From b8a3392b5908ebe3e6e07da8232cd8fd79718688 Mon Sep 17 00:00:00 2001 From: Dimitris Date: Fri, 30 Oct 2020 14:07:21 +0200 Subject: [PATCH 001/106] 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 0000000000..b56257ee54 --- /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 0000000000..ffc7c74cd1 --- /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 0000000000..50b951cbc2 --- /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 0000000000..749687ec56 --- /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 0000000000..0e0e013cfc --- /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 0000000000..347d3de21e --- /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 0000000000..65816518f3 --- /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 0000000000..6e015acf4f --- /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 0000000000..1708a1c648 --- /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 0000000000..295e98280f --- /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 0000000000..405b58bd5b --- /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 0000000000..988c23b488 --- /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 0000000000..b5c8073787 --- /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 0000000000..8d62a85a9f --- /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 002/106] 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 ffc7c74cd1..29dd5648bf 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 749687ec56..6947381c95 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 0e0e013cfc..7a61b1f469 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 65816518f3..7a64e48d24 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 6e015acf4f..6625c381b0 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 405b58bd5b..ae901dfa53 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 003/106] 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 0000000000..14b543a579 --- /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 0000000000..e6da7eff3e --- /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 0000000000..196238ea2b --- /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 0000000000..7b3db3115e --- /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 0000000000..28c4f30a12 --- /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 0000000000..f8d51a8825 --- /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 0000000000..b5c8073787 --- /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 0000000000..3a81e497d7 --- /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 0000000000..338b2a2c54 --- /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 0000000000..f76644c836 --- /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 0000000000..774dcf0b7d --- /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 0000000000..090f76ff5c --- /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 0000000000..88550579b1 --- /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 0000000000..ef76360997 --- /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 0000000000..681105de4a --- /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 0000000000..e0225d49a9 --- /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 0000000000..6f020daa08 --- /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 0000000000..54ed286cbe --- /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 0000000000..c4ee7d63ce --- /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 0000000000..988c23b488 --- /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 0000000000..b5c8073787 --- /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 0000000000..a6600516d9 --- /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 6947381c95..011c905323 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 347d3de21e..747b5ce0e4 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 7a64e48d24..8f7fffa9f4 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 6625c381b0..6d5bdfac0b 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 71dfc6f61e..06e350c9ee 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 ae901dfa53..405b58bd5b 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 004/106] 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 774dcf0b7d..81e34b3e7e 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 090f76ff5c..bb8d8565e7 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 ef76360997..c20781767c 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 681105de4a..5cc9ec5635 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 e0225d49a9..4903d95995 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 54ed286cbe..4ca20c52e6 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 c4ee7d63ce..bf2187569c 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 0000000000..f400239f5d --- /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 0000000000..8f0f8eae7d --- /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 0000000000..3f958abba4 --- /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 0000000000..4f34adc04e --- /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 0000000000..ea3ac59489 --- /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 0000000000..a165c6eab1 --- /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 0000000000..2d224075fd --- /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 0000000000..43abb1681d --- /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 0000000000..3f121288e4 --- /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 0000000000..b5c8073787 --- /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 0000000000..37700539b5 --- /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 211aa04726bb1789006dde33e5755ba3894d7ed7 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 9 Dec 2020 18:08:51 +0100 Subject: [PATCH 005/106] allow orcid_pending to be percolate to the XML graph serialization --- .../dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java index 9cdf1cd2ee..f3fbca47de 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java @@ -8,6 +8,7 @@ import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; @@ -272,11 +273,7 @@ public class CreateRelatedEntitiesJob_phase2 { .filter(Objects::nonNull) .map(Qualifier::getClassid) .filter(StringUtils::isNotBlank) - .anyMatch(c -> "orcid".equals(c.toLowerCase())); - } - - private static FilterFunction filterEmptyEntityFn() { - return (FilterFunction) v -> Objects.nonNull(v.getEntity()); + .anyMatch(c -> c.toLowerCase().contains(ModelConstants.ORCID)); } private static void removeOutputDir(SparkSession spark, String path) { From ff72fcd91a501d3c824f7adee375d48118a6052b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 9 Dec 2020 19:04:50 +0100 Subject: [PATCH 006/106] allow orcid_pending to be percolate to the XML graph serialization --- .../eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java index 0e742365ab..74d35bf5ee 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java @@ -7,13 +7,15 @@ import java.util.Set; import com.google.common.collect.Sets; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; public class GraphMappingUtils { public static final String SEPARATOR = "_"; - public static Set authorPidTypes = Sets.newHashSet("orcid", "magidentifier"); + public static Set authorPidTypes = Sets.newHashSet( + ModelConstants.ORCID, ModelConstants.ORCID_PENDING, "magidentifier"); public static String removePrefix(final String s) { if (s.contains("|")) From 94bfed1c848fc003a60c6b6c922700bc1f3bae15 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 10 Dec 2020 11:59:28 +0100 Subject: [PATCH 007/106] 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 5ca865e8fc..951afb6c5e 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 e9644122f3..1e060d824f 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 d8b8dd8079..04985a6ab9 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 008/106] 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 951afb6c5e..416ee5024f 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 cfee360c57..9e128d49e5 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 d5c53ea360..c44aead5e9 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 d3cbe0034f..929c316004 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 792a2354a4..e1d2e7d245 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 762bfbb903..106528666c 