 index f8d51a882..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/export/datasets_usagestats_parameters.json +++ /dev/null @@ -1,56 +0,0 @@ -[ - { - "paramName": "dbu", - "paramLongName": "dataciteBaseURL", - "paramDescription": "URL of Datacite Reports Endpoint", - "paramRequired": true - }, - { - "paramName": "drp", - "paramLongName": "dataciteReportPath", - "paramDescription": "Path for Datacite Reports", - "paramRequired": true - }, - { - "paramName": "dbhu", - "paramLongName": "dbHiveUrl", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "dbiu", - "paramLongName": "dbImpalaUrl", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "dusdbs", - "paramLongName": "datasetUsageStatsDBSchema", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "sdbs", - "paramLongName": "statsDBSchema", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "rdbt", - "paramLongName": "recreateDbAndTables", - "paramDescription": "Re-create database and initial tables?", - "paramRequired": true - }, - { - "paramName": "pwed", - "paramLongName": "datasetsEmptyDirs", - "paramDescription": "Empty piwik directories?", - "paramRequired": true - }, - { - "paramName": "ftvi", - "paramLongName": "finalTablesVisibleToImpala", - "paramDescription": "Make the dataset_usage_stats, visible to Impala", - "paramRequired": true - } -] diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/config-default.xml b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/config-default.xml deleted file mode 100644 index b5c807378..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/config-default.xml +++ /dev/null @@ -1,38 +0,0 @@ - - - jobTracker - ${jobTracker} - - - nameNode - ${nameNode} - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1 - - - impalaJdbcUrl - jdbc:hive2://iis-cdh5-test-gw.ocean.icm.edu.pl:21050/;auth=noSasl; - - - oozie.wf.workflow.notification.url - {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status - - - oozie.use.system.libpath - true - - diff --git a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/workflow.xml b/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/workflow.xml deleted file mode 100644 index 3a81e497d..000000000 --- a/dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/workflow.xml +++ /dev/null @@ -1,70 +0,0 @@ - - - - hiveMetastoreUris - Hive server metastore URIs - - - hiveJdbcUrl - Hive server jdbc url - - - impalaJdbcUrl - Impala server jdbc url - - - - - ${jobTracker} - ${nameNode} - - - hive.metastore.uris - ${hiveMetastoreUris} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - eu.dnetlib.oa.graph.datasetsusagestats.export.ExecuteWorkflow - --dataciteBaseURL - ${dataciteBaseURL} - --dataciteReportPath - ${dataciteReportPath} - --dbHiveUrl - ${hiveJdbcUrl} - --dbImpalaUrl - ${impalaJdbcUrl} - --datasetUsageStatsDBSchema - ${datasetUsageStatsDBSchema} - --statsDBSchema - ${statsDBSchema} - --recreateDbAndTables - ${recreateDbAndTables} - --datasetsEmptyDirs - ${datasetsEmptyDirs} - --finalTablesVisibleToImpala - ${finalTablesVisibleToImpala} - - - - - - - - diff --git a/dhp-workflows/dhp-usage-stats-update/pom.xml b/dhp-workflows/dhp-usage-stats-update/pom.xml deleted file mode 100644 index b56257ee5..000000000 --- a/dhp-workflows/dhp-usage-stats-update/pom.xml +++ /dev/null @@ -1,78 +0,0 @@ - - - - - - - - - dhp-workflows - eu.dnetlib.dhp - 1.1.7-SNAPSHOT - - 4.0.0 - dhp-usage-stats-update - - - UTF-8 - UTF-8 - 0.13.1-cdh5.2.1 - 2.5.0-cdh5.2.1 - - - - - org.apache.spark - spark-core_2.11 - 2.2.0 - - - org.apache.spark - spark-sql_2.11 - 2.4.5 - - - com.googlecode.json-simple - json-simple - 1.1.1 - - - org.json - json - 20180130 - jar - - - org.apache.hive - hive-jdbc - ${cdh.hive.version} - - - org.apache.hadoop - hadoop-common - ${cdh.hadoop.version} - - - eu.dnetlib.dhp - dhp-common - ${project.version} - - - c3p0 - c3p0 - 0.9.1.2 - jar - - - diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java deleted file mode 100644 index 29dd5648b..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java +++ /dev/null @@ -1,125 +0,0 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ - -package eu.dnetlib.oa.graph.usagestats.export; - -import java.sql.Connection; -import java.sql.DriverManager; -import java.sql.SQLException; -import java.sql.Statement; -import java.util.Properties; - -import org.apache.log4j.Logger; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -/** - * @author D. Pierrakos, S. Zoupanos - */ -import com.mchange.v2.c3p0.ComboPooledDataSource; - -public abstract class ConnectDB { - - public static Connection DB_HIVE_CONNECTION; - public static Connection DB_IMPALA_CONNECTION; - - private static String dbHiveUrl; - private static String dbImpalaUrl; - private static String usageStatsDBSchema; - private static String statsDBSchema; - private final static Logger log = Logger.getLogger(ConnectDB.class); - - static void init() throws ClassNotFoundException { - - dbHiveUrl = ExecuteWorkflow.dbHiveUrl; - dbImpalaUrl = ExecuteWorkflow.dbImpalaUrl; - usageStatsDBSchema = ExecuteWorkflow.usageStatsDBSchema; - statsDBSchema = ExecuteWorkflow.statsDBSchema; - - Class.forName("org.apache.hive.jdbc.HiveDriver"); - } - - public static Connection getHiveConnection() throws SQLException { - if (DB_HIVE_CONNECTION != null && !DB_HIVE_CONNECTION.isClosed()) { - return DB_HIVE_CONNECTION; - } else { - DB_HIVE_CONNECTION = connectHive(); - - return DB_HIVE_CONNECTION; - } - } - - public static Connection getImpalaConnection() throws SQLException { - if (DB_IMPALA_CONNECTION != null && !DB_IMPALA_CONNECTION.isClosed()) { - return DB_IMPALA_CONNECTION; - } else { - DB_IMPALA_CONNECTION = connectImpala(); - - return DB_IMPALA_CONNECTION; - } - } - - public static String getUsageStatsDBSchema() { - return ConnectDB.usageStatsDBSchema; - } - - public static String getStatsDBSchema() { - return ConnectDB.statsDBSchema; - } - - private static Connection connectHive() throws SQLException { - /* - * Connection connection = DriverManager.getConnection(dbHiveUrl); Statement stmt = - * connection.createStatement(); log.debug("Opened database successfully"); return connection; - */ - ComboPooledDataSource cpds = new ComboPooledDataSource(); - cpds.setJdbcUrl(dbHiveUrl); - cpds.setAcquireIncrement(1); - cpds.setMaxPoolSize(100); - cpds.setMinPoolSize(1); - cpds.setInitialPoolSize(1); - cpds.setMaxIdleTime(300); - cpds.setMaxConnectionAge(36000); - - cpds.setAcquireRetryAttempts(5); - cpds.setAcquireRetryDelay(2000); - cpds.setBreakAfterAcquireFailure(false); - - cpds.setCheckoutTimeout(0); - cpds.setPreferredTestQuery("SELECT 1"); - cpds.setIdleConnectionTestPeriod(60); - return cpds.getConnection(); - - } - - private static Connection connectImpala() throws SQLException { - /* - * Connection connection = DriverManager.getConnection(dbImpalaUrl); Statement stmt = - * connection.createStatement(); log.debug("Opened database successfully"); return connection; - */ - ComboPooledDataSource cpds = new ComboPooledDataSource(); - cpds.setJdbcUrl(dbImpalaUrl); - cpds.setAcquireIncrement(1); - cpds.setMaxPoolSize(100); - cpds.setMinPoolSize(1); - cpds.setInitialPoolSize(1); - cpds.setMaxIdleTime(300); - cpds.setMaxConnectionAge(36000); - - cpds.setAcquireRetryAttempts(5); - cpds.setAcquireRetryDelay(2000); - cpds.setBreakAfterAcquireFailure(false); - - cpds.setCheckoutTimeout(0); - cpds.setPreferredTestQuery("SELECT 1"); - cpds.setIdleConnectionTestPeriod(60); - - return cpds.getConnection(); - - } - -} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ExecuteWorkflow.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ExecuteWorkflow.java deleted file mode 100644 index 50b951cbc..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ExecuteWorkflow.java +++ /dev/null @@ -1,197 +0,0 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ - -package eu.dnetlib.oa.graph.usagestats.export; - -import java.text.SimpleDateFormat; -import java.util.Calendar; -import java.util.Date; - -import org.apache.commons.io.IOUtils; -import org.apache.log4j.BasicConfigurator; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -public class ExecuteWorkflow { - - static String matomoAuthToken; - static String matomoBaseURL; - static String repoLogPath; - static String portalLogPath; - static String portalMatomoID; - static String irusUKBaseURL; - static String irusUKReportPath; - static String sarcsReportPathArray; - static String sarcsReportPathNonArray; - static String lareferenciaLogPath; - static String lareferenciaBaseURL; - static String lareferenciaAuthToken; - static String dbHiveUrl; - static String dbImpalaUrl; - static String usageStatsDBSchema; - static String statsDBSchema; - static boolean recreateDbAndTables; - - static boolean piwikEmptyDirs; - static boolean downloadPiwikLogs; - static boolean processPiwikLogs; - - static Calendar startingLogPeriod; - static Calendar endingLogPeriod; - static int numberOfPiwikIdsToDownload; - static int numberOfSiteIdsToDownload; - - static boolean laReferenciaEmptyDirs; - static boolean downloadLaReferenciaLogs; - static boolean processLaReferenciaLogs; - - static boolean irusCreateTablesEmptyDirs; - static boolean irusDownloadReports; - static boolean irusProcessStats; - static int irusNumberOfOpendoarsToDownload; - - static boolean sarcCreateTablesEmptyDirs; - static boolean sarcDownloadReports; - static boolean sarcProcessStats; - static int sarcNumberOfIssnToDownload; - - static boolean finalizeStats; - static boolean finalTablesVisibleToImpala; - - static int numberOfDownloadThreads; - - public static void main(String args[]) throws Exception { - - // Sending the logs to the console - BasicConfigurator.configure(); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - UsageStatsExporter.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/usagestats/export/usagestats_parameters.json"))); - parser.parseArgument(args); - - // Setting up the initial parameters - matomoAuthToken = parser.get("matomoAuthToken"); - matomoBaseURL = parser.get("matomoBaseURL"); - repoLogPath = parser.get("repoLogPath"); - portalLogPath = parser.get("portalLogPath"); - portalMatomoID = parser.get("portalMatomoID"); - irusUKBaseURL = parser.get("irusUKBaseURL"); - irusUKReportPath = parser.get("irusUKReportPath"); - sarcsReportPathArray = parser.get("sarcsReportPathArray"); - sarcsReportPathNonArray = parser.get("sarcsReportPathNonArray"); - lareferenciaLogPath = parser.get("lareferenciaLogPath"); - lareferenciaBaseURL = parser.get("lareferenciaBaseURL"); - lareferenciaAuthToken = parser.get("lareferenciaAuthToken"); - - dbHiveUrl = parser.get("dbHiveUrl"); - dbImpalaUrl = parser.get("dbImpalaUrl"); - usageStatsDBSchema = parser.get("usageStatsDBSchema"); - statsDBSchema = parser.get("statsDBSchema"); - - if (parser.get("recreateDbAndTables").toLowerCase().equals("true")) - recreateDbAndTables = true; - else - recreateDbAndTables = false; - - if (parser.get("piwikEmptyDirs").toLowerCase().equals("true")) - piwikEmptyDirs = true; - else - piwikEmptyDirs = false; - - if (parser.get("downloadPiwikLogs").toLowerCase().equals("true")) - downloadPiwikLogs = true; - else - downloadPiwikLogs = false; - - if (parser.get("processPiwikLogs").toLowerCase().equals("true")) - processPiwikLogs = true; - else - processPiwikLogs = false; - - String startingLogPeriodStr = parser.get("startingLogPeriod"); - Date startingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(startingLogPeriodStr); - startingLogPeriod = startingLogPeriodStr(startingLogPeriodDate); - - String endingLogPeriodStr = parser.get("endingLogPeriod"); - Date endingLogPeriodDate = new SimpleDateFormat("MM/yyyy").parse(endingLogPeriodStr); - endingLogPeriod = startingLogPeriodStr(endingLogPeriodDate); - - numberOfPiwikIdsToDownload = Integer.parseInt(parser.get("numberOfPiwikIdsToDownload")); - numberOfSiteIdsToDownload = Integer.parseInt(parser.get("numberOfSiteIdsToDownload")); - - if (parser.get("laReferenciaEmptyDirs").toLowerCase().equals("true")) - laReferenciaEmptyDirs = true; - else - laReferenciaEmptyDirs = false; - - if (parser.get("downloadLaReferenciaLogs").toLowerCase().equals("true")) - downloadLaReferenciaLogs = true; - else - downloadLaReferenciaLogs = false; - - if (parser.get("processLaReferenciaLogs").toLowerCase().equals("true")) - processLaReferenciaLogs = true; - else - processLaReferenciaLogs = false; - - if (parser.get("irusCreateTablesEmptyDirs").toLowerCase().equals("true")) - irusCreateTablesEmptyDirs = true; - else - irusCreateTablesEmptyDirs = false; - if (parser.get("irusDownloadReports").toLowerCase().equals("true")) - irusDownloadReports = true; - else - irusDownloadReports = false; - if (parser.get("irusProcessStats").toLowerCase().equals("true")) - irusProcessStats = true; - else - irusProcessStats = false; - irusNumberOfOpendoarsToDownload = Integer.parseInt(parser.get("irusNumberOfOpendoarsToDownload")); - - if (parser.get("sarcCreateTablesEmptyDirs").toLowerCase().equals("true")) - sarcCreateTablesEmptyDirs = true; - else - sarcCreateTablesEmptyDirs = false; - if (parser.get("sarcDownloadReports").toLowerCase().equals("true")) - sarcDownloadReports = true; - else - sarcDownloadReports = false; - if (parser.get("sarcProcessStats").toLowerCase().equals("true")) - sarcProcessStats = true; - else - sarcProcessStats = false; - sarcNumberOfIssnToDownload = Integer.parseInt(parser.get("sarcNumberOfIssnToDownload")); - - if (parser.get("finalizeStats").toLowerCase().equals("true")) - finalizeStats = true; - else - finalizeStats = false; - if (parser.get("finalTablesVisibleToImpala").toLowerCase().equals("true")) - finalTablesVisibleToImpala = true; - else - finalTablesVisibleToImpala = false; - - numberOfDownloadThreads = Integer.parseInt(parser.get("numberOfDownloadThreads")); - - UsageStatsExporter usagestatsExport = new UsageStatsExporter(); - usagestatsExport.export(); - } - - private static Calendar startingLogPeriodStr(Date date) { - - Calendar calendar = Calendar.getInstance(); - calendar.setTime(date); - return calendar; - - } -} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java deleted file mode 100644 index 011c90532..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java +++ /dev/null @@ -1,419 +0,0 @@ -package eu.dnetlib.oa.graph.usagestats.export; - -import java.io.*; -import java.net.URL; -import java.net.URLConnection; -import java.sql.PreparedStatement; -import java.sql.ResultSet; -import java.sql.Statement; -import java.text.SimpleDateFormat; -import java.util.ArrayList; -import java.util.Calendar; -import java.util.Date; -import java.util.List; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.json.simple.JSONArray; -import org.json.simple.JSONObject; -import org.json.simple.parser.JSONParser; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -public class IrusStats { - - private String irusUKURL; - - private static final Logger logger = LoggerFactory.getLogger(IrusStats.class); - - public IrusStats(String irusUKURL) throws Exception { - this.irusUKURL = irusUKURL; - // The following may not be needed - It will be created when JSON tables are created -// createTmpTables(); - } - - public void reCreateLogDirs() throws Exception { - FileSystem dfs = FileSystem.get(new Configuration()); - - logger.info("Deleting irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); - dfs.delete(new Path(ExecuteWorkflow.irusUKReportPath), true); - - logger.info("Creating irusUKReport directory: " + ExecuteWorkflow.irusUKReportPath); - dfs.mkdirs(new Path(ExecuteWorkflow.irusUKReportPath)); - } - - public void createTables() throws Exception { - try { - logger.info("Creating sushilog"); - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog(source STRING, " - + "repository STRING, rid STRING, date STRING, metric_type STRING, count INT) clustered by (source, " - + "repository, rid, date, metric_type) into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTableSushiLog); - logger.info("Created sushilog"); - - // To see how to apply to the ignore duplicate rules and indexes -// stmt.executeUpdate(sqlCreateTableSushiLog); -// String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " -// + " ON INSERT TO sushilog " -// + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," -// + "sushilog.rid, sushilog.date " -// + "FROM sushilog " -// + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; -// stmt.executeUpdate(sqlcreateRuleSushiLog); -// String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; -// stmt.executeUpdate(createSushiIndex); - stmt.close(); - ConnectDB.getHiveConnection().close(); - logger.info("Sushi Tables Created"); - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - } - } - -// // The following may not be needed - It will be created when JSON tables are created -// private void createTmpTables() throws Exception { -// try { -// -// Statement stmt = ConnectDB.getConnection().createStatement(); -// String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilogtmp(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; -// stmt.executeUpdate(sqlCreateTableSushiLog); -// -// // stmt.executeUpdate("CREATE TABLE IF NOT EXISTS public.sushilog AS TABLE sushilog;"); -// // String sqlCopyPublicSushiLog = "INSERT INTO sushilog SELECT * FROM public.sushilog;"; -// // stmt.executeUpdate(sqlCopyPublicSushiLog); -// String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " -// + " ON INSERT TO sushilogtmp " -// + " WHERE (EXISTS ( SELECT sushilogtmp.source, sushilogtmp.repository," -// + "sushilogtmp.rid, sushilogtmp.date " -// + "FROM sushilogtmp " -// + "WHERE sushilogtmp.source = new.source AND sushilogtmp.repository = new.repository AND sushilogtmp.rid = new.rid AND sushilogtmp.date = new.date AND sushilogtmp.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; -// stmt.executeUpdate(sqlcreateRuleSushiLog); -// -// stmt.close(); -// ConnectDB.getConnection().close(); -// log.info("Sushi Tmp Tables Created"); -// } catch (Exception e) { -// log.error("Failed to create tables: " + e); -// throw new Exception("Failed to create tables: " + e.toString(), e); -// } -// } - public void processIrusStats() throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Adding JSON Serde jar"); - stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); - logger.info("Added JSON Serde jar"); - - logger.info("Dropping sushilogtmp_json table"); - String dropSushilogtmpJson = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".sushilogtmp_json"; - stmt.executeUpdate(dropSushilogtmpJson); - logger.info("Dropped sushilogtmp_json table"); - - logger.info("Creating irus_sushilogtmp_json table"); - String createSushilogtmpJson = "CREATE EXTERNAL TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json(\n" - + " `ItemIdentifier` ARRAY<\n" - + " struct<\n" - + " Type: STRING,\n" - + " Value: STRING\n" - + " >\n" - + " >,\n" - + " `ItemPerformance` ARRAY<\n" - + " struct<\n" - + " `Period`: struct<\n" - + " `Begin`: STRING,\n" - + " `End`: STRING\n" - + " >,\n" - + " `Instance`: struct<\n" - + " `Count`: STRING,\n" - + " `MetricType`: STRING\n" - + " >\n" - + " >\n" - + " >\n" - + ")\n" - + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" - + "LOCATION '" + ExecuteWorkflow.irusUKReportPath + "'\n" - + "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(createSushilogtmpJson); - logger.info("Created irus_sushilogtmp_json table"); - - logger.info("Dropping irus_sushilogtmp table"); - String dropSushilogtmp = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".irus_sushilogtmp"; - stmt.executeUpdate(dropSushilogtmp); - logger.info("Dropped irus_sushilogtmp table"); - - logger.info("Creating irus_sushilogtmp table"); - String createSushilogtmp = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() - + ".irus_sushilogtmp(source STRING, repository STRING, " - + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " - + "tblproperties('transactional'='true')"; - stmt.executeUpdate(createSushilogtmp); - logger.info("Created irus_sushilogtmp table"); - - logger.info("Inserting to irus_sushilogtmp table"); - String insertSushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp " - + "SELECT 'IRUS-UK', CONCAT('opendoar____::', split(split(INPUT__FILE__NAME,'IrusIRReport_')[1],'_')[0]), " - + "`ItemIdent`.`Value`, `ItemPerf`.`Period`.`Begin`, " - + "`ItemPerf`.`Instance`.`MetricType`, `ItemPerf`.`Instance`.`Count` " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp_json " - + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " - + "LATERAL VIEW posexplode(ItemPerformance) ItemPerformanceTable AS seqp, ItemPerf " - + "WHERE `ItemIdent`.`Type`= 'OAI'"; - stmt.executeUpdate(insertSushilogtmp); - logger.info("Inserted to irus_sushilogtmp table"); - - logger.info("Creating downloads_stats table"); - String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats " - + "(`source` string, " - + "`repository_id` string, " - + "`result_id` string, " - + "`date` string, " - + "`count` bigint, " - + "`openaire` bigint)"; - stmt.executeUpdate(createDownloadsStats); - logger.info("Created downloads_stats table"); - - logger.info("Inserting into downloads_stats"); - String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " - + "SELECT s.source, d.id AS repository_id, " - + "ro.id as result_id, CONCAT(YEAR(date), '/', LPAD(MONTH(date), 2, '0')) as date, s.count, '0' " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".irus_sushilogtmp s, " - + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " - + ConnectDB.getStatsDBSchema() + ".result_oids ro " - + "WHERE s.repository=d.oid AND s.rid=ro.oid AND metric_type='ft_total' AND s.source='IRUS-UK'"; - stmt.executeUpdate(insertDStats); - logger.info("Inserted into downloads_stats"); - - logger.info("Creating sushilog table"); - String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog " - + "(`source` string, " - + "`repository_id` string, " - + "`rid` string, " - + "`date` string, " - + "`metric_type` string, " - + "`count` int)"; - stmt.executeUpdate(createSushilog); - logger.info("Created sushilog table"); - - logger.info("Inserting to sushilog table"); - String insertToShushilog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sushilog SELECT * FROM " - + ConnectDB.getUsageStatsDBSchema() - + ".irus_sushilogtmp"; - stmt.executeUpdate(insertToShushilog); - logger.info("Inserted to sushilog table"); - - ConnectDB.getHiveConnection().close(); - } - - public void getIrusRRReport(String irusUKReportPath) throws Exception { - SimpleDateFormat sdf = new SimpleDateFormat("YYYY-MM"); - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("(getIrusRRReport) Starting period for log download: " + sdf.format(start.getTime())); - - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("(getIrusRRReport) Ending period for log download: " + sdf.format(end.getTime())); - - String reportUrl = irusUKURL + "GetReport/?Report=RR1&Release=4&RequestorID=OpenAIRE&BeginDate=" - + sdf.format(start.getTime()) + "&EndDate=" + sdf.format(end.getTime()) - + "&RepositoryIdentifier=&ItemDataType=&NewJiscBand=&Granularity=Monthly&Callback="; - - logger.info("(getIrusRRReport) Getting report: " + reportUrl); - - String text = getJson(reportUrl, "", ""); - - List opendoarsToVisit = new ArrayList(); - JSONParser parser = new JSONParser(); - JSONObject jsonObject = (JSONObject) parser.parse(text); - jsonObject = (JSONObject) jsonObject.get("ReportResponse"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Customer"); - JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); - int i = 0; - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - JSONArray itemIdentifier = (JSONArray) jsonObjectRow.get("ItemIdentifier"); - for (Object identifier : itemIdentifier) { - JSONObject opendoar = (JSONObject) identifier; - if (opendoar.get("Type").toString().equals("OpenDOAR")) { - i++; - opendoarsToVisit.add(opendoar.get("Value").toString()); - break; - } - } - // break; - } - - logger.info("(getIrusRRReport) Found the following opendoars for download: " + opendoarsToVisit); - - if (ExecuteWorkflow.irusNumberOfOpendoarsToDownload > 0 - && ExecuteWorkflow.irusNumberOfOpendoarsToDownload <= opendoarsToVisit.size()) { - logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.irusNumberOfOpendoarsToDownload); - opendoarsToVisit = opendoarsToVisit.subList(0, ExecuteWorkflow.irusNumberOfOpendoarsToDownload); - } - - logger.info("(getIrusRRReport) Downloading the followins opendoars: " + opendoarsToVisit); - - for (String opendoar : opendoarsToVisit) { - logger.info("Now working on openDoar: " + opendoar); - this.getIrusIRReport(opendoar, irusUKReportPath); - } - - logger.info("(getIrusRRReport) Finished with report: " + reportUrl); - } - - private void getIrusIRReport(String opendoar, String irusUKReportPath) throws Exception { - - logger.info("(getIrusIRReport) Getting report(s) with opendoar: " + opendoar); - - ConnectDB.getHiveConnection().setAutoCommit(false); - - SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); - - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("(getIrusIRReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); - - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("(getIrusIRReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); - - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - PreparedStatement st = ConnectDB - .getHiveConnection() - .prepareStatement( - "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); - st.setString(1, "opendoar____::" + opendoar); - ResultSet rs_date = st.executeQuery(); - Date dateMax = null; - while (rs_date.next()) { - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - dateMax = sdf.parse(rs_date.getString(1)); - } - } - rs_date.close(); - int batch_size = 0; - - if (dateMax != null && start.getTime().compareTo(dateMax) <= 0) { - logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + opendoar); - } else { - while (start.before(end)) { - logger.info("date: " + simpleDateFormat.format(start.getTime())); - String reportUrl = this.irusUKURL + "GetReport/?Report=IR1&Release=4&RequestorID=OpenAIRE&BeginDate=" - + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()) - + "&RepositoryIdentifier=opendoar%3A" + opendoar - + "&ItemIdentifier=&ItemDataType=&hasDOI=&Granularity=Monthly&Callback="; - start.add(Calendar.MONTH, 1); - - logger.info("Downloading file: " + reportUrl); - String text = getJson(reportUrl, "", ""); - if (text == null) { - continue; - } - - FileSystem fs = FileSystem.get(new Configuration()); - String filePath = irusUKReportPath + "/" + "IrusIRReport_" - + opendoar + "_" + simpleDateFormat.format(start.getTime()) + ".json"; - logger.info("Storing to file: " + filePath); - FSDataOutputStream fin = fs.create(new Path(filePath), true); - - JSONParser parser = new JSONParser(); - JSONObject jsonObject = (JSONObject) parser.parse(text); - jsonObject = (JSONObject) jsonObject.get("ReportResponse"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Report"); - jsonObject = (JSONObject) jsonObject.get("Customer"); - JSONArray jsonArray = (JSONArray) jsonObject.get("ReportItems"); - if (jsonArray == null) { - continue; - } - String oai = ""; - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - fin.write(jsonObjectRow.toJSONString().getBytes()); - fin.writeChar('\n'); - } - - fin.close(); - } - - } - //ConnectDB.getHiveConnection().close(); - - logger.info("(getIrusIRReport) Finished downloading report(s) with opendoar: " + opendoar); - } - - private String getJson(String url) throws Exception { - try { - System.out.println("===> Connecting to: " + url); - URL website = new URL(url); - System.out.println("Connection url -----> " + url); - URLConnection connection = website.openConnection(); - - // connection.setRequestProperty ("Authorization", "Basic "+encoded); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); -// response.append("\n"); - } - } - - System.out.println("response ====> " + response.toString()); - - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL: " + e); - System.out.println("Failed to get URL: " + e); - throw new Exception("Failed to get URL: " + e.toString(), e); - } - } - - private String getJson(String url, String username, String password) throws Exception { - // String cred=username+":"+password; - // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); - try { - URL website = new URL(url); - URLConnection connection = website.openConnection(); - // connection.setRequestProperty ("Authorization", "Basic "+encoded); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); - response.append("\n"); - } - } - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL", e); - return null; - } - } -} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java deleted file mode 100644 index 7a61b1f46..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java +++ /dev/null @@ -1,265 +0,0 @@ -package eu.dnetlib.oa.graph.usagestats.export; - -import java.io.*; -import java.net.URL; -import java.net.URLConnection; -import java.sql.PreparedStatement; -import java.sql.ResultSet; -import java.sql.Statement; -import java.text.SimpleDateFormat; -import java.util.ArrayList; -import java.util.Calendar; -import java.util.Date; -import java.util.List; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.json.simple.JSONArray; -import org.json.simple.JSONObject; -import org.json.simple.parser.JSONParser; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -public class LaReferenciaDownloadLogs { - - private final String piwikUrl; - private Date startDate; - private final String tokenAuth; - - /* - * The Piwik's API method - */ - private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; - private final String format = "&format=json"; - private final String ApimethodGetAllSites = "?module=API&method=SitesManager.getSitesWithViewAccess"; - - private static final Logger logger = LoggerFactory.getLogger(LaReferenciaDownloadLogs.class); - - public LaReferenciaDownloadLogs(String piwikUrl, String tokenAuth) throws Exception { - this.piwikUrl = piwikUrl; - this.tokenAuth = tokenAuth; - this.createTables(); -// this.createTmpTables(); - } - - public void reCreateLogDirs() throws IllegalArgumentException, IOException { - FileSystem dfs = FileSystem.get(new Configuration()); - - logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); - dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); - - logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); - dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); - } - - private void createTables() throws Exception { - try { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - - logger.info("Creating LaReferencia tables"); - String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " - + "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " - + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " - + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " - + "stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTableLareferenciaLog); - logger.info("Created LaReferencia tables"); -// String sqlcreateRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " -// + " ON INSERT TO lareferencialog " -// + " WHERE (EXISTS ( SELECT lareferencialog.matomoid, lareferencialog.source, lareferencialog.id_visit," -// + "lareferencialog.action, lareferencialog.\"timestamp\", lareferencialog.entity_id " -// + "FROM lareferencialog " -// + "WHERE lareferencialog.matomoid=new.matomoid AND lareferencialog.source = new.source AND lareferencialog.id_visit = new.id_visit AND lareferencialog.action = new.action AND lareferencialog.entity_id = new.entity_id AND lareferencialog.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; -// String sqlCreateRuleIndexLaReferenciaLog = "create index if not exists lareferencialog_rule on lareferencialog(matomoid, source, id_visit, action, entity_id, \"timestamp\");"; -// stmt.executeUpdate(sqlcreateRuleLaReferenciaLog); -// stmt.executeUpdate(sqlCreateRuleIndexLaReferenciaLog); - - stmt.close(); - ConnectDB.getHiveConnection().close(); - logger.info("Lareferencia Tables Created"); - - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - // System.exit(0); - } - } - -// private void createTmpTables() throws Exception { -// -// try { -// Statement stmt = ConnectDB.getConnection().createStatement(); -// String sqlCreateTmpTableLaReferenciaLog = "CREATE TABLE IF NOT EXISTS lareferencialogtmp(matomoid INTEGER, source TEXT, id_visit TEXT, country TEXT, action TEXT, url TEXT, entity_id TEXT, source_item_type TEXT, timestamp TEXT, referrer_name TEXT, agent TEXT, PRIMARY KEY(source, id_visit, action, timestamp, entity_id));"; -// String sqlcreateTmpRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " -// + " ON INSERT TO lareferencialogtmp " -// + " WHERE (EXISTS ( SELECT lareferencialogtmp.matomoid, lareferencialogtmp.source, lareferencialogtmp.id_visit," -// + "lareferencialogtmp.action, lareferencialogtmp.\"timestamp\", lareferencialogtmp.entity_id " -// + "FROM lareferencialogtmp " -// + "WHERE lareferencialogtmp.matomoid=new.matomoid AND lareferencialogtmp.source = new.source AND lareferencialogtmp.id_visit = new.id_visit AND lareferencialogtmp.action = new.action AND lareferencialogtmp.entity_id = new.entity_id AND lareferencialogtmp.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; -// stmt.executeUpdate(sqlCreateTmpTableLaReferenciaLog); -// stmt.executeUpdate(sqlcreateTmpRuleLaReferenciaLog); -// -// stmt.close(); -// log.info("Lareferencia Tmp Tables Created"); -// -// } catch (Exception e) { -// log.error("Failed to create tmptables: " + e); -// throw new Exception("Failed to create tmp tables: " + e.toString(), e); -// // System.exit(0); -// } -// } - private String getPiwikLogUrl() { - return piwikUrl + "/"; - } - - private String getJson(String url) throws Exception { - try { - URL website = new URL(url); - URLConnection connection = website.openConnection(); - - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); -// response.append("\n"); - } - } - - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL: " + e); - throw new Exception("Failed to get URL: " + e.toString(), e); - } - } - - public void GetLaReferenciaRepos(String repoLogsPath) throws Exception { - - String baseApiUrl = getPiwikLogUrl() + ApimethodGetAllSites + format + "&token_auth=" + this.tokenAuth; - String content = ""; - - List siteIdsToVisit = new ArrayList(); - - // Getting all the siteIds in a list for logging reasons & limiting the list - // to the max number of siteIds - content = getJson(baseApiUrl); - JSONParser parser = new JSONParser(); - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - siteIdsToVisit.add(Integer.parseInt(jsonObjectRow.get("idsite").toString())); - } - logger.info("Found the following siteIds for download: " + siteIdsToVisit); - - if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 - && ExecuteWorkflow.numberOfPiwikIdsToDownload <= siteIdsToVisit.size()) { - logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); - siteIdsToVisit = siteIdsToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); - } - - logger.info("Downloading from repos with the followins siteIds: " + siteIdsToVisit); - - for (int siteId : siteIdsToVisit) { - logger.info("Now working on LaReferencia MatomoId: " + siteId); - this.GetLaReFerenciaLogs(repoLogsPath, siteId); - } - } - - public void GetLaReFerenciaLogs(String repoLogsPath, - int laReferencialMatomoID) throws Exception { - - logger.info("Downloading logs for LaReferencia repoid " + laReferencialMatomoID); - - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("Starting period for log download: " + sdf.format(start.getTime())); - - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("Ending period for log download: " + sdf.format(end.getTime())); - - PreparedStatement st = ConnectDB - .getHiveConnection() - .prepareStatement( - "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() - + ".lareferencialog WHERE matomoid=?"); - st.setInt(1, laReferencialMatomoID); - Date dateMax = null; - - ResultSet rs_date = st.executeQuery(); - while (rs_date.next()) { - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - dateMax = sdf.parse(rs_date.getString(1)); - } - } - rs_date.close(); - - for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { - Date date = currDay.getTime(); - if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { - logger.info("Date found in logs " + dateMax + " and not downloanding Matomo logs for " + laReferencialMatomoID); - } else { - logger - .info( - "Downloading logs for LaReferencia repoid " + laReferencialMatomoID + " and for " - + sdf.format(date)); - - String period = "&period=day&date=" + sdf.format(date); - String outFolder = ""; - outFolder = repoLogsPath; - - FileSystem fs = FileSystem.get(new Configuration()); - FSDataOutputStream fin = fs - .create( - new Path(outFolder + "/" + laReferencialMatomoID + "_LaRefPiwiklog" + sdf.format((date)) + ".json"), - true); - - String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + laReferencialMatomoID + period + format - + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; - String content = ""; - int i = 0; - - JSONParser parser = new JSONParser(); - do { - String apiUrl = baseApiUrl; - - if (i > 0) { - apiUrl += "&filter_offset=" + (i * 1000); - } - - content = getJson(apiUrl); - if (content.length() == 0 || content.equals("[]")) { - break; - } - - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRaw = (JSONObject) aJsonArray; - fin.write(jsonObjectRaw.toJSONString().getBytes()); - fin.writeChar('\n'); - } - - logger - .info( - "Downloaded part " + i + " of logs for LaReferencia repoid " + laReferencialMatomoID - + " and for " - + sdf.format(date)); - i++; - } while (true); - fin.close(); - } - } - } -} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java deleted file mode 100644 index 747b5ce0e..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java +++ /dev/null @@ -1,436 +0,0 @@ - -package eu.dnetlib.oa.graph.usagestats.export; - -import java.io.*; -import java.net.URLDecoder; -import java.sql.Connection; -import java.sql.PreparedStatement; -import java.sql.SQLException; -import java.sql.Statement; -import java.sql.Timestamp; -import java.text.SimpleDateFormat; -import java.util.