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 39fa76e43d..01778ad74f 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 8e502f7366..82c3619e10 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 55ab497f07..bd6135d413 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 4d06f6f133..18e8c00b2a 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 b53d7e39b9..9655303620 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 1e060d824f..ec694f5d36 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 eb9add00de..a575328e8d 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 0cfc1adcbb..8c2879b38d 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 166372a7f4..0c23181274 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 e988366c8c..1952b5d9c9 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 724acc4dce..d6ac27fc51 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 d15565d0d7..c4ccf4af68 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 d3c7113ec0..cf44506038 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 0000000000..2584b78fcc --- /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 adee1888a1..0d942cd59f 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 14e33b0916..1a1df418b8 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 bab8081932..a482ee2dc6 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 ac1dbf7867..079709ad89 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 4921bc03e2..441249661e 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 5eea894c8e..63e9b12637 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 879c0d3490..c73b3fb524 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${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json index 10ba926abf..12cd6a391c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the path where the temporary data will be stored", + "paramLongName": "outputDir", + "paramDescription": "the path where the data will be stored", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index dba3c9f73b..83fe47c758 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the opendoar IDs whitelist (comma separated) - workingPath + outputDir the path where the the generated data will be stored @@ -87,7 +87,7 @@ --conf spark.eventLog.dir=${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 15d7d251f6..2388b1c1f4 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 009/106] 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 416ee5024f..d42c692f7b 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 9e128d49e5..457b82517c 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 c44aead5e9..2772f8fd16 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 929c316004..72efc9e6b3 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 e1d2e7d245..29fc72d04b 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 106528666c..006cde48cb 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 ec694f5d36..08c74a291b 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 010/106] 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 1547056b94..c8fab5207c 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 011/106] 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 33def91b39..f57b8dcafd 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 012/106] 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 992ab26e81..0f1912cc32 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 0000000000..b6b183b154 --- /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": 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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 0000000000..a65c4514a3 --- /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 14b543a579..5593d4d872 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 0000000000..9b4325508d --- /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 e6da7eff3e..25b30e8adf 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 0000000000..88db1f8191 --- /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 196238ea2b..a73b299ec5 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 7b3db3115e..b28578e4bf 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 0000000000..ccb3eebd30 --- /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 28c4f30a12..7b07fbc258 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 338b2a2c54..44f28ff565 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 0000000000..4465dae217 --- /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 f76644c836..5b2e6804b9 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 81e34b3e7e..e0e0d3687a 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 bb8d8565e7..7ec5b0fca2 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 88550579b1..904290af8d 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 c20781767c..bcf1711cb3 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 5cc9ec5635..a84d6743f6 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 4903d95995..9144620b75 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 4ca20c52e6..e85c972f54 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 bf2187569c..07e15605fd 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 988c23b488..1aa5ad6f80 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 a6600516d9..022a107abe 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 f400239f5d..79fabb603b 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 0000000000..191fb24c61 --- /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 8f0f8eae7d..e53709f1a5 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 3f958abba4..26e44b1f6f 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 4f34adc04e..4439f848ed 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 ea3ac59489..0d34ebef38 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 a165c6eab1..253dc03b54 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 2d224075fd..880233f00c 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 43abb1681d..47986f52aa 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 3f121288e4..407370ada7 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 37700539b5..71e8a50d61 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 014/106] 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 457b82517c..1ae241e340 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 1ab56cc346..103751f954 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 1a1df418b8..ea81c90d04 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 a482ee2dc6..e803bb5b90 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 0000000000..2e0ed9aeea --- /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 0000000000..43c26f3a3e --- /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${brokerApiBaseUrl} + + + + + + + + + + \ No newline at end of file From d03756c962c31b8dc7929242dcca9e990b28a51a Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 14 Dec 2020 11:11:41 +0100 Subject: [PATCH 015/106] mkdir of output dir --- .../dhp/broker/oa/generate_all/oozie_app/workflow.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index ea81c90d04..250f928f8e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -116,15 +116,15 @@ - + Action failed, error message[${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 016/106] 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 0000000000..7391569ed9 --- /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 eba7362287..9f16e99d8a 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 0f1912cc32..8ae8a55c39 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 b6b183b154..ea7a300513 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 017/106] 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 72efc9e6b3..e18a7ef560 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 29fc72d04b..75f4eb066d 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 006cde48cb..380a689e4d 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 250f928f8e..d06eec87e3 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 079709ad89..f7e072d0fb 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 441249661e..0046490bbb 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 63e9b12637..370b484115 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 c73b3fb524..248326d57e 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${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml index 43c26f3a3e..9095004ad5 