*; -import java.util.regex.Matcher; -import java.util.regex.Pattern; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.LocatedFileStatus; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.fs.RemoteIterator; -import org.json.simple.JSONArray; -import org.json.simple.JSONObject; -import org.json.simple.parser.JSONParser; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -public class LaReferenciaStats { - - private static final Logger logger = LoggerFactory.getLogger(LaReferenciaStats.class); - - private String logRepoPath; - - private Statement stmt = null; - - private String CounterRobotsURL; - private ArrayList robotsList; - - public LaReferenciaStats(String logRepoPath) throws Exception { - this.logRepoPath = logRepoPath; - this.createTables(); -// this.createTmpTables(); - } - - /* - * private void connectDB() throws Exception { try { ConnectDB connectDB = new ConnectDB(); } catch (Exception e) { - * log.error("Connect to db failed: " + e); throw new Exception("Failed to connect to db: " + e.toString(), e); } } - */ - private void createTables() throws Exception { - try { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - - logger.info("Creating LaReferencia tables"); - String sqlCreateTableLareferenciaLog = "CREATE TABLE IF NOT EXISTS " + - ConnectDB.getUsageStatsDBSchema() + ".lareferencialog(matomoid INT, " + - "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + - "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + - "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + - "stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTableLareferenciaLog); - logger.info("Created LaReferencia tables"); -// String sqlcreateRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " -// + " ON INSERT TO lareferencialog " -// + " WHERE (EXISTS ( SELECT lareferencialog.matomoid, lareferencialog.source, lareferencialog.id_visit," -// + "lareferencialog.action, lareferencialog.\"timestamp\", lareferencialog.entity_id " -// + "FROM lareferencialog " -// + "WHERE lareferencialog.matomoid=new.matomoid AND lareferencialog.source = new.source AND lareferencialog.id_visit = new.id_visit AND lareferencialog.action = new.action AND lareferencialog.entity_id = new.entity_id AND lareferencialog.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; -// String sqlCreateRuleIndexLaReferenciaLog = "create index if not exists lareferencialog_rule on lareferencialog(matomoid, source, id_visit, action, entity_id, \"timestamp\");"; -// stmt.executeUpdate(sqlcreateRuleLaReferenciaLog); -// stmt.executeUpdate(sqlCreateRuleIndexLaReferenciaLog); - - stmt.close(); - ConnectDB.getHiveConnection().close(); - logger.info("Lareferencia Tables Created"); - - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - // System.exit(0); - } - } - -// private void createTmpTables() throws Exception { -// -// try { -// Statement stmt = ConnectDB.getConnection().createStatement(); -// String sqlCreateTmpTableLaReferenciaLog = "CREATE TABLE IF NOT EXISTS lareferencialogtmp(matomoid INTEGER, source TEXT, id_visit TEXT, country TEXT, action TEXT, url TEXT, entity_id TEXT, source_item_type TEXT, timestamp TEXT, referrer_name TEXT, agent TEXT, PRIMARY KEY(source, id_visit, action, timestamp, entity_id));"; -// String sqlcreateTmpRuleLaReferenciaLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " -// + " ON INSERT TO lareferencialogtmp " -// + " WHERE (EXISTS ( SELECT lareferencialogtmp.matomoid, lareferencialogtmp.source, lareferencialogtmp.id_visit," -// + "lareferencialogtmp.action, lareferencialogtmp.\"timestamp\", lareferencialogtmp.entity_id " -// + "FROM lareferencialogtmp " -// + "WHERE lareferencialogtmp.matomoid=new.matomoid AND lareferencialogtmp.source = new.source AND lareferencialogtmp.id_visit = new.id_visit AND lareferencialogtmp.action = new.action AND lareferencialogtmp.entity_id = new.entity_id AND lareferencialogtmp.\"timestamp\" = new.\"timestamp\")) DO INSTEAD NOTHING;"; -// stmt.executeUpdate(sqlCreateTmpTableLaReferenciaLog); -// stmt.executeUpdate(sqlcreateTmpRuleLaReferenciaLog); -// -// stmt.close(); -// log.info("Lareferencia Tmp Tables Created"); -// -// } catch (Exception e) { -// log.error("Failed to create tmptables: " + e); -// throw new Exception("Failed to create tmp tables: " + e.toString(), e); -// // System.exit(0); -// } -// } - - public void processLogs() throws Exception { - try { - logger.info("Processing LaReferencia repository logs"); - processlaReferenciaLog(); - logger.info("LaReferencia repository logs process done"); - - logger.info("LaReferencia removing double clicks"); - removeDoubleClicks(); - logger.info("LaReferencia removed double clicks"); - - logger.info("LaReferencia creating viewsStats"); - viewsStats(); - logger.info("LaReferencia created viewsStats"); - logger.info("LaReferencia creating downloadsStats"); - downloadsStats(); - logger.info("LaReferencia created downloadsStats"); - logger.info("LaReferencia updating Production Tables"); - updateProdTables(); - logger.info("LaReferencia updated Production Tables"); - - } catch (Exception e) { - logger.error("Failed to process logs: " + e); - throw new Exception("Failed to process logs: " + e.toString(), e); - } - } - - public void processlaReferenciaLog() throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Adding JSON Serde jar"); - stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); - logger.info("Added JSON Serde jar"); - - logger.info("Dropping lareferencialogtmp_json table"); - String drop_lareferencialogtmp_json = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".lareferencialogtmp_json"; - stmt.executeUpdate(drop_lareferencialogtmp_json); - logger.info("Dropped lareferencialogtmp_json table"); - - logger.info("Creating lareferencialogtmp_json"); - String create_lareferencialogtmp_json = "CREATE EXTERNAL TABLE IF NOT EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".lareferencialogtmp_json(\n" + - " `idSite` STRING,\n" + - " `idVisit` STRING,\n" + - " `country` STRING,\n" + - " `referrerName` STRING,\n" + - " `browser` STRING,\n" + - " `repItem` STRING,\n" + - " `actionDetails` ARRAY<\n" + - " struct<\n" + - " timestamp: STRING,\n" + - " type: STRING,\n" + - " url: STRING,\n" + - " `customVariables`: struct<\n" + - " `1`: struct<\n" + - " `customVariablePageValue1`: STRING\n" + - " >,\n" + - " `2`: struct<\n" + - " `customVariablePageValue2`: STRING\n" + - " >\n" + - " >\n" + - " >\n" + - " >" + - ")\n" + - "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + - "LOCATION '" + ExecuteWorkflow.lareferenciaLogPath + "'\n" + - "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(create_lareferencialogtmp_json); - logger.info("Created lareferencialogtmp_json"); - - logger.info("Dropping lareferencialogtmp table"); - String drop_lareferencialogtmp = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".lareferencialogtmp"; - stmt.executeUpdate(drop_lareferencialogtmp); - logger.info("Dropped lareferencialogtmp table"); - - logger.info("Creating lareferencialogtmp"); - String create_lareferencialogtmp = "CREATE TABLE " + - ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp(matomoid INT, " + - "source STRING, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " + - "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + - "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " + - "stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(create_lareferencialogtmp); - logger.info("Created lareferencialogtmp"); - - logger.info("Inserting into lareferencialogtmp"); - String insert_lareferencialogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp " + - "SELECT DISTINCT cast(idSite as INT) as matomoid, CONCAT('opendoar____::', " + - "actiondetail.customVariables.`2`.customVariablePageValue2) as source, idVisit as id_Visit, country, " + - "actiondetail.type as action, actiondetail.url as url, " + - "actiondetail.customVariables.`1`.`customVariablePageValue1` as entity_id, " + - "'repItem' as source_item_type, from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, " + - "referrerName as referrer_name, browser as agent " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp_json " + - "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; - stmt.executeUpdate(insert_lareferencialogtmp); - logger.info("Inserted into lareferencialogtmp"); - - stmt.close(); - } - - public void removeDoubleClicks() throws Exception { - - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Cleaning download double clicks"); - // clean download double clicks - String sql = "DELETE from " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp WHERE EXISTS (" + - "SELECT DISTINCT p1.source, p1.id_visit, p1.action, p1.entity_id, p1.timestamp " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp p1, " + - ConnectDB.getUsageStatsDBSchema() + ".lareferencialogtmp p2 " + - "WHERE p1.source=p2.source AND p1.id_visit=p2.id_visit AND p1.entity_id=p2.entity_id " + - "AND p1.action=p2.action AND p1.action='download' AND p1.timestamp!=p2.timestamp " + - "AND p1.timestamp listHdfsDir(String dir) throws Exception { - FileSystem hdfs = FileSystem.get(new Configuration()); - RemoteIterator Files; - ArrayList fileNames = new ArrayList<>(); - - try { - Path exportPath = new Path(hdfs.getUri() + dir); - Files = hdfs.listFiles(exportPath, false); - while (Files.hasNext()) { - String fileName = Files.next().getPath().toString(); - // log.info("Found hdfs file " + fileName); - fileNames.add(fileName); - } - // hdfs.close(); - } catch (Exception e) { - logger.error("HDFS file path with exported data does not exist : " + new Path(hdfs.getUri() + logRepoPath)); - throw new Exception("HDFS file path with exported data does not exist : " + logRepoPath, e); - } - - return fileNames; - } - - private String readHDFSFile(String filename) throws Exception { - String result; - try { - - FileSystem fs = FileSystem.get(new Configuration()); - // log.info("reading file : " + filename); - - BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(new Path(filename)))); - - StringBuilder sb = new StringBuilder(); - String line = br.readLine(); - - while (line != null) { - if (!line.equals("[]")) { - sb.append(line); - } - // sb.append(line); - line = br.readLine(); - } - result = sb.toString().replace("][{\"idSite\"", ",{\"idSite\""); - if (result.equals("")) { - result = "[]"; - } - - // fs.close(); - } catch (Exception e) { - logger.error(e.getMessage()); - throw new Exception(e); - } - - return result; - } - -} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java deleted file mode 100644 index 8f7fffa9f..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java +++ /dev/null @@ -1,325 +0,0 @@ -package eu.dnetlib.oa.graph.usagestats.export; - -import java.io.*; -import java.net.Authenticator; -import java.net.URL; -import java.net.URLConnection; -import java.sql.PreparedStatement; -import java.sql.ResultSet; -import java.sql.Statement; -import java.text.SimpleDateFormat; -import java.util.ArrayList; -import java.util.Calendar; -import java.util.Date; -import java.util.List; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.Executors; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.json.simple.JSONArray; -import org.json.simple.JSONObject; -import org.json.simple.parser.JSONParser; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -public class PiwikDownloadLogs { - - private final String piwikUrl; - private Date startDate; - private final String tokenAuth; - - /* - * The Piwik's API method - */ - private final String APImethod = "?module=API&method=Live.getLastVisitsDetails"; - private final String format = "&format=json"; - - private static final Logger logger = LoggerFactory.getLogger(PiwikDownloadLogs.class); - - public PiwikDownloadLogs(String piwikUrl, String tokenAuth) { - this.piwikUrl = piwikUrl; - this.tokenAuth = tokenAuth; - - } - - private String getPiwikLogUrl() { - return "https://" + piwikUrl + "/"; - } - - private String getJson(String url) throws Exception { - try { - logger.debug("Connecting to download the JSON: " + url); - URL website = new URL(url); - URLConnection connection = website.openConnection(); - - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); - } - } - return response.toString(); - } catch (Exception e) { - logger.error("Failed to get URL: " + url + " Exception: " + e); - throw new Exception("Failed to get URL: " + url + " Exception: " + e.toString(), e); - } - } - - class WorkerThread implements Runnable { - - private Calendar currDay; - private int siteId; - private String repoLogsPath; - private String portalLogPath; - private String portalMatomoID; - - public WorkerThread(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, - String portalMatomoID) throws IOException { - this.currDay = (Calendar) currDay.clone(); - this.siteId = new Integer(siteId); - this.repoLogsPath = new String(repoLogsPath); - this.portalLogPath = new String(portalLogPath); - this.portalMatomoID = new String(portalMatomoID); - } - - public void run() { - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - System.out - .println( - Thread.currentThread().getName() + " (Start) Thread for " - + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId - + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath - + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); - try { - GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); - - } catch (Exception e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - System.out - .println( - Thread.currentThread().getName() + " (End) Thread for " - + "parameters: currDay=" + sdf.format(currDay.getTime()) + ", siteId=" + siteId - + ", repoLogsPath=" + repoLogsPath + ", portalLogPath=" + portalLogPath - + ", portalLogPath=" + portalLogPath + ", portalMatomoID=" + portalMatomoID); - } - - public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, - String portalMatomoID) throws Exception { - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - - Date date = currDay.getTime(); - logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); - - String period = "&period=day&date=" + sdf.format(date); - String outFolder = ""; - if (siteId == Integer.parseInt(portalMatomoID)) { - outFolder = portalLogPath; - } else { - outFolder = repoLogsPath; - } - - String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format - + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; - String content = ""; - - int i = 0; - - JSONParser parser = new JSONParser(); - StringBuffer totalContent = new StringBuffer(); - FileSystem fs = FileSystem.get(new Configuration()); - - do { - int writtenBytes = 0; - String apiUrl = baseApiUrl; - - if (i > 0) { - apiUrl += "&filter_offset=" + (i * 1000); - } - - content = getJson(apiUrl); - if (content.length() == 0 || content.equals("[]")) { - break; - } - - FSDataOutputStream fin = fs - .create( - new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"), - true); - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRaw = (JSONObject) aJsonArray; - byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); - fin.write(jsonObjectRawBytes); - fin.writeChar('\n'); - - writtenBytes += jsonObjectRawBytes.length + 1; - } - - fin.close(); - System.out - .println( - Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes - + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"); - - i++; - } while (true); - - fs.close(); - } - } - - public void GetOpenAIRELogs(String repoLogsPath, String portalLogPath, String portalMatomoID) throws Exception { - - Statement statement = ConnectDB.getHiveConnection().createStatement(); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - - ResultSet rs = statement - .executeQuery( - "SELECT distinct piwik_id from " + ConnectDB.getStatsDBSchema() - + ".datasource where piwik_id is not null and piwik_id <> 0 order by piwik_id"); - - // Getting all the piwikids in a list for logging reasons & limitting the list - // to the max number of piwikids - List piwikIdToVisit = new ArrayList(); - while (rs.next()) - piwikIdToVisit.add(rs.getInt(1)); - logger.info("Found the following piwikIds for download: " + piwikIdToVisit); - - if (ExecuteWorkflow.numberOfPiwikIdsToDownload > 0 - && ExecuteWorkflow.numberOfPiwikIdsToDownload <= piwikIdToVisit.size()) { - logger.info("Trimming piwikIds list to the size of: " + ExecuteWorkflow.numberOfPiwikIdsToDownload); - piwikIdToVisit = piwikIdToVisit.subList(0, ExecuteWorkflow.numberOfPiwikIdsToDownload); - } - - logger.info("Downloading from repos with the followins piwikIds: " + piwikIdToVisit); - - // ExecutorService executor = Executors.newFixedThreadPool(ExecuteWorkflow.numberOfDownloadThreads); - for (int siteId : piwikIdToVisit) { - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("Starting period for log download: " + sdf.format(start.getTime())); - - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("Ending period for log download: " + sdf.format(end.getTime())); - - logger.info("Now working on piwikId: " + siteId); - - PreparedStatement st = ConnectDB.DB_HIVE_CONNECTION - .prepareStatement( - "SELECT max(timestamp) FROM " + ConnectDB.getUsageStatsDBSchema() - + ".piwiklog WHERE source=?"); - st.setInt(1, siteId); - Date dateMax = null; - ResultSet rs_date = st.executeQuery(); - while (rs_date.next()) { - logger.info("Found max date: " + rs_date.getString(1) + " for repository " + siteId); - - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - dateMax = sdf.parse(rs_date.getString(1)); - } - } - rs_date.close(); - - for (Calendar currDay = (Calendar) start.clone(); currDay.before(end); currDay.add(Calendar.DATE, 1)) { - // logger.info("Date used " + currDay.toString()); - // Runnable worker = new WorkerThread(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); - // executor.execute(worker);// calling execute method of ExecutorService - logger.info("Date used " + currDay.getTime().toString()); - - if (dateMax != null && currDay.getTime().compareTo(dateMax) <= 0) { - logger.info("Date found in logs " + dateMax + " and not downloanding Matomo logs for " + siteId); - } else { - GetOpenAIRELogsForDate(currDay, siteId, repoLogsPath, portalLogPath, portalMatomoID); - } - - } - } - // executor.shutdown(); - // while (!executor.isTerminated()) { - // } - // System.out.println("Finished all threads"); - } - - public void GetOpenAIRELogsForDate(Calendar currDay, int siteId, String repoLogsPath, String portalLogPath, - String portalMatomoID) throws Exception { - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - - Date date = currDay.getTime(); - logger.info("Downloading logs for repoid " + siteId + " and for " + sdf.format(date)); - - String period = "&period=day&date=" + sdf.format(date); - String outFolder = ""; - if (siteId == Integer.parseInt(portalMatomoID)) { - outFolder = portalLogPath; - } else { - outFolder = repoLogsPath; - } - - String baseApiUrl = getPiwikLogUrl() + APImethod + "&idSite=" + siteId + period + format - + "&expanded=5&filter_limit=1000&token_auth=" + tokenAuth; - String content = ""; - - int i = 0; - - JSONParser parser = new JSONParser(); - StringBuffer totalContent = new StringBuffer(); - FileSystem fs = FileSystem.get(new Configuration()); - - do { - int writtenBytes = 0; - String apiUrl = baseApiUrl; - - if (i > 0) { - apiUrl += "&filter_offset=" + (i * 1000); - } - - content = getJson(apiUrl); - if (content.length() == 0 || content.equals("[]")) { - break; - } - - FSDataOutputStream fin = fs - .create( - new Path(outFolder + "/" + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"), - true); - JSONArray jsonArray = (JSONArray) parser.parse(content); - for (Object aJsonArray : jsonArray) { - JSONObject jsonObjectRaw = (JSONObject) aJsonArray; - byte[] jsonObjectRawBytes = jsonObjectRaw.toJSONString().getBytes(); - fin.write(jsonObjectRawBytes); - fin.writeChar('\n'); - - writtenBytes += jsonObjectRawBytes.length + 1; - } - - fin.close(); - System.out - .println( - Thread.currentThread().getName() + " (Finished writing) Wrote " + writtenBytes - + " bytes. Filename: " + siteId + "_Piwiklog" + sdf.format((date)) + "_offset_" + i - + ".json"); - - i++; - } while (true); - - fs.close(); - } -} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java deleted file mode 100644 index 6d5bdfac0..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java +++ /dev/null @@ -1,1262 +0,0 @@ - -package eu.dnetlib.oa.graph.usagestats.export; - -import java.io.*; -import java.net.URLDecoder; -import java.sql.Connection; -import java.sql.SQLException; -import java.sql.Statement; -import java.text.SimpleDateFormat; -import java.util.*; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.LocatedFileStatus; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.fs.RemoteIterator; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -public class PiwikStatsDB { - - private String logPath; - private String logRepoPath; - private String logPortalPath; - - private Statement stmt = null; - - private static final Logger logger = LoggerFactory.getLogger(PiwikStatsDB.class); - - private String CounterRobotsURL; - private ArrayList robotsList; - - public PiwikStatsDB(String logRepoPath, String logPortalPath) throws Exception { - this.logRepoPath = logRepoPath; - this.logPortalPath = logPortalPath; - - } - - public void reCreateLogDirs() throws IllegalArgumentException, IOException { - FileSystem dfs = FileSystem.get(new Configuration()); - - logger.info("Deleting repoLog directory: " + ExecuteWorkflow.repoLogPath); - dfs.delete(new Path(ExecuteWorkflow.repoLogPath), true); - - logger.info("Deleting portalLog directory: " + ExecuteWorkflow.portalLogPath); - dfs.delete(new Path(ExecuteWorkflow.portalLogPath), true); - - logger.info("Creating repoLog directory: " + ExecuteWorkflow.repoLogPath); - dfs.mkdirs(new Path(ExecuteWorkflow.repoLogPath)); - - logger.info("Creating portalLog directory: " + ExecuteWorkflow.portalLogPath); - dfs.mkdirs(new Path(ExecuteWorkflow.portalLogPath)); - } - - public void recreateDBAndTables() throws Exception { - this.createDatabase(); - this.createTables(); - // The piwiklog table is not needed since it is built - // on top of JSON files - this.createTmpTables(); - } - - public ArrayList getRobotsList() { - return robotsList; - } - - public void setRobotsList(ArrayList robotsList) { - this.robotsList = robotsList; - } - - public String getCounterRobotsURL() { - return CounterRobotsURL; - } - - public void setCounterRobotsURL(String CounterRobotsURL) { - this.CounterRobotsURL = CounterRobotsURL; - } - - private void createDatabase() throws Exception { - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - logger.info("Dropping usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); - String dropDatabase = "DROP DATABASE IF EXISTS " + ConnectDB.getUsageStatsDBSchema() + " CASCADE"; - stmt.executeUpdate(dropDatabase); - } catch (Exception e) { - logger.error("Failed to drop database: " + e); - throw new Exception("Failed to drop database: " + e.toString(), e); - } - - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - logger.info("Creating usagestats DB: " + ConnectDB.getUsageStatsDBSchema()); - String createDatabase = "CREATE DATABASE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema(); - stmt.executeUpdate(createDatabase); - - } catch (Exception e) { - logger.error("Failed to create database: " + e); - throw new Exception("Failed to create database: " + e.toString(), e); - } - } - - private void createTables() throws Exception { - try { - stmt = ConnectDB.getHiveConnection().createStatement(); - - // Create Piwiklog table - This table should exist - String sqlCreateTablePiwikLog = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".piwiklog(source INT, id_visit STRING, country STRING, action STRING, url STRING, " - + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " - + "clustered by (source, id_visit, action, timestamp, entity_id) " - + "into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTablePiwikLog); - - ///////////////////////////////////////// - // Rule for duplicate inserts @ piwiklog - ///////////////////////////////////////// - - String sqlCreateTablePortalLog = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".process_portal_log(source INT, id_visit STRING, country STRING, action STRING, url STRING, " - + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " - + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTablePortalLog); - - ////////////////////////////////////////////////// - // Rule for duplicate inserts @ process_portal_log - ////////////////////////////////////////////////// - - stmt.close(); - ConnectDB.getHiveConnection().close(); - - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - } - } - - private void createTmpTables() throws Exception { - try { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - String sqlCreateTmpTablePiwikLog = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".piwiklogtmp(source INT, id_visit STRING, country STRING, action STRING, url STRING, entity_id STRING, " - + "source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " - + "clustered by (source, id_visit, action, timestamp, entity_id) into 100 buckets " - + "stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTmpTablePiwikLog); - - ////////////////////////////////////////////////// - // Rule for duplicate inserts @ piwiklogtmp - ////////////////////////////////////////////////// - - ////////////////////////////////////////////////// - // Copy from public.piwiklog to piwiklog - ////////////////////////////////////////////////// - // String sqlCopyPublicPiwiklog="insert into piwiklog select * from public.piwiklog;"; - // stmt.executeUpdate(sqlCopyPublicPiwiklog); - - String sqlCreateTmpTablePortalLog = "CREATE TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".process_portal_log_tmp(source INT, id_visit STRING, country STRING, action STRING, url STRING, " - + "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " - + "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(sqlCreateTmpTablePortalLog); - - ////////////////////////////////////////////////// - // Rule for duplicate inserts @ process_portal_log_tmp - ////////////////////////////////////////////////// - - stmt.close(); - - } catch (Exception e) { - logger.error("Failed to create tmptables: " + e); - throw new Exception("Failed to create tmp tables: " + e.toString(), e); - // System.exit(0); - } - } - - public void processLogs() throws Exception { - try { - ReadCounterRobotsList counterRobots = new ReadCounterRobotsList(this.getCounterRobotsURL()); - this.robotsList = counterRobots.getRobotsPatterns(); - - logger.info("Processing repository logs"); - processRepositoryLog(); - logger.info("Repository logs process done"); - - logger.info("Removing double clicks"); - removeDoubleClicks(); - logger.info("Removing double clicks done"); - - logger.info("Cleaning oai"); - cleanOAI(); - logger.info("Cleaning oai done"); - - logger.info("Processing portal logs"); - processPortalLog(); - logger.info("Portal logs process done"); - - logger.info("Processing portal usagestats"); - portalStats(); - logger.info("Portal usagestats process done"); - - logger.info("ViewsStats processing starts"); - viewsStats(); - logger.info("ViewsStats processing ends"); - - logger.info("DownloadsStats processing starts"); - downloadsStats(); - logger.info("DownloadsStats processing starts"); - - logger.info("Updating Production Tables"); - updateProdTables(); - logger.info("Updated Production Tables"); - - } catch (Exception e) { - logger.error("Failed to process logs: " + e); - throw new Exception("Failed to process logs: " + e.toString(), e); - } - } - - public void processRepositoryLog() throws Exception { - - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Adding JSON Serde jar"); - stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); - logger.info("Added JSON Serde jar"); - - logger.info("Dropping piwiklogtmp_json table"); - String drop_piwiklogtmp_json = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".piwiklogtmp_json"; - stmt.executeUpdate(drop_piwiklogtmp_json); - logger.info("Dropped piwiklogtmp_json table"); - - logger.info("Creating piwiklogtmp_json"); - String create_piwiklogtmp_json = "CREATE EXTERNAL TABLE IF NOT EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".piwiklogtmp_json(\n" + - " `idSite` STRING,\n" + - " `idVisit` STRING,\n" + - " `country` STRING,\n" + - " `referrerName` STRING,\n" + - " `browser` STRING,\n" + - " `actionDetails` ARRAY<\n" + - " struct<\n" + - " type: STRING,\n" + - " url: STRING,\n" + - " `customVariables`: struct<\n" + - " `1`: struct<\n" + - " `customVariablePageValue1`: STRING\n" + - " >\n" + - " >,\n" + - " timestamp: String\n" + - " >\n" + - " >\n" + - ")\n" + - "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + - "LOCATION '" + ExecuteWorkflow.repoLogPath + "'\n" + - "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(create_piwiklogtmp_json); - logger.info("Created piwiklogtmp_json"); - - logger.info("Dropping piwiklogtmp table"); - String drop_piwiklogtmp = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".piwiklogtmp"; - stmt.executeUpdate(drop_piwiklogtmp); - logger.info("Dropped piwiklogtmp"); - - logger.info("Creating piwiklogtmp"); - String create_piwiklogtmp = "CREATE TABLE " + - ConnectDB.getUsageStatsDBSchema() + - ".piwiklogtmp (source BIGINT, id_Visit STRING, country STRING, action STRING, url STRING, " + - "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + - "clustered by (source) into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(create_piwiklogtmp); - logger.info("Created piwiklogtmp"); - - logger.info("Inserting into piwiklogtmp"); - String insert_piwiklogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, " + - "actiondetail.type as action, actiondetail.url as url, " + - "actiondetail.customVariables.`1`.`customVariablePageValue1` as entity_id, " + - "'repItem' as source_item_type, from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, " + - "referrerName as referrer_name, browser as agent\n" + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp_json\n" + - "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; - stmt.executeUpdate(insert_piwiklogtmp); - logger.info("Inserted into piwiklogtmp"); - - stmt.close(); - } - - public void removeDoubleClicks() throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Cleaning download double clicks"); - // clean download double clicks - String sql = "DELETE from " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "WHERE EXISTS (\n" + - "SELECT DISTINCT p1.source, p1.id_visit, p1.action, p1.entity_id, p1.timestamp \n" + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p1, " + - ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp p2\n" + - "WHERE p1.source=p2.source AND p1.id_visit=p2.id_visit AND p1.entity_id=p2.entity_id \n" - + - "AND p1.action=p2.action AND p1.action='download' AND p1.timestamp!=p2.timestamp \n" + - "AND p1.timestamp\n" + - " >\n" + - ")\n" + - "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" + - "LOCATION '" + ExecuteWorkflow.portalLogPath + "'\n" + - "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(create_process_portal_log_tmp_json); - logger.info("Created process_portal_log_tmp_json"); - - logger.info("Droping process_portal_log_tmp table"); - String drop_process_portal_log_tmp = "DROP TABLE IF EXISTS " + - ConnectDB.getUsageStatsDBSchema() + - ".process_portal_log_tmp"; - stmt.executeUpdate(drop_process_portal_log_tmp); - logger.info("Dropped process_portal_log_tmp"); - - logger.info("Creating process_portal_log_tmp"); - String create_process_portal_log_tmp = "CREATE TABLE " + - ConnectDB.getUsageStatsDBSchema() + - ".process_portal_log_tmp (source BIGINT, id_visit STRING, country STRING, action STRING, url STRING, " + - "entity_id STRING, source_item_type STRING, timestamp STRING, referrer_name STRING, agent STRING) " + - "clustered by (source, id_visit, timestamp) into 100 buckets stored as orc tblproperties('transactional'='true')"; - stmt.executeUpdate(create_process_portal_log_tmp); - logger.info("Created process_portal_log_tmp"); - - logger.info("Inserting into process_portal_log_tmp"); - String insert_process_portal_log_tmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() - + ".process_portal_log_tmp " + - "SELECT DISTINCT cast(idSite as BIGINT) as source, idVisit as id_Visit, country, actiondetail.type as action, " - + - "actiondetail.url as url, " + - "CASE\n" + - " WHEN (actiondetail.url like '%datasourceId=%') THEN split(actiondetail.url,'datasourceId=')[1] " + - " WHEN (actiondetail.url like '%datasource=%') THEN split(actiondetail.url,'datasource=')[1] " + - " WHEN (actiondetail.url like '%datasourceFilter=%') THEN split(actiondetail.url,'datasourceFilter=')[1] " - + - " WHEN (actiondetail.url like '%articleId=%') THEN split(actiondetail.url,'articleId=')[1] " + - " WHEN (actiondetail.url like '%datasetId=%') THEN split(actiondetail.url,'datasetId=')[1] " + - " WHEN (actiondetail.url like '%projectId=%') THEN split(actiondetail.url,'projectId=')[1] " + - " WHEN (actiondetail.url like '%organizationId=%') THEN split(actiondetail.url,'organizationId=')[1] " + - " ELSE '' " + - "END AS entity_id, " + - "CASE " + - " WHEN (actiondetail.url like '%datasourceId=%') THEN 'datasource' " + - " WHEN (actiondetail.url like '%datasource=%') THEN 'datasource' " + - " WHEN (actiondetail.url like '%datasourceFilter=%') THEN 'datasource' " + - " WHEN (actiondetail.url like '%articleId=%') THEN 'result' " + - " WHEN (actiondetail.url like '%datasetId=%') THEN 'result' " + - " WHEN (actiondetail.url like '%projectId=%') THEN 'project' " + - " WHEN (actiondetail.url like '%organizationId=%') THEN 'organization' " + - " ELSE '' " + - "END AS source_item_type, " + - "from_unixtime(cast(actiondetail.timestamp as BIGINT)) as timestamp, referrerName as referrer_name, " + - "browser as agent " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp_json " + - "LATERAL VIEW explode(actiondetails) actiondetailsTable AS actiondetail"; - stmt.executeUpdate(insert_process_portal_log_tmp); - logger.info("Inserted into process_portal_log_tmp"); - - stmt.close(); - } - - public void portalStats() throws SQLException { - Connection con = ConnectDB.getHiveConnection(); - Statement stmt = con.createStatement(); - con.setAutoCommit(false); - -// Original queries where of the style -// -// SELECT DISTINCT source, id_visit, country, action, url, roid.oid, 'oaItem', `timestamp`, referrer_name, agent -// FROM usagestats_20200907.process_portal_log_tmp2, -// openaire_prod_stats_20200821.result_oids roid -// WHERE entity_id IS NOT null AND entity_id=roid.oid AND roid.oid IS NOT null -// -// The following query is an example of how queries should be -// -// -// INSERT INTO usagestats_20200907.piwiklogtmp -// SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent -// FROM usagestats_20200907.process_portal_log_tmp -// WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id -// IN (SELECT roid.oid FROM openaire_prod_stats_20200821.result_oids roid WHERE roid.oid IS NOT NULL); -// -// We should consider if we would like the queries to be as the following -// -// INSERT INTO usagestats_20200907.piwiklogtmp -// SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent -// FROM usagestats_20200907.process_portal_log_tmp -// WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id != '' AND process_portal_log_tmp.entity_id -// IN (SELECT roid.oid FROM openaire_prod_stats_20200821.result_oids roid WHERE roid.oid IS NOT NULL AND -// roid.oid != ''); - - logger.info("PortalStats - Step 1"); - String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'oaItem', `timestamp`, referrer_name, agent " - + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + - "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + - "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() - + ".result_oids roid WHERE roid.id IS NOT NULL)"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("PortalStats - Step 2"); - stmt = con.createStatement(); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'datasource', `timestamp`, referrer_name, agent " - + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + - "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + - "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() - + ".datasource_oids roid WHERE roid.id IS NOT NULL)"; - stmt.executeUpdate(sql); - stmt.close(); - - /* - * logger.info("PortalStats - Step 3"); stmt = con.createStatement(); sql = "INSERT INTO " + - * ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - * "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'organization', `timestamp`, referrer_name, agent " - * + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + - * "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + - * "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() + - * ".organization_oids roid WHERE roid.id IS NOT NULL)"; // stmt.executeUpdate(sql); stmt.close(); - */ - logger.info("PortalStats - Step 3"); - stmt = con.createStatement(); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SELECT DISTINCT source, id_visit, country, action, url, entity_id, 'project', `timestamp`, referrer_name, agent " - + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp " + - "WHERE process_portal_log_tmp.entity_id IS NOT NULL AND process_portal_log_tmp.entity_id " + - "IN (SELECT roid.id FROM " + ConnectDB.getStatsDBSchema() - + ".project_oids roid WHERE roid.id IS NOT NULL)"; - stmt.executeUpdate(sql); - stmt.close(); - - con.close(); - } - - private void cleanOAI() throws Exception { - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Cleaning oai - Step 1"); - stmt = ConnectDB.getHiveConnection().createStatement(); - String sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chlc.min-saude.pt/'," + - "'oai:repositorio.chlc.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.chlc.min-saude.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 2"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hospitaldebraga.pt/'," + - "'oai:repositorio.hospitaldebraga.pt:') WHERE entity_id LIKE 'oai:repositorio.hospitaldebraga.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 3"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipl.pt/'," + - "'oai:repositorio.ipl.pt:') WHERE entity_id LIKE 'oai:repositorio.ipl.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 4"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:bibliotecadigital.ipb.pt/'," + - "'oai:bibliotecadigital.ipb.pt:') WHERE entity_id LIKE 'oai:bibliotecadigital.ipb.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 5"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ismai.pt/'," + - "'oai:repositorio.ismai.pt:') WHERE entity_id LIKE 'oai:repositorio.ismai.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 6"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorioaberto.uab.pt/'," + - "'oai:repositorioaberto.uab.pt:') WHERE entity_id LIKE 'oai:repositorioaberto.uab.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 7"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.uac.pt/'," + - "'oai:repositorio.uac.pt:') WHERE entity_id LIKE 'oai:repositorio.uac.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 8"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.insa.pt/'," + - "'oai:repositorio.insa.pt:') WHERE entity_id LIKE 'oai:repositorio.insa.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 9"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipcb.pt/'," + - "'oai:repositorio.ipcb.pt:') WHERE entity_id LIKE 'oai:repositorio.ipcb.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 10"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ispa.pt/'," + - "'oai:repositorio.ispa.pt:') WHERE entity_id LIKE 'oai:repositorio.ispa.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 11"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.chporto.pt/'," + - "'oai:repositorio.chporto.pt:') WHERE entity_id LIKE 'oai:repositorio.chporto.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 12"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ucp.pt/'," + - "'oai:repositorio.ucp.pt:') WHERE entity_id LIKE 'oai:repositorio.ucp.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 13"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:rihuc.huc.min-saude.pt/'," + - "'oai:rihuc.huc.min-saude.pt:') WHERE entity_id LIKE 'oai:rihuc.huc.min-saude.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 14"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipv.pt/'," + - "'oai:repositorio.ipv.pt:') WHERE entity_id LIKE 'oai:repositorio.ipv.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 15"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:www.repository.utl.pt/'," + - "'oai:www.repository.utl.pt:') WHERE entity_id LIKE 'oai:www.repository.utl.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 16"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:run.unl.pt/'," + - "'oai:run.unl.pt:') WHERE entity_id LIKE 'oai:run.unl.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 17"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:sapientia.ualg.pt/'," + - "'oai:sapientia.ualg.pt:') WHERE entity_id LIKE 'oai:sapientia.ualg.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 18"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ipsantarem.pt/'," + - "'oai:repositorio.ipsantarem.pt:') WHERE entity_id LIKE 'oai:repositorio.ipsantarem.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 19"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:arca.igc.gulbenkian.pt/'," + - "'oai:arca.igc.gulbenkian.pt:') WHERE entity_id LIKE 'oai:arca.igc.gulbenkian.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 20"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:ubibliorum.ubi.pt/'," + - "'oai:ubibliorum.ubi.pt:') WHERE entity_id LIKE 'oai:ubibliorum.ubi.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 21"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:digituma.uma.pt/'," + - "'oai:digituma.uma.pt:') WHERE entity_id LIKE 'oai:digituma.uma.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 22"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.ul.pt/'," + - "'oai:repositorio.ul.pt:') WHERE entity_id LIKE 'oai:repositorio.ul.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 23"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.hff.min-saude.pt/'," + - "'oai:repositorio.hff.min-saude.pt:') WHERE entity_id LIKE 'oai:repositorio.hff.min-saude.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 24"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorium.sdum.uminho.pt/'," + - "'oai:repositorium.sdum.uminho.pt:') WHERE entity_id LIKE 'oai:repositorium.sdum.uminho.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 25"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:recipp.ipp.pt/'," + - "'oai:recipp.ipp.pt:') WHERE entity_id LIKE 'oai:recipp.ipp.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 26"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:bdigital.ufp.pt/'," + - "'oai:bdigital.ufp.pt:') WHERE entity_id LIKE 'oai:bdigital.ufp.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 27"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:repositorio.lneg.pt/'," + - "'oai:repositorio.lneg.pt:') WHERE entity_id LIKE 'oai:repositorio.lneg.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 28"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:iconline.ipleiria.pt/'," + - "'oai:iconline.ipleiria.pt:') WHERE entity_id LIKE 'oai:iconline.ipleiria.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Step 29"); - stmt = ConnectDB.getHiveConnection().createStatement(); - sql = "UPDATE " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp " + - "SET entity_id = regexp_replace(entity_id, '^oai:comum.rcaap.pt/'," + - "'oai:comum.rcaap.pt:') WHERE entity_id LIKE 'oai:comum.rcaap.pt/%'"; - stmt.executeUpdate(sql); - stmt.close(); - - logger.info("Cleaning oai - Done, closing connection"); - ConnectDB.getHiveConnection().close(); - } - - private String processPortalURL(String url) { - - if (url.indexOf("explore.openaire.eu") > 0) { - try { - url = URLDecoder.decode(url, "UTF-8"); - } catch (Exception e) { - logger.info("Error when decoding the following URL: " + url); - } - if (url.indexOf("datasourceId=") > 0 && url.substring(url.indexOf("datasourceId=") + 13).length() >= 46) { - url = "datasource|" - + url.substring(url.indexOf("datasourceId=") + 13, url.indexOf("datasourceId=") + 59); - } else if (url.indexOf("datasource=") > 0 - && url.substring(url.indexOf("datasource=") + 11).length() >= 46) { - url = "datasource|" + url.substring(url.indexOf("datasource=") + 11, url.indexOf("datasource=") + 57); - } else if (url.indexOf("datasourceFilter=") > 0 - && url.substring(url.indexOf("datasourceFilter=") + 17).length() >= 46) { - url = "datasource|" - + url.substring(url.indexOf("datasourceFilter=") + 17, url.indexOf("datasourceFilter=") + 63); - } else if (url.indexOf("articleId=") > 0 && url.substring(url.indexOf("articleId=") + 10).length() >= 46) { - url = "result|" + url.substring(url.indexOf("articleId=") + 10, url.indexOf("articleId=") + 56); - } else if (url.indexOf("datasetId=") > 0 && url.substring(url.indexOf("datasetId=") + 10).length() >= 46) { - url = "result|" + url.substring(url.indexOf("datasetId=") + 10, url.indexOf("datasetId=") + 56); - } else if (url.indexOf("projectId=") > 0 && url.substring(url.indexOf("projectId=") + 10).length() >= 46 - && !url.contains("oai:dnet:corda")) { - url = "project|" + url.substring(url.indexOf("projectId=") + 10, url.indexOf("projectId=") + 56); - } else if (url.indexOf("organizationId=") > 0 - && url.substring(url.indexOf("organizationId=") + 15).length() >= 46) { - url = "organization|" - + url.substring(url.indexOf("organizationId=") + 15, url.indexOf("organizationId=") + 61); - } else { - url = ""; - } - } else { - url = ""; - } - - return url; - } - - private void updateProdTables() throws SQLException { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Inserting data to piwiklog"); - String sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".piwiklog " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".piwiklogtmp"; - stmt.executeUpdate(sql); - - logger.info("Inserting data to views_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".views_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp"; - stmt.executeUpdate(sql); - - logger.info("Inserting data to downloads_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp"; - stmt.executeUpdate(sql); - - logger.info("Inserting data to pageviews_stats"); - sql = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats " + - "SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats_tmp"; - stmt.executeUpdate(sql); - - logger.info("Creating usage_stats table"); - String createUsageStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats " + - "AS SELECT coalesce(ds.source, vs.source) as source, " + - "coalesce(ds.repository_id, vs.repository_id) as repository_id, " + - "coalesce(ds.result_id, vs.result_id) as result_id, coalesce(ds.date, vs.date) as date, " + - "coalesce(ds.count, 0) as downloads, coalesce(vs.count, 0) as views, " + - "coalesce(ds.openaire, 0) as openaire_downloads, " + - "coalesce(vs.openaire, 0) as openaire_views " + - "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats AS ds FULL OUTER JOIN " + - ConnectDB.getUsageStatsDBSchema() + ".views_stats AS vs ON ds.source=vs.source " + - "AND ds.repository_id=vs.repository_id AND ds.result_id=vs.result_id AND ds.date=vs.date"; - stmt.executeUpdate(createUsageStats); - logger.info("Created usage_stats table"); - - - /* - * logger.info("Dropping table views_stats_tmp"); sql = "DROP TABLE IF EXISTS " + - * ConnectDB.getUsageStatsDBSchema() + ".views_stats_tmp"; stmt.executeUpdate(sql); - * logger.info("Dropping table downloads_stats_tmp"); sql = "DROP TABLE IF EXISTS " + - * ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_tmp"; stmt.executeUpdate(sql); - * logger.info("Dropping table pageviews_stats_tmp"); sql = "DROP TABLE IF EXISTS " + - * ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats_tmp"; stmt.executeUpdate(sql); - * logger.info("Dropping table process_portal_log_tmp"); sql = "DROP TABLE IF EXISTS " + - * ConnectDB.getUsageStatsDBSchema() + ".process_portal_log_tmp"; stmt.executeUpdate(sql); - */ - stmt.close(); - ConnectDB.getHiveConnection().close(); - - } - - private ArrayList listHdfsDir(String dir) throws Exception { - - FileSystem hdfs = FileSystem.get(new Configuration()); - RemoteIterator Files; - ArrayList fileNames = new ArrayList<>(); - - try { - Path exportPath = new Path(hdfs.getUri() + dir); - Files = hdfs.listFiles(exportPath, false); - while (Files.hasNext()) { - String fileName = Files.next().getPath().toString(); - fileNames.add(fileName); - } - - hdfs.close(); - } catch (Exception e) { - logger.error("HDFS file path with exported data does not exist : " + new Path(hdfs.getUri() + logPath)); - throw new Exception("HDFS file path with exported data does not exist : " + logPath, e); - } - - return fileNames; - } - - private String readHDFSFile(String filename) throws Exception { - String result; - try { - - FileSystem fs = FileSystem.get(new Configuration()); - // log.info("reading file : " + filename); - - BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(new Path(filename)))); - - StringBuilder sb = new StringBuilder(); - String line = br.readLine(); - - while (line != null) { - if (!line.equals("[]")) { - sb.append(line); - } - // sb.append(line); - line = br.readLine(); - } - result = sb.toString().replace("][{\"idSite\"", ",{\"idSite\""); - if (result.equals("")) { - result = "[]"; - } - - // fs.close(); - } catch (Exception e) { - logger.error(e.getMessage()); - throw new Exception(e); - } - - return result; - } - - private Connection getConnection() throws SQLException { - return ConnectDB.getHiveConnection(); - } -} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ReadCounterRobotsList.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ReadCounterRobotsList.java deleted file mode 100644 index 1708a1c64..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ReadCounterRobotsList.java +++ /dev/null @@ -1,54 +0,0 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ - -package eu.dnetlib.oa.graph.usagestats.export; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -/** - * @author D. Pierrakos, S. Zoupanos - */ -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.net.MalformedURLException; -import java.net.URL; -import java.nio.charset.Charset; -import java.util.ArrayList; - -import org.json.JSONException; -import org.json.simple.JSONArray; -import org.json.simple.parser.JSONParser; -import org.json.simple.parser.ParseException; - -public class ReadCounterRobotsList { - - private ArrayList robotsPatterns = new ArrayList(); - private String COUNTER_ROBOTS_URL; - - public ReadCounterRobotsList(String url) throws IOException, JSONException, ParseException { - COUNTER_ROBOTS_URL = url; - robotsPatterns = readRobotsPartners(COUNTER_ROBOTS_URL); - } - - private ArrayList readRobotsPartners(String url) throws MalformedURLException, IOException, ParseException { - InputStream is = new URL(url).openStream(); - JSONParser parser = new JSONParser(); - BufferedReader reader = new BufferedReader(new InputStreamReader(is, Charset.forName("ISO-8859-1"))); - JSONArray jsonArray = (JSONArray) parser.parse(reader); - for (Object aJsonArray : jsonArray) { - org.json.simple.JSONObject jsonObjectRow = (org.json.simple.JSONObject) aJsonArray; - robotsPatterns.add(jsonObjectRow.get("pattern").toString().replace("\\", "\\\\")); - } - return robotsPatterns; - } - - public ArrayList getRobotsPatterns() { - return robotsPatterns; - } -} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java deleted file mode 100644 index 06e350c9e..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java +++ /dev/null @@ -1,575 +0,0 @@ -package eu.dnetlib.oa.graph.usagestats.export; - -import java.io.*; -// import java.io.BufferedReader; -// import java.io.InputStreamReader; -import java.net.URL; -import java.net.URLConnection; -import java.sql.PreparedStatement; -import java.sql.ResultSet; -import java.sql.SQLException; -import java.sql.Statement; -import java.text.SimpleDateFormat; -import java.util.ArrayList; -import java.util.Calendar; -import java.util.Date; -import java.util.HashSet; -import java.util.List; -import java.util.Set; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.json.simple.JSONArray; -import org.json.simple.JSONObject; -import org.json.simple.parser.JSONParser; -import org.json.simple.parser.ParseException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * @author D. Pierrakos, S. Zoupanos - */ -public class SarcStats { - - private Statement stmtHive = null; - private Statement stmtImpala = null; - - private static final Logger logger = LoggerFactory.getLogger(SarcStats.class); - - public SarcStats() throws Exception { -// createTables(); - } - - private void createTables() throws Exception { - try { - - stmtHive = ConnectDB.getHiveConnection().createStatement(); - String sqlCreateTableSushiLog = "CREATE TABLE IF NOT EXISTS sushilog(source TEXT, repository TEXT, rid TEXT, date TEXT, metric_type TEXT, count INT, PRIMARY KEY(source, repository, rid, date, metric_type));"; - stmtHive.executeUpdate(sqlCreateTableSushiLog); - - // String sqlCopyPublicSushiLog="INSERT INTO sushilog SELECT * FROM public.sushilog;"; - // stmt.executeUpdate(sqlCopyPublicSushiLog); - String sqlcreateRuleSushiLog = "CREATE OR REPLACE RULE ignore_duplicate_inserts AS " - + " ON INSERT TO sushilog " - + " WHERE (EXISTS ( SELECT sushilog.source, sushilog.repository," - + "sushilog.rid, sushilog.date " - + "FROM sushilog " - + "WHERE sushilog.source = new.source AND sushilog.repository = new.repository AND sushilog.rid = new.rid AND sushilog.date = new.date AND sushilog.metric_type = new.metric_type)) DO INSTEAD NOTHING;"; - stmtHive.executeUpdate(sqlcreateRuleSushiLog); - String createSushiIndex = "create index if not exists sushilog_duplicates on sushilog(source, repository, rid, date, metric_type);"; - stmtHive.executeUpdate(createSushiIndex); - - stmtHive.close(); - ConnectDB.getHiveConnection().close(); - logger.info("Sushi Tables Created"); - } catch (Exception e) { - logger.error("Failed to create tables: " + e); - throw new Exception("Failed to create tables: " + e.toString(), e); - } - } - - public void reCreateLogDirs() throws IOException { - FileSystem dfs = FileSystem.get(new Configuration()); - - logger.info("Deleting sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); - dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathArray), true); - - logger.info("Deleting sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); - dfs.delete(new Path(ExecuteWorkflow.sarcsReportPathNonArray), true); - - logger.info("Creating sarcsReport (Array) directory: " + ExecuteWorkflow.sarcsReportPathArray); - dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathArray)); - - logger.info("Creating sarcsReport (NonArray) directory: " + ExecuteWorkflow.sarcsReportPathNonArray); - dfs.mkdirs(new Path(ExecuteWorkflow.sarcsReportPathNonArray)); - } - - public void processSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Adding JSON Serde jar"); - stmt.executeUpdate("add jar /usr/share/cmf/common_jars/hive-hcatalog-core-1.1.0-cdh5.14.0.jar"); - logger.info("Added JSON Serde jar"); - - logger.info("Dropping sarc_sushilogtmp_json_array table"); - String drop_sarc_sushilogtmp_json_array = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array"; - stmt.executeUpdate(drop_sarc_sushilogtmp_json_array); - logger.info("Dropped sarc_sushilogtmp_json_array table"); - - logger.info("Creating sarc_sushilogtmp_json_array table"); - String create_sarc_sushilogtmp_json_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array(\n" - + " `ItemIdentifier` ARRAY<\n" - + " struct<\n" - + " `Type`: STRING,\n" - + " `Value`: STRING\n" - + " >\n" - + " >,\n" - + " `ItemPerformance` struct<\n" - + " `Period`: struct<\n" - + " `Begin`: STRING,\n" - + " `End`: STRING\n" - + " >,\n" - + " `Instance`: struct<\n" - + " `Count`: STRING,\n" - + " `MetricType`: STRING\n" - + " >\n" - + " >\n" - + ")" - + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" - + "LOCATION '" + sarcsReportPathArray + "/'\n" - + "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(create_sarc_sushilogtmp_json_array); - logger.info("Created sarc_sushilogtmp_json_array table"); - - logger.info("Dropping sarc_sushilogtmp_json_non_array table"); - String drop_sarc_sushilogtmp_json_non_array = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp_json_non_array"; - stmt.executeUpdate(drop_sarc_sushilogtmp_json_non_array); - logger.info("Dropped sarc_sushilogtmp_json_non_array table"); - - logger.info("Creating sarc_sushilogtmp_json_non_array table"); - String create_sarc_sushilogtmp_json_non_array = "CREATE EXTERNAL TABLE IF NOT EXISTS " - + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array (\n" - + " `ItemIdentifier` struct<\n" - + " `Type`: STRING,\n" - + " `Value`: STRING\n" - + " >,\n" - + " `ItemPerformance` struct<\n" - + " `Period`: struct<\n" - + " `Begin`: STRING,\n" - + " `End`: STRING\n" - + " >,\n" - + " `Instance`: struct<\n" - + " `Count`: STRING,\n" - + " `MetricType`: STRING\n" - + " >\n" - + " >" - + ")" - + "ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'\n" - + "LOCATION '" + sarcsReportPathNonArray + "/'\n" - + "TBLPROPERTIES (\"transactional\"=\"false\")"; - stmt.executeUpdate(create_sarc_sushilogtmp_json_non_array); - logger.info("Created sarc_sushilogtmp_json_non_array table"); - - logger.info("Creating sarc_sushilogtmp table"); - String create_sarc_sushilogtmp = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp(source STRING, repository STRING, " - + "rid STRING, date STRING, metric_type STRING, count INT) clustered by (source) into 100 buckets stored as orc " - + "tblproperties('transactional'='true')"; - stmt.executeUpdate(create_sarc_sushilogtmp); - logger.info("Created sarc_sushilogtmp table"); - - logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); - String insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " - + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " - + " `ItemIdent`.`Value`, `ItemPerformance`.`Period`.`Begin`, " - + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_array " - + "LATERAL VIEW posexplode(ItemIdentifier) ItemIdentifierTable AS seqi, ItemIdent " - + "WHERE `ItemIdent`.`Type`='DOI'"; - stmt.executeUpdate(insert_sarc_sushilogtmp); - logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_array)"); - - logger.info("Inserting to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); - insert_sarc_sushilogtmp = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp " - + "SELECT 'SARC-OJS', split(split(INPUT__FILE__NAME,'SarcsARReport_')[1],'_')[0], " - + "`ItemIdentifier`.`Value`, `ItemPerformance`.`Period`.`Begin`, " - + "`ItemPerformance`.`Instance`.`MetricType`, `ItemPerformance`.`Instance`.`Count` " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_json_non_array"; - stmt.executeUpdate(insert_sarc_sushilogtmp); - logger.info("Inserted to sarc_sushilogtmp table (sarc_sushilogtmp_json_non_array)"); - - ConnectDB.getHiveConnection().close(); - } - - public void getAndProcessSarc(String sarcsReportPathArray, String sarcsReportPathNonArray) throws Exception { - - Statement stmt = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - - logger.info("Creating sushilog table"); - String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog " - + "(`source` string, " - + "`repository` string, " - + "`rid` string, " - + "`date` string, " - + "`metric_type` string, " - + "`count` int)"; - stmt.executeUpdate(createSushilog); - logger.info("Created sushilog table"); - - logger.info("Dropping sarc_sushilogtmp table"); - String drop_sarc_sushilogtmp = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp"; - stmt.executeUpdate(drop_sarc_sushilogtmp); - logger.info("Dropped sarc_sushilogtmp table"); - ConnectDB.getHiveConnection().close(); - - List issnAndUrls = new ArrayList(); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/motricidade/sushiLite/v1_7/", "1646-107X" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/antropologicas/sushiLite/v1_7/", "0873-819X" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/interaccoes/sushiLite/v1_7/", "1646-2335" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/cct/sushiLite/v1_7/", "2182-3030" - }); - issnAndUrls.add(new String[]{ - "https://actapediatrica.spp.pt/sushiLite/v1_7/", "0873-9781" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/sociologiapp/sushiLite/v1_7/", "0873-6529" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/finisterra/sushiLite/v1_7/", "0430-5027" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/sisyphus/sushiLite/v1_7/", "2182-8474" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/anestesiologia/sushiLite/v1_7/", "0871-6099" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/rpe/sushiLite/v1_7/", "0871-9187" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/psilogos/sushiLite/v1_7/", "1646-091X" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/juridica/sushiLite/v1_7/", "2183-5799" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/ecr/sushiLite/v1_7/", "1647-2098" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/nascercrescer/sushiLite/v1_7/", "0872-0754" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/cea/sushiLite/v1_7/", "1645-3794" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/proelium/sushiLite/v1_7/", "1645-8826" - }); - issnAndUrls.add(new String[]{ - "https://revistas.rcaap.pt/millenium/sushiLite/v1_7/", "0873-3015" - }); - - if (ExecuteWorkflow.sarcNumberOfIssnToDownload > 0 - && ExecuteWorkflow.sarcNumberOfIssnToDownload <= issnAndUrls.size()) { - logger.info("Trimming siteIds list to the size of: " + ExecuteWorkflow.sarcNumberOfIssnToDownload); - issnAndUrls = issnAndUrls.subList(0, ExecuteWorkflow.sarcNumberOfIssnToDownload); - } - - logger.info("(getAndProcessSarc) Downloading the followins opendoars: " + issnAndUrls); - - for (String[] issnAndUrl : issnAndUrls) { - logger.info("Now working on ISSN: " + issnAndUrl[1]); - getARReport(sarcsReportPathArray, sarcsReportPathNonArray, issnAndUrl[0], issnAndUrl[1]); - } - - } - - public void finalizeSarcStats() throws Exception { - stmtHive = ConnectDB.getHiveConnection().createStatement(); - ConnectDB.getHiveConnection().setAutoCommit(false); - stmtImpala = ConnectDB.getImpalaConnection().createStatement(); - - logger.info("Creating downloads_stats table_tmp"); - String createDownloadsStats = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_tmp " - + "(`source` string, " - + "`repository_id` string, " - + "`result_id` string, " - + "`date` string, " - + "`count` bigint, " - + "`openaire` bigint)"; - stmtHive.executeUpdate(createDownloadsStats); - logger.info("Created downloads_stats_tmp table"); - - logger.info("Dropping sarc_sushilogtmp_impala table"); - String drop_sarc_sushilogtmp_impala = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp_impala"; - stmtHive.executeUpdate(drop_sarc_sushilogtmp_impala); - logger.info("Dropped sarc_sushilogtmp_impala table"); - - logger.info("Creating sarc_sushilogtmp_impala, a table readable by impala"); - String createSarcSushilogtmpImpala = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp_impala " - + "STORED AS PARQUET AS SELECT * FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; - stmtHive.executeUpdate(createSarcSushilogtmpImpala); - logger.info("Created sarc_sushilogtmp_impala"); - - logger.info("Making sarc_sushilogtmp visible to impala"); - String invalidateMetadata = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() - + ".sarc_sushilogtmp_impala;"; - stmtImpala.executeUpdate(invalidateMetadata); - - logger.info("Dropping downloads_stats_impala table"); - String drop_downloads_stats_impala = "DROP TABLE IF EXISTS " - + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_impala"; - stmtHive.executeUpdate(drop_downloads_stats_impala); - logger.info("Dropped downloads_stats_impala table"); - - logger.info("Making downloads_stats_impala deletion visible to impala"); - try { - String invalidateMetadataDownloadsStatsImpala = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_impala;"; - stmtImpala.executeUpdate(invalidateMetadataDownloadsStatsImpala); - } catch (SQLException sqle) { - } - - // We run the following query in Impala because it is faster - logger.info("Creating downloads_stats_impala"); - String createDownloadsStatsImpala = "CREATE TABLE " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_impala AS " - + "SELECT s.source, d.id AS repository_id, " - + "ro.id as result_id, CONCAT(CAST(YEAR(`date`) AS STRING), '/', " - + "LPAD(CAST(MONTH(`date`) AS STRING), 2, '0')) AS `date`, s.count, '0' " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp_impala s, " - + ConnectDB.getStatsDBSchema() + ".datasource_oids d, " - + ConnectDB.getStatsDBSchema() + ".result_pids ro " - + "WHERE d.oid LIKE CONCAT('%', s.repository, '%') AND d.id like CONCAT('%', 'sarcservicod', '%') " - + "AND s.rid=ro.pid AND ro.type='Digital Object Identifier' AND s.metric_type='ft_total' AND s.source='SARC-OJS'"; - stmtImpala.executeUpdate(createDownloadsStatsImpala); - logger.info("Creating downloads_stats_impala"); - - // Insert into downloads_stats - logger.info("Inserting data from downloads_stats_impala into downloads_stats_tmp"); - String insertDStats = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() - + ".downloads_stats_tmp SELECT * " - + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats_impala"; - stmtHive.executeUpdate(insertDStats); - logger.info("Inserted into downloads_stats_tmp"); - - logger.info("Creating sushilog table"); - String createSushilog = "CREATE TABLE IF NOT EXISTS " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog " - + "(`source` string, " - + "`repository_id` string, " - + "`rid` string, " - + "`date` string, " - + "`metric_type` string, " - + "`count` int)"; - stmtHive.executeUpdate(createSushilog); - logger.info("Created sushilog table"); - - // Insert into sushilog - logger.info("Inserting into sushilog"); - String insertSushiLog = "INSERT INTO " + ConnectDB.getUsageStatsDBSchema() - + ".sushilog SELECT * " + "FROM " + ConnectDB.getUsageStatsDBSchema() + ".sarc_sushilogtmp"; - stmtHive.executeUpdate(insertSushiLog); - logger.info("Inserted into sushilog"); - - stmtHive.close(); - ConnectDB.getHiveConnection().close(); - } - - public void getARReport(String sarcsReportPathArray, String sarcsReportPathNonArray, - String url, String issn) throws Exception { - logger.info("Processing SARC! issn: " + issn + " with url: " + url); - ConnectDB.getHiveConnection().setAutoCommit(false); - - SimpleDateFormat simpleDateFormat = new SimpleDateFormat("YYYY-MM"); - // Setting the starting period - Calendar start = (Calendar) ExecuteWorkflow.startingLogPeriod.clone(); - logger.info("(getARReport) Starting period for log download: " + simpleDateFormat.format(start.getTime())); - - // Setting the ending period (last day of the month) - Calendar end = (Calendar) ExecuteWorkflow.endingLogPeriod.clone(); - end.add(Calendar.MONTH, +1); - end.add(Calendar.DAY_OF_MONTH, -1); - logger.info("(getARReport) Ending period for log download: " + simpleDateFormat.format(end.getTime())); - - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - PreparedStatement st = ConnectDB - .getHiveConnection() - .prepareStatement( - "SELECT max(date) FROM " + ConnectDB.getUsageStatsDBSchema() + ".sushilog WHERE repository=?"); - st.setString(1, issn); - ResultSet rs_date = st.executeQuery(); - Date dateMax = null; - while (rs_date.next()) { - if (rs_date.getString(1) != null && !rs_date.getString(1).equals("null") - && !rs_date.getString(1).equals("")) { - start.setTime(sdf.parse(rs_date.getString(1))); - dateMax = sdf.parse(rs_date.getString(1)); - } - } - rs_date.close(); - - // Creating the needed configuration for the correct storing of data - Configuration config = new Configuration(); - config.addResource(new Path("/etc/hadoop/conf/core-site.xml")); - config.addResource(new Path("/etc/hadoop/conf/hdfs-site.xml")); - config - .set( - "fs.hdfs.impl", - org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); - config - .set( - "fs.file.impl", - org.apache.hadoop.fs.LocalFileSystem.class.getName()); - FileSystem dfs = FileSystem.get(config); - - if (dateMax != null && start.getTime().compareTo(dateMax) <= 0) { - logger.info("Date found in logs " + dateMax + " and not downloanding logs for " + issn); - } else { - - while (start.before(end)) { - String reportUrl = url + "GetReport/?Report=AR1&Format=json&BeginDate=" - + simpleDateFormat.format(start.getTime()) + "&EndDate=" + simpleDateFormat.format(start.getTime()); - start.add(Calendar.MONTH, 1); - - logger.info("(getARReport) Getting report: " + reportUrl); - String text = getJson(reportUrl); - if (text == null) { - continue; - } - - JSONParser parser = new JSONParser(); - JSONObject jsonObject = null; - try { - jsonObject = (JSONObject) parser.parse(text); - } // if there is a parsing error continue with the next url - catch (ParseException pe) { - continue; - } - - jsonObject = (JSONObject) jsonObject.get("sc:ReportResponse"); - jsonObject = (JSONObject) jsonObject.get("sc:Report"); - if (jsonObject == null) { - continue; - } - jsonObject = (JSONObject) jsonObject.get("c:Report"); - jsonObject = (JSONObject) jsonObject.get("c:Customer"); - Object obj = jsonObject.get("c:ReportItems"); - JSONArray jsonArray = new JSONArray(); - if (obj instanceof JSONObject) { - jsonArray.add(obj); - } else { - jsonArray = (JSONArray) obj; - // jsonArray = (JSONArray) jsonObject.get("c:ReportItems"); - } - if (jsonArray == null) { - continue; - } - - // Creating the file in the filesystem for the ItemIdentifier as array object - String filePathArray = sarcsReportPathArray + "/SarcsARReport_" + issn + "_" - + simpleDateFormat.format(start.getTime()) + ".json"; - logger.info("Storing to file: " + filePathArray); - FSDataOutputStream finArray = dfs.create(new Path(filePathArray), true); - - // Creating the file in the filesystem for the ItemIdentifier as array object - String filePathNonArray = sarcsReportPathNonArray + "/SarcsARReport_" + issn + "_" - + simpleDateFormat.format(start.getTime()) + ".json"; - logger.info("Storing to file: " + filePathNonArray); - FSDataOutputStream finNonArray = dfs.create(new Path(filePathNonArray), true); - - for (Object aJsonArray : jsonArray) { - - JSONObject jsonObjectRow = (JSONObject) aJsonArray; - renameKeysRecursively(":", jsonObjectRow); - - if (jsonObjectRow.get("ItemIdentifier") instanceof JSONObject) { - finNonArray.write(jsonObjectRow.toJSONString().getBytes()); - finNonArray.writeChar('\n'); - } else { - finArray.write(jsonObjectRow.toJSONString().getBytes()); - finArray.writeChar('\n'); - } - } - - finArray.close(); - finNonArray.close(); - - // Check the file size and if it is too big, delete it - File fileArray = new File(filePathArray); - if (fileArray.length() == 0) - fileArray.delete(); - File fileNonArray = new File(filePathNonArray); - if (fileNonArray.length() == 0) - fileNonArray.delete(); - - } - - dfs.close(); - } - //ConnectDB.getHiveConnection().close(); - } - - private void renameKeysRecursively(String delimiter, JSONArray givenJsonObj) throws Exception { - for (Object jjval : givenJsonObj) { - if (jjval instanceof JSONArray) { - renameKeysRecursively(delimiter, (JSONArray) jjval); - } else if (jjval instanceof JSONObject) { - renameKeysRecursively(delimiter, (JSONObject) jjval); - } // All other types of vals - else - ; - } - } - - private void renameKeysRecursively(String delimiter, JSONObject givenJsonObj) throws Exception { - Set jkeys = new HashSet(givenJsonObj.keySet()); - for (String jkey : jkeys) { - - String[] splitArray = jkey.split(delimiter); - String newJkey = splitArray[splitArray.length - 1]; - - Object jval = givenJsonObj.get(jkey); - givenJsonObj.remove(jkey); - givenJsonObj.put(newJkey, jval); - - if (jval instanceof JSONObject) { - renameKeysRecursively(delimiter, (JSONObject) jval); - } - - if (jval instanceof JSONArray) { - renameKeysRecursively(delimiter, (JSONArray) jval); - } - } - } - - private String getJson(String url) throws Exception { - // String cred=username+":"+password; - // String encoded = new sun.misc.BASE64Encoder().encode (cred.getBytes()); - try { - URL website = new URL(url); - URLConnection connection = website.openConnection(); - // connection.setRequestProperty ("Authorization", "Basic "+encoded); - StringBuilder response; - try (BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()))) { - response = new StringBuilder(); - String inputLine; - while ((inputLine = in.readLine()) != null) { - response.append(inputLine); - response.append("\n"); - } - } - return response.toString(); - } catch (Exception e) { - - // Logging error and silently continuing - logger.error("Failed to get URL: " + e); - System.out.println("Failed to get URL: " + e); -// return null; -// throw new Exception("Failed to get URL: " + e.toString(), e); - } - return ""; - } -} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java b/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java deleted file mode 100644 index 405b58bd5..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java +++ /dev/null @@ -1,179 +0,0 @@ - -package eu.dnetlib.oa.graph.usagestats.export; - -import java.io.IOException; -import java.sql.SQLException; -import java.sql.Statement; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * Main class for downloading and processing Usage statistics - * - * @author D. Pierrakos, S. Zoupanos - */ -public class UsageStatsExporter { - - public UsageStatsExporter() { - - } - - private static final Logger logger = LoggerFactory.getLogger(UsageStatsExporter.class); - - private void reCreateLogDirs() throws IllegalArgumentException, IOException { - FileSystem dfs = FileSystem.get(new Configuration()); - - logger.info("Deleting repoLog directory: " + ExecuteWorkflow.repoLogPath); - dfs.delete(new Path(ExecuteWorkflow.repoLogPath), true); - - logger.info("Deleting portalLog directory: " + ExecuteWorkflow.portalLogPath); - dfs.delete(new Path(ExecuteWorkflow.portalLogPath), true); - - logger.info("Deleting lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); - dfs.delete(new Path(ExecuteWorkflow.lareferenciaLogPath), true); - - logger.info("Creating repoLog directory: " + ExecuteWorkflow.repoLogPath); - dfs.mkdirs(new Path(ExecuteWorkflow.repoLogPath)); - - logger.info("Creating portalLog directory: " + ExecuteWorkflow.portalLogPath); - dfs.mkdirs(new Path(ExecuteWorkflow.portalLogPath)); - - logger.info("Creating lareferenciaLog directory: " + ExecuteWorkflow.lareferenciaLogPath); - dfs.mkdirs(new Path(ExecuteWorkflow.lareferenciaLogPath)); - } - - public void export() throws Exception { - - logger.info("Initialising DB properties"); - ConnectDB.init(); - -// runImpalaQuery(); - - PiwikStatsDB piwikstatsdb = new PiwikStatsDB(ExecuteWorkflow.repoLogPath, ExecuteWorkflow.portalLogPath); - - logger.info("Re-creating database and tables"); - if (ExecuteWorkflow.recreateDbAndTables) - piwikstatsdb.recreateDBAndTables(); - ; - - logger.info("Initializing the download logs module"); - PiwikDownloadLogs piwd = new PiwikDownloadLogs(ExecuteWorkflow.matomoBaseURL, ExecuteWorkflow.matomoAuthToken); - - if (ExecuteWorkflow.piwikEmptyDirs) { - logger.info("Recreating Piwik log directories"); - piwikstatsdb.reCreateLogDirs(); - } - - // Downloading piwik logs (also managing directory creation) - if (ExecuteWorkflow.downloadPiwikLogs) { - logger.info("Downloading piwik logs"); - piwd - .GetOpenAIRELogs( - ExecuteWorkflow.repoLogPath, - ExecuteWorkflow.portalLogPath, ExecuteWorkflow.portalMatomoID); - } - logger.info("Downloaded piwik logs"); - - // Create DB tables, insert/update statistics - String cRobotsUrl = "https://raw.githubusercontent.com/atmire/COUNTER-Robots/master/COUNTER_Robots_list.json"; - piwikstatsdb.setCounterRobotsURL(cRobotsUrl); - - if (ExecuteWorkflow.processPiwikLogs) { - logger.info("Processing logs"); - piwikstatsdb.processLogs(); - } - - logger.info("Creating LaReferencia tables"); - LaReferenciaDownloadLogs lrf = new LaReferenciaDownloadLogs(ExecuteWorkflow.lareferenciaBaseURL, - ExecuteWorkflow.lareferenciaAuthToken); - - if (ExecuteWorkflow.laReferenciaEmptyDirs) { - logger.info("Recreating LaReferencia log directories"); - lrf.reCreateLogDirs(); - } - - if (ExecuteWorkflow.downloadLaReferenciaLogs) { - logger.info("Downloading LaReferencia logs"); - lrf.GetLaReferenciaRepos(ExecuteWorkflow.lareferenciaLogPath); - logger.info("Downloaded LaReferencia logs"); - } - LaReferenciaStats lastats = new LaReferenciaStats(ExecuteWorkflow.lareferenciaLogPath); - - if (ExecuteWorkflow.processLaReferenciaLogs) { - logger.info("Processing LaReferencia logs"); - lastats.processLogs(); - logger.info("LaReferencia logs done"); - } - - IrusStats irusstats = new IrusStats(ExecuteWorkflow.irusUKBaseURL); - if (ExecuteWorkflow.irusCreateTablesEmptyDirs) { - logger.info("Creating Irus Stats tables"); - irusstats.createTables(); - logger.info("Created Irus Stats tables"); - - logger.info("Re-create log dirs"); - irusstats.reCreateLogDirs(); - logger.info("Re-created log dirs"); - } - - if (ExecuteWorkflow.irusDownloadReports) { - irusstats.getIrusRRReport(ExecuteWorkflow.irusUKReportPath); - } - if (ExecuteWorkflow.irusProcessStats) { - irusstats.processIrusStats(); - logger.info("Irus done"); - } - - SarcStats sarcStats = new SarcStats(); - if (ExecuteWorkflow.sarcCreateTablesEmptyDirs) { - sarcStats.reCreateLogDirs(); - } - if (ExecuteWorkflow.sarcDownloadReports) { - sarcStats.getAndProcessSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); - } - if (ExecuteWorkflow.sarcProcessStats) { - sarcStats.processSarc(ExecuteWorkflow.sarcsReportPathArray, ExecuteWorkflow.sarcsReportPathNonArray); - sarcStats.finalizeSarcStats(); - } - logger.info("Sarc done"); - - // finalize usagestats - if (ExecuteWorkflow.finalizeStats) { - piwikstatsdb.finalizeStats(); - logger.info("Finalized stats"); - } - - // Make the tables available to Impala - if (ExecuteWorkflow.finalTablesVisibleToImpala) { - logger.info("Making tables visible to Impala"); - invalidateMetadata(); - } - - logger.info("End"); - } - - private void invalidateMetadata() throws SQLException { - Statement stmt = null; - - stmt = ConnectDB.getImpalaConnection().createStatement(); - - String sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".downloads_stats"; - stmt.executeUpdate(sql); - - sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".views_stats"; - stmt.executeUpdate(sql); - - sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".usage_stats"; - stmt.executeUpdate(sql); - - sql = "INVALIDATE METADATA " + ConnectDB.getUsageStatsDBSchema() + ".pageviews_stats"; - stmt.executeUpdate(sql); - - stmt.close(); - ConnectDB.getHiveConnection().close(); - } -} diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/export/usagestats_parameters.json b/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/export/usagestats_parameters.json deleted file mode 100644 index 988c23b48..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/export/usagestats_parameters.json +++ /dev/null @@ -1,231 +0,0 @@ -[ - { - "paramName": "mat", - "paramLongName": "matomoAuthToken", - "paramDescription": "when true will stop SparkSession after job execution", - "paramRequired": false - }, - { - "paramName": "mbu", - "paramLongName": "matomoBaseURL", - "paramDescription": "URL of the isLookUp Service", - "paramRequired": true - }, - { - "paramName": "rlp", - "paramLongName": "repoLogPath", - "paramDescription": "nameNode of the source cluster", - "paramRequired": true - }, - { - "paramName": "plp", - "paramLongName": "portalLogPath", - "paramDescription": "namoNode of the target cluster", - "paramRequired": true - }, - { - "paramName": "pmi", - "paramLongName": "portalMatomoID", - "paramDescription": "namoNode of the target cluster", - "paramRequired": true - }, - { - "paramName": "iukbuw", - "paramLongName": "irusUKBaseURL", - "paramDescription": "working directory", - "paramRequired": true - }, - { - "paramName": "iukrp", - "paramLongName": "irusUKReportPath", - "paramDescription": "maximum number of map tasks used in the distcp process", - "paramRequired": true - }, - { - "paramName": "srpa", - "paramLongName": "sarcsReportPathArray", - "paramDescription": "memory for distcp action copying actionsets from remote cluster", - "paramRequired": true - }, - { - "paramName": "srpna", - "paramLongName": "sarcsReportPathNonArray", - "paramDescription": "timeout for distcp copying actions from remote cluster", - "paramRequired": true - }, - { - "paramName": "llp", - "paramLongName": "lareferenciaLogPath", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "lbu", - "paramLongName": "lareferenciaBaseURL", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "lat", - "paramLongName": "lareferenciaAuthToken", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "dbhu", - "paramLongName": "dbHiveUrl", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "dbiu", - "paramLongName": "dbImpalaUrl", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "usdbs", - "paramLongName": "usageStatsDBSchema", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "sdbs", - "paramLongName": "statsDBSchema", - "paramDescription": "activate tranform-only mode. Only apply transformation step", - "paramRequired": true - }, - { - "paramName": "rdbt", - "paramLongName": "recreateDbAndTables", - "paramDescription": "Re-create database and initial tables?", - "paramRequired": true - }, - { - "paramName": "pwed", - "paramLongName": "piwikEmptyDirs", - "paramDescription": "Empty piwik directories?", - "paramRequired": true - }, - { - "paramName": "ppwl", - "paramLongName": "processPiwikLogs", - "paramDescription": "Process the piwiklogs (create & fill in the needed tables and process the data) based on the downloaded data", - "paramRequired": true - }, - { - "paramName": "dpwl", - "paramLongName": "downloadPiwikLogs", - "paramDescription": "download piwik logs?", - "paramRequired": true - }, - { - "paramName": "slp", - "paramLongName": "startingLogPeriod", - "paramDescription": "Starting log period", - "paramRequired": true - }, - { - "paramName": "elp", - "paramLongName": "endingLogPeriod", - "paramDescription": "Ending log period", - "paramRequired": true - }, - { - "paramName": "npidd", - "paramLongName": "numberOfPiwikIdsToDownload", - "paramDescription": "Limit the number of the downloaded piwikids to the first numberOfPiwikIdsToDownload", - "paramRequired": true - }, - { - "paramName": "nsidd", - "paramLongName": "numberOfSiteIdsToDownload", - "paramDescription": "Limit the number of the downloaded siteids (La Referencia logs) to the first numberOfSiteIdsToDownload", - "paramRequired": true - }, - { - "paramName": "lerd", - "paramLongName": "laReferenciaEmptyDirs", - "paramDescription": "Empty LaReferencia directories?", - "paramRequired": true - }, - { - "paramName": "plrl", - "paramLongName": "processLaReferenciaLogs", - "paramDescription": "Process the La Referencia logs (create & fill in the needed tables and process the data) based on the downloaded data", - "paramRequired": true - }, - { - "paramName": "dlrl", - "paramLongName": "downloadLaReferenciaLogs", - "paramDescription": "download La Referencia logs?", - "paramRequired": true - }, - { - "paramName": "icted", - "paramLongName": "irusCreateTablesEmptyDirs", - "paramDescription": "Irus section: Create tables and empty JSON directories?", - "paramRequired": true - }, - { - "paramName": "idr", - "paramLongName": "irusDownloadReports", - "paramDescription": "Irus section: Download reports?", - "paramRequired": true - }, - { - "paramName": "ipr", - "paramLongName": "irusProcessStats", - "paramDescription": "Irus section: Process stats?", - "paramRequired": true - }, - { - "paramName": "inod", - "paramLongName": "irusNumberOfOpendoarsToDownload", - "paramDescription": "Limit the number of the downloaded Opendoars (Irus) to the first irusNumberOfOpendoarsToDownload", - "paramRequired": true - }, - { - "paramName": "icted", - "paramLongName": "sarcCreateTablesEmptyDirs", - "paramDescription": "Sarc section: Create tables and empty JSON directories?", - "paramRequired": true - }, - { - "paramName": "idr", - "paramLongName": "sarcDownloadReports", - "paramDescription": "Sarc section: Download reports?", - "paramRequired": true - }, - { - "paramName": "ipr", - "paramLongName": "sarcProcessStats", - "paramDescription": "Sarc section: Process stats?", - "paramRequired": true - }, - { - "paramName": "inod", - "paramLongName": "sarcNumberOfIssnToDownload", - "paramDescription": "Limit the number of the downloaded ISSN (Sarc) to the first sarcNumberOfIssnToDownload", - "paramRequired": true - }, - - { - "paramName": "fs", - "paramLongName": "finalizeStats", - "paramDescription": "Create the usage_stats table?", - "paramRequired": true - }, - { - "paramName": "ftvi", - "paramLongName": "finalTablesVisibleToImpala", - "paramDescription": "Make the usage_stats, views_stats and downloads_stats tables visible to Impala", - "paramRequired": true - }, - { - "paramName": "nodt", - "paramLongName": "numberOfDownloadThreads", - "paramDescription": "Number of download threads", - "paramRequired": true - } -] diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/config-default.xml b/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/config-default.xml deleted file mode 100644 index b5c807378..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/config-default.xml +++ /dev/null @@ -1,38 +0,0 @@ - - - jobTracker - ${jobTracker} - - - nameNode - ${nameNode} - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1 - - - impalaJdbcUrl - jdbc:hive2://iis-cdh5-test-gw.ocean.icm.edu.pl:21050/;auth=noSasl; - - - oozie.wf.workflow.notification.url - {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status - - - oozie.use.system.libpath - true - - diff --git a/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/workflow.xml b/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/workflow.xml deleted file mode 100644 index 8d62a85a9..000000000 --- a/dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/workflow.xml +++ /dev/null @@ -1,90 +0,0 @@ - - - - hiveMetastoreUris - Hive server metastore URIs - - - hiveJdbcUrl - Hive server jdbc url - - - impalaJdbcUrl - Impala server jdbc url - - - - - ${jobTracker} - ${nameNode} - - - hive.metastore.uris - ${hiveMetastoreUris} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - eu.dnetlib.oa.graph.usagestats.export.ExecuteWorkflow - --matomoAuthToken${matomoAuthToken} - --matomoBaseURL${matomoBaseURL} - --repoLogPath${repoLogPath} - --portalLogPath${portalLogPath} - --portalMatomoID${portalMatomoID} - --irusUKBaseURL${irusUKBaseURL} - --irusUKReportPath${irusUKReportPath} - --sarcsReportPathArray${sarcsReportPathArray} - --sarcsReportPathNonArray${sarcsReportPathNonArray} - --lareferenciaLogPath${lareferenciaLogPath} - --lareferenciaBaseURL${lareferenciaBaseURL} - --lareferenciaAuthToken${lareferenciaAuthToken} - --dbHiveUrl${hiveJdbcUrl} - --dbImpalaUrl${impalaJdbcUrl} - --usageStatsDBSchema${usageStatsDBSchema} - --statsDBSchema${statsDBSchema} - --recreateDbAndTables${recreateDbAndTables} - --piwikEmptyDirs${piwikEmptyDirs} - --downloadPiwikLogs${downloadPiwikLogs} - --processPiwikLogs${processPiwikLogs} - --startingLogPeriod${startingLogPeriod} - --endingLogPeriod${endingLogPeriod} - --numberOfPiwikIdsToDownload${numberOfPiwikIdsToDownload} - --numberOfSiteIdsToDownload${numberOfSiteIdsToDownload} - --laReferenciaEmptyDirs${laReferenciaEmptyDirs} - --downloadLaReferenciaLogs${downloadLaReferenciaLogs} - --processLaReferenciaLogs${processLaReferenciaLogs} - --irusCreateTablesEmptyDirs${irusCreateTablesEmptyDirs} - --irusDownloadReports${irusDownloadReports} - --irusProcessStats${irusProcessStats} - --irusNumberOfOpendoarsToDownload${irusNumberOfOpendoarsToDownload} - --sarcCreateTablesEmptyDirs${sarcCreateTablesEmptyDirs} - --sarcDownloadReports${sarcDownloadReports} - --sarcProcessStats${sarcProcessStats} - --sarcNumberOfIssnToDownload${sarcNumberOfIssnToDownload} - --finalizeStats${finalizeStats} - --finalTablesVisibleToImpala${finalTablesVisibleToImpala} - --numberOfDownloadThreads${numberOfDownloadThreads} - - - - - - - - From 34d653de41e6264174c6bbecf26b1d356235c2ec Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 22 Jan 2021 14:16:33 +0100 Subject: [PATCH 138/149] [Cleaning] updated cleaning rule for DOIs --- .../java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index 885d761c5..0cbf7219a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -15,7 +15,7 @@ import eu.dnetlib.dhp.schema.oaf.*; public class CleaningFunctions { - public static final String DOI_URL_PREFIX_REGEX = "(^http(s?):\\/\\/)(((dx\\.)?doi\\.org)|(handle\\.test\\.datacite\\.org))\\/"; + public static final String DOI_PREFIX_REGEX = "^10\\."; public static final String ORCID_CLEANING_REGEX = ".*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9x]{4})"; public static final int ORCID_LEN = 19; @@ -308,7 +308,7 @@ public class CleaningFunctions { // TODO add cleaning for more PID types as needed case "doi": - pid.setValue(value.toLowerCase().replaceAll(DOI_URL_PREFIX_REGEX, "")); + pid.setValue(value.toLowerCase().replaceAll(DOI_PREFIX_REGEX, "10.")); break; } return pid; From 646dab7f680f641f9600b231920f1f624b7f2bcc Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 22 Jan 2021 18:24:34 +0100 Subject: [PATCH 139/149] trying to avoid NPEs --- .../src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index 0026ee9aa..845c4c982 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -323,13 +323,13 @@ public class Result extends OafEntity implements Serializable { if (a.size() == b.size()) { int msa = a .stream() - .filter(i -> i.getValue() != null) + .filter(i -> i != null && i.getValue() != null) .map(i -> i.getValue().length()) .max(Comparator.naturalOrder()) .orElse(0); int msb = b .stream() - .filter(i -> i.getValue() != null) + .filter(i -> i != null && i.getValue() != null) .map(i -> i.getValue().length()) .max(Comparator.naturalOrder()) .orElse(0); From 07a0ccfc96d50be6e75909da39730d3d55c7bbf9 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 Jan 2021 13:36:01 +0100 Subject: [PATCH 140/149] [Cleaning] trying to avoid NPEs --- .../dhp/oa/graph/clean/CleaningFunctions.java | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index 0cbf7219a..42ce7f90b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -59,12 +59,16 @@ public class CleaningFunctions { } } if (Objects.nonNull(r.getAuthor())) { - r.getAuthor().forEach(a -> { - if (Objects.nonNull(a.getPid())) { - a.getPid().forEach(p -> { - fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES); - }); - } + r.getAuthor() + .stream() + .filter(Objects::nonNull) + .forEach(a -> { + if (Objects.nonNull(a.getPid())) { + a.getPid() + .stream() + .filter(Objects::nonNull) + .forEach(p -> fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES)); + } }); } if (value instanceof Publication) { From 3465c8ccee3e2cb53792968264add0e3994fa04f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 Jan 2021 16:54:53 +0100 Subject: [PATCH 141/149] [Cleaning] trying to avoid NPEs --- .../dhp/oa/graph/clean/CleaningFunctions.java | 25 +++++++++++-------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index 42ce7f90b..1d0e35125 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -59,17 +59,19 @@ public class CleaningFunctions { } } if (Objects.nonNull(r.getAuthor())) { - r.getAuthor() - .stream() - .filter(Objects::nonNull) - .forEach(a -> { - if (Objects.nonNull(a.getPid())) { - a.getPid() - .stream() - .filter(Objects::nonNull) - .forEach(p -> fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES)); - } - }); + r + .getAuthor() + .stream() + .filter(Objects::nonNull) + .forEach(a -> { + if (Objects.nonNull(a.getPid())) { + a + .getPid() + .stream() + .filter(Objects::nonNull) + .forEach(p -> fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES)); + } + }); } if (value instanceof Publication) { @@ -208,6 +210,7 @@ public class CleaningFunctions { a .getPid() .stream() + .filter(Objects::nonNull) .filter(p -> Objects.nonNull(p.getQualifier())) .filter(p -> StringUtils.isNotBlank(p.getValue())) .map(p -> { From ded6ed8d7d328d2bec562d6438185a5b01289f8a Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Mon, 25 Jan 2021 17:57:51 +0100 Subject: [PATCH 142/149] no ',' author, if there are no author in ODF records --- .../dhp/oa/graph/raw/OdfToOafMapper.java | 46 +++---- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 9 ++ .../dhp/oa/graph/raw/textgrid-noauthor.xml | 117 ++++++++++++++++++ 3 files changed, 151 insertions(+), 21 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid-noauthor.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 6d2e28ba8..9dc0bb44b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -51,31 +51,35 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final Node n = (Node) o; final Author author = new Author(); final String fullname = n.valueOf("./datacite:creatorName"); - author.setFullname(fullname); - - final PacePerson pp = new PacePerson(fullname, false); final String name = n.valueOf("./datacite:givenName"); - if (StringUtils.isBlank(name) & pp.isAccurate()) { - author.setName(pp.getNormalisedFirstName()); - } else { - author.setName(name); - } - final String surname = n.valueOf("./datacite:familyName"); - if (StringUtils.isBlank(surname) & pp.isAccurate()) { - author.setSurname(pp.getNormalisedSurname()); - } else { - author.setSurname(surname); - } + if(StringUtils.isNotBlank(fullname) || StringUtils.isNotBlank(name) || StringUtils.isNotBlank(surname)){ + author.setFullname(fullname); - if (StringUtils.isBlank(author.getFullname())) { - author.setFullname(String.format("%s, %s", author.getSurname(), author.getName())); - } + final PacePerson pp = new PacePerson(fullname, false); - author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info)); - author.setPid(preparePids(n, info)); - author.setRank(pos++); - res.add(author); + if (StringUtils.isBlank(name) & pp.isAccurate()) { + author.setName(pp.getNormalisedFirstName()); + } else { + author.setName(name); + } + + + if (StringUtils.isBlank(surname) & pp.isAccurate()) { + author.setSurname(pp.getNormalisedSurname()); + } else { + author.setSurname(surname); + } + + if (StringUtils.isBlank(author.getFullname())) { + author.setFullname(String.format("%s, %s", author.getSurname(), author.getName())); + } + + author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info)); + author.setPid(preparePids(n, info)); + author.setRank(pos++); + res.add(author); + } } return res; } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 2a62e25b2..ae203b3a7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -379,6 +379,15 @@ public class MappersTest { System.out.println(p.getPid().get(0).getValue()); } + @Test + void testTextGridNoAuthor() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("textgrid-noauthor.xml")); + final List list = new OdfToOafMapper(vocs, false).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + } @Test void testBologna() throws IOException { final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf-bologna.xml")); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid-noauthor.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid-noauthor.xml new file mode 100644 index 000000000..53256bed0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid-noauthor.xml @@ -0,0 +1,117 @@ + + + + r3f52792889d::00002412cb25f2f3047712d00ab2c8eb + hdl:11858/00-1734-0000-0003-EE73-2 + 2020-12-16T10:04:03.148Z + r3f52792889d + textgrid:rn8z.0 + 2012-01-29T20:54:12Z + 2020-12-16T16:02:37.562Z + + + + hdl:11858/00-1734-0000-0003-EE73-2 + + + + + + + + Auf dem Trocknen + Detlev von Liliencron: Gute Nacht. Hinterlassene Gedichte, Berlin: Schuster & Loeffler, 1909. + + TextGrid + 2012 + + + tvitt@textgrid.de + + + Digitale Bibliothek + TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c + + + + 2012-01-29T20:54:12Z + 2012-01-29T20:54:12Z + 2012-01-29T20:54:12Z + + + + textgrid:rn8z.0 + http://hdl.handle.net/hdl:11858/00-1734-0000-0003-EE73-2 + + + hdl:11858/00-1734-0000-0003-EE72-4 + + + 527 Bytes + + + text/tg.edition+tg.aggregation+xml + + 0 + + Der annotierte Datenbestand der Digitalen Bibliothek inklusive + Metadaten sowie davon einzeln zugängliche Teile sind eine Abwandlung + des Datenbestandes von www.editura.de durch TextGrid und werden + unter der Lizenz Creative Commons Namensnennung 3.0 Deutschland + Lizenz (by-Nennung TextGrid) veröffentlicht. Die Lizenz bezieht sich + nicht auf die der Annotation zu Grunde liegenden allgemeinfreien + Texte (Siehe auch Punkt 2 der Lizenzbestimmungen). + + + + + + + + Berlin + + + + hdl:11858/00-1734-0000-0003-EE73-2 + 0021 + 0002 + 2012-01-29 + OPEN + http://creativecommons.org/licenses/by/3.0/de/legalcode + und + DE + + + + + + + https%3A%2F%2Fdev.textgridlab.org%2F1.0%2Ftgoaipmh%2Foai + textgrid:rn8z.0 + 2012-01-29T20:54:12Z + + + + + false + false + 0.9 + + + + + + From 505477f36fe2be46ca46fceba474d03c5e1c39b8 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Mon, 25 Jan 2021 18:02:49 +0100 Subject: [PATCH 143/149] format code --- .../main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java | 3 +-- .../src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 1 + 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 9dc0bb44b..683b37630 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -53,7 +53,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final String fullname = n.valueOf("./datacite:creatorName"); final String name = n.valueOf("./datacite:givenName"); final String surname = n.valueOf("./datacite:familyName"); - if(StringUtils.isNotBlank(fullname) || StringUtils.isNotBlank(name) || StringUtils.isNotBlank(surname)){ + if (StringUtils.isNotBlank(fullname) || StringUtils.isNotBlank(name) || StringUtils.isNotBlank(surname)) { author.setFullname(fullname); final PacePerson pp = new PacePerson(fullname, false); @@ -64,7 +64,6 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { author.setName(name); } - if (StringUtils.isBlank(surname) & pp.isAccurate()) { author.setSurname(pp.getNormalisedSurname()); } else { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index ae203b3a7..9827dcc99 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -388,6 +388,7 @@ public class MappersTest { System.out.println(new ObjectMapper().writeValueAsString(list)); System.out.println("***************"); } + @Test void testBologna() throws IOException { final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf-bologna.xml")); From cd379eb5e324ade3ee6ff2448e2cb18870bca490 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 Jan 2021 18:11:49 +0100 Subject: [PATCH 144/149] [Cleaning] trying to avoid NPEs, this time by ruling out authors without a defined fullname --- .../eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index 1d0e35125..7a12a92d6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -190,6 +190,15 @@ public class CleaningFunctions { } } if (Objects.nonNull(r.getAuthor())) { + r + .setAuthor( + r + .getAuthor() + .stream() + .filter(a -> Objects.nonNull(a)) + .filter(a -> StringUtils.isNotBlank(StringUtils.trim(a.getFullname()))) + .collect(Collectors.toList())); + boolean nullRank = r .getAuthor() .stream() From 2890511613aa80db927617e9564e039ca0c7d569 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 26 Jan 2021 09:41:44 +0100 Subject: [PATCH 145/149] [Cleaning] normalise missing Result.country --- .../dnetlib/dhp/oa/graph/clean/CleaningFunctions.java | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index 7a12a92d6..0d69a448e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -110,6 +110,16 @@ public class CleaningFunctions { .setLanguage( qualifier("und", "Undetermined", ModelConstants.DNET_LANGUAGES)); } + if (Objects.nonNull(r.getCountry())) { + r + .setCountry( + r + .getCountry() + .stream() + .filter(Objects::nonNull) + .filter(c -> StringUtils.isNotBlank(c.getClassid())) + .collect(Collectors.toList())); + } if (Objects.nonNull(r.getSubject())) { r .setSubject( From 885e0dd926a50212dbab9f583f1b72d162d94be5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 26 Jan 2021 09:48:53 +0100 Subject: [PATCH 146/149] [Cleaning] filter authors not providing word characters in the fullname --- .../java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index 0d69a448e..db7d34ec9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -206,7 +206,8 @@ public class CleaningFunctions { .getAuthor() .stream() .filter(a -> Objects.nonNull(a)) - .filter(a -> StringUtils.isNotBlank(StringUtils.trim(a.getFullname()))) + .filter(a -> StringUtils.isNotBlank(a.getFullname())) + .filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", ""))) .collect(Collectors.toList())); boolean nullRank = r From f1a852f27848f3ecd5852dc4260627381736ae38 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 26 Jan 2021 15:42:42 +0100 Subject: [PATCH 147/149] align usage-stats workflow poms with latest snapshot version --- .../dhp-usage-raw-data-update/pom.xml | 18 +---------------- dhp-workflows/dhp-usage-stats-build/pom.xml | 20 ++----------------- 2 files changed, 3 insertions(+), 35 deletions(-) diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index 44f28ff56..a78f92d41 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -1,25 +1,9 @@ - - - - - dhp-workflows eu.dnetlib.dhp - 1.1.7-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index 79fabb603..20d2f5b76 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -1,29 +1,13 @@ - - - - - dhp-workflows eu.dnetlib.dhp - 1.1.7-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-usage-stats-build - + pl.project13.maven From fd705404a13875c7b2bdc7205df808827388ffd4 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 3 Feb 2021 10:28:17 +0100 Subject: [PATCH 148/149] tests for EU Open Data portal dataset mapping --- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 29 ++ .../eu/dnetlib/dhp/oa/graph/raw/eu_odp.xml | 367 ++++++++++++++++++ 2 files changed, 396 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/eu_odp.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 9827dcc99..ffe71aa03 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -19,6 +19,7 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; +import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest; @@ -406,6 +407,34 @@ public class MappersTest { System.out.println(p.getTitle().get(0).getValue()); } + @Test + void testEUOpenDataPortal() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("eu_odp.xml")); + final List list = new OdfToOafMapper(vocs, false).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + final Dataset p = (Dataset) list.get(0); + assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertEquals(0, p.getAuthor().size()); + assertEquals(0, p.getPid().size()); + assertEquals("OPEN", p.getBestaccessright().getClassid()); + assertEquals("dataset", p.getResulttype().getClassname()); + assertEquals(1, p.getInstance().size()); + assertEquals("OPEN", p.getInstance().get(0).getAccessright().getClassid()); + assertValidId(p.getInstance().get(0).getCollectedfrom().getKey()); + assertValidId(p.getInstance().get(0).getHostedby().getKey()); + assertEquals( + "CC_BY_4_0", p.getInstance().get(0).getLicense().getValue()); + assertEquals(1, p.getInstance().get(0).getUrl().size()); + assertEquals(1, p.getInstance().size()); + System.out.println(p.getInstance().get(0).getUrl().get(0)); + System.out.println(p.getInstance().get(0).getHostedby().getValue()); + } + private void assertValidId(final String id) { assertEquals(49, id.length()); assertEquals('|', id.charAt(2)); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/eu_odp.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/eu_odp.xml new file mode 100644 index 000000000..2fd7cfa2d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/eu_odp.xml @@ -0,0 +1,367 @@ + + + + r3c4b2081b22::0007d64b38bb2b399120f9993f95d911 + 60a0a5b0-b63c-473f-b8bc-207ea037eb3b + 2021-01-28T17:24:33.095+01:00 + r3c4b2081b22 + 2021-02-03T10:16:27.948+01:00 + + + + http://data.europa.eu/88u/dataset/60a0a5b0-b63c-473f-b8bc-207ea037eb3b + + + GMIS - Favourable feeding habitat of adult Atlantic bluefin tuna (ABFT) Monthly 1998-2017 (frequency of occurence, %) + + JRC + 2019 + + 2019-07-09 + + Dataset + + The favourable feeding habitat of the Atlantic bluefin tuna is daily identified linking their ecological traits with environmental variables from satellite remote sensing and physical ocean models. The feeding habitat is mostly related to the occurrence of productive oceanic features (such as eddies) that are detected by satellite sensors of ocean colour (chlorophyll-a fronts). The physical variables used are sea surface temperature and sea surface height anomaly. More information: https://fishreg.jrc.ec.europa.eu/fish-habitat, Peer-reviewed publication: http://www.sciencedirect.com/science/article/pii/S0079661116000070 + + + protected area + environmental monitoring + oceanography + ocean + Environmental Monitoring Facilities + Environment + Protected Sites + Oceanographic Geographical Features + environmental data + http://publications.europa.eu/resource/authority/data-theme/TECH + http://publications.europa.eu/resource/authority/data-theme/ENVI + http://eurovoc.europa.eu/2114 + http://eurovoc.europa.eu/2107 + http://eurovoc.europa.eu/4801 + http://eurovoc.europa.eu/3140 + + + http://publications.europa.eu/resource/authority/file-type/OP_DATPRO + + + + http://publications.europa.eu/resource/authority/country/ESH + + + http://publications.europa.eu/resource/authority/country/ESP + + + http://publications.europa.eu/resource/authority/country/EST + + + http://publications.europa.eu/resource/authority/country/ETH + + + http://publications.europa.eu/resource/authority/country/DNK + + + http://publications.europa.eu/resource/authority/country/DZA + + + http://publications.europa.eu/resource/authority/country/EGY + + + http://publications.europa.eu/resource/authority/country/ERI + + + http://publications.europa.eu/resource/authority/country/FIN + + + http://publications.europa.eu/resource/authority/country/FRA + + + http://publications.europa.eu/resource/authority/country/1A0 + + + http://publications.europa.eu/resource/authority/country/AUT + + + http://publications.europa.eu/resource/authority/country/BGR + + + http://publications.europa.eu/resource/authority/country/MDA + + + http://publications.europa.eu/resource/authority/country/MCO + + + http://publications.europa.eu/resource/authority/country/LUX + + + http://publications.europa.eu/resource/authority/country/LTU + + + http://publications.europa.eu/resource/authority/country/MAR + + + http://publications.europa.eu/resource/authority/country/LVA + + + http://publications.europa.eu/resource/authority/country/LBN + + + http://publications.europa.eu/resource/authority/country/JOR + + + http://publications.europa.eu/resource/authority/country/LIE + + + http://publications.europa.eu/resource/authority/country/LBY + + + http://publications.europa.eu/resource/authority/country/TUN + + + http://publications.europa.eu/resource/authority/country/TUR + + + http://publications.europa.eu/resource/authority/country/SVK + + + http://publications.europa.eu/resource/authority/country/SVN + + + http://publications.europa.eu/resource/authority/country/SRB + + + http://publications.europa.eu/resource/authority/country/SSD + + + http://publications.europa.eu/resource/authority/country/TCD + + + http://publications.europa.eu/resource/authority/country/TGO + + + http://publications.europa.eu/resource/authority/country/SWE + + + http://publications.europa.eu/resource/authority/country/SYR + + + http://publications.europa.eu/resource/authority/country/AND + + + http://publications.europa.eu/resource/authority/country/BFA + + + http://publications.europa.eu/resource/authority/country/GRC + + + http://publications.europa.eu/resource/authority/country/GNB + + + http://publications.europa.eu/resource/authority/country/GGY + + + http://publications.europa.eu/resource/authority/country/GEO + + + http://publications.europa.eu/resource/authority/country/GBR + + + http://publications.europa.eu/resource/authority/country/FRO + + + http://publications.europa.eu/resource/authority/country/GMB + + + http://publications.europa.eu/resource/authority/country/GIN + + + http://publications.europa.eu/resource/authority/country/GIB + + + http://publications.europa.eu/resource/authority/country/GHA + + + http://publications.europa.eu/resource/authority/country/MKD + + + http://publications.europa.eu/resource/authority/country/MLI + + + http://publications.europa.eu/resource/authority/country/MLT + + + http://publications.europa.eu/resource/authority/country/MNE + + + http://publications.europa.eu/resource/authority/country/MRT + + + http://publications.europa.eu/resource/authority/country/NER + + + http://publications.europa.eu/resource/authority/country/NGA + + + http://publications.europa.eu/resource/authority/country/NLD + + + http://publications.europa.eu/resource/authority/country/NOR + + + http://publications.europa.eu/resource/authority/country/POL + + + http://publications.europa.eu/resource/authority/country/ALB + + + http://publications.europa.eu/resource/authority/country/BEN + + + http://publications.europa.eu/resource/authority/country/VAT + + + http://publications.europa.eu/resource/authority/country/UKR + + + http://publications.europa.eu/resource/authority/country/CAF + + + http://publications.europa.eu/resource/authority/country/BLR + + + http://publications.europa.eu/resource/authority/country/CIV + + + http://publications.europa.eu/resource/authority/country/CHE + + + http://publications.europa.eu/resource/authority/country/CPV + + + http://publications.europa.eu/resource/authority/country/CMR + + + http://publications.europa.eu/resource/authority/country/CZE + + + http://publications.europa.eu/resource/authority/country/CYP + + + http://publications.europa.eu/resource/authority/country/DJI + + + http://publications.europa.eu/resource/authority/country/DEU + + + http://publications.europa.eu/resource/authority/country/ITA + + + http://publications.europa.eu/resource/authority/country/JEY + + + http://publications.europa.eu/resource/authority/country/ISL + + + http://publications.europa.eu/resource/authority/country/ISR + + + http://publications.europa.eu/resource/authority/country/IRL + + + http://publications.europa.eu/resource/authority/country/IRQ + + + http://publications.europa.eu/resource/authority/country/HUN + + + http://publications.europa.eu/resource/authority/country/IMN + + + http://publications.europa.eu/resource/authority/country/GRL + + + http://publications.europa.eu/resource/authority/country/HRV + + + http://publications.europa.eu/resource/authority/country/ALA + + + http://publications.europa.eu/resource/authority/country/BEL + + + http://publications.europa.eu/resource/authority/country/BIH + + + http://publications.europa.eu/resource/authority/country/SLE + + + http://publications.europa.eu/resource/authority/country/SEN + + + http://publications.europa.eu/resource/authority/country/SDN + + + http://publications.europa.eu/resource/authority/country/SAU + + + http://publications.europa.eu/resource/authority/country/RUS + + + http://publications.europa.eu/resource/authority/country/ROU + + + http://publications.europa.eu/resource/authority/country/PSE + + + http://publications.europa.eu/resource/authority/country/PRT + + + http://publications.europa.eu/resource/authority/country/SOM + + + http://publications.europa.eu/resource/authority/country/SMR + + + + EU + OPEN + 0021 + 2019-07-09 + + + CC_BY_4_0 + ENG + + + + + https%3A%2F%2Fdata.europa.eu%2Feuodp%2Fdata%2Fapiodp%2Faction%2Fpackage_search + + + + + + + false + false + 0.9 + + + + + + From c67329d3ad556c153db3e95cfe2941f037f8ee5f Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 3 Feb 2021 17:06:48 +0100 Subject: [PATCH 149/149] updated test for EU Open Data portal datasets --- .../src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 2 +- .../src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt | 1 + .../src/test/resources/eu/dnetlib/dhp/oa/graph/raw/eu_odp.xml | 3 ++- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index ffe71aa03..853106cd8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -420,7 +420,7 @@ public class MappersTest { assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); assertEquals(0, p.getAuthor().size()); - assertEquals(0, p.getPid().size()); + assertEquals(1, p.getPid().size()); assertEquals("OPEN", p.getBestaccessright().getClassid()); assertEquals("dataset", p.getResulttype().getClassname()); assertEquals(1, p.getInstance().size()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt index 67c070d1d..ba47aaf5c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt @@ -1047,6 +1047,7 @@ dnet:pid_types @=@ dnet:pid_types @=@ urn @=@ urn dnet:pid_types @=@ dnet:pid_types @=@ who @=@ WHO Identifier dnet:pid_types @=@ dnet:pid_types @=@ drks @=@ DRKS Identifier dnet:pid_types @=@ dnet:pid_types @=@ handle @=@ Handle +dnet:pid_types @=@ dnet:pid_types @=@ data.europa.eu @=@ EU Persistent URL dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ACM @=@ An ACM classification term that can be associated to your publications dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ARXIV @=@ An ARXIV classification term that can be associated to your publications dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/DDC @=@ A Dewey Decimal classification term (DDC) that can be associated to your publications diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/eu_odp.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/eu_odp.xml index 2fd7cfa2d..c363d026c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/eu_odp.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/eu_odp.xml @@ -7,7 +7,7 @@ 60a0a5b0-b63c-473f-b8bc-207ea037eb3b 2021-01-28T17:24:33.095+01:00 r3c4b2081b22 - 2021-02-03T10:16:27.948+01:00 + 2021-02-03T16:57:03.099+01:00 + http://data.europa.eu/88u/dataset/60a0a5b0-b63c-473f-b8bc-207ea037eb3b EU OPEN 0021