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml @@ -13,6 +13,26 @@ esIndexHost the elasticsearch host + + esBatchWriteRetryCount + 8 + an ES configuration property + + + esBatchWriteRetryWait + 60s + an ES configuration property + + + esBatchSizeEntries + 200 + an ES configuration property + + + esNodesWanOnly + true + an ES configuration property + maxIndexedEventsForDsAndTopic the max number of events for each couple (ds/topic) @@ -102,6 +122,10 @@ --outputDir${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 018/106] 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 a8e1ab8414..7709e00a85 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 019/106] 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 66297e1779..60ad438598 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 0c613d1b4a..5ac1176931 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 020/106] 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 f4f5baa7bb..494123fdf5 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 b698c957d0..4be4d5d30c 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 021/106] 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 c8fab5207c..0d44d8e5eb 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 022/106] 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 053627a5fb..0856814881 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 023/106] 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 b6210013cb..3adbd244c6 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 0390c11aa3..f912d3ce92 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 024/106] 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 a575328e8d..dc156cbcf9 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 8c2879b38d..9bdf32a642 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 1952b5d9c9..9498c0f337 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 d6ac27fc51..8270500fd4 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 c4ccf4af68..16b4507338 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 04985a6ab9..9ce64f6bde 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 0856814881..ecbfd821ea 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 75c4625ce4..c693be93c5 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 025/106] 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 9c9221b272..8d906fa15f 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 5ba01357e7..d1ceb9a072 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 026/106] 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 26ebbb7c03..cb3ea54645 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 bbe6609d75..1f6edf96e7 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 027/106] [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 dd8342980d..b3ef3a1121 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 028/106] 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 eddbc1ec43..7ad7c4d6bd 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 029/106] 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 78a4c68015..c0c14d10de 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 d5b2ced7cb..0000000000 --- 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 da9a4bd0ce..0000000000 --- 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 0bebe2fb0e..0000000000 --- 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 6909a96344..0000000000 --- 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 493e944177..0000000000 --- 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 7cc21b44da..0000000000 --- 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 23764f38e4..0000000000 --- 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 67911eef1f..0000000000 --- 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 ae844a0c9c..0000000000 --- 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 a1755f329b..0000000000 --- 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 ea2e9f58ab..0000000000 --- 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 4b02e7485c..0000000000 --- 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 a4f3fa8b82..0000000000 --- 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 030/106] 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 da9a4bd0ce..2475466949 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 23764f38e4..50bda898c0 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 031/106] 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 9cf75f2080..0d1ec1ad1a 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 032/106] 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 dcd034166f..7bd9ce1b6a 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 033/106] 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 fbb20f1433..798eae4ddd 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 034/106] 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 17482c0198..5ad4598a6d 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 0000000000..1ff9753beb --- /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 0000000000..600181ba56 --- /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. BANKIER", "affiliation":null, "pid":null, "surname":"BANKIER", "name":"ALEXANDER A." } ], "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" } ], "relevantdate":[ { "qualifier":{ "classid":"created", "schemeid":"dnet:dataCite_date", "schemename":"dnet:dataCite_date", "classname":"created" }, "dataInfo":null, "value":"2002-09-19T13:54:50Z" } ], "dateofacceptance":{ "dataInfo":null, "value":"2002-09-19T13:54:50Z" }, "publisher":{ "dataInfo":null, "value":"Elsevier BV" }, "embargoenddate":null, "fulltext":null, "contributor":null, "resourcetype":{ "classid":"0001", "schemeid":"dnet:dataCite_resource", "schemename":"dnet:dataCite_resource", 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"value":"https://www.elsevier.com/tdm/userlicense/1.0/" }, "accessright":{ "classid":"RESTRICTED", "schemeid":"dnet:access_modes", "schemename":"dnet:access_modes", "classname":"Restricted" }, "dateofacceptance":{ "dataInfo":null, "value":"2002-09-19T13:54:50Z" }, "collectedfrom":{ "dataInfo":null, "value":"Crossref", "key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2" }, "url":[ "https://api.elsevier.com/content/article/PII:S0009926000904987?httpAccept=text/xml", "https://api.elsevier.com/content/article/PII:S0009926000904987?httpAccept=text/plain", "http://dx.doi.org/10.1053/crad.2000.0498" ] } ], "context":null, "country":null, "originalId":[ "S0009926000904987", "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":"2020-02-06T20:40:22Z", "dateoftransformation":null, "oaiprovenance":null, "extraInfo":null, 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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, "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":"0.40295774", "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":"Pulmonary function testing" } ], "language":null, "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 035/106] 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 7bd9ce1b6a..ceaa47794c 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 036/106] 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 5ad4598a6d..b3d84c40f9 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 1ff9753beb..02e694770a 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 037/106] 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 b3d84c40f9..0b602b7746 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 02e694770a..d7b3bc36f1 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 038/106] 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 798eae4ddd..859fc074c3 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 039/106] 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 30cfebe799..882483e22d 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 040/106] 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 d7b3bc36f1..9c4e622148 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 1efa865862..bff92ecf98 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 882483e22d..c35bbf424d 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 8646ac7422..9bc90d51da 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 572824e3db..7adf992cd2 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 8d906fa15f..683986de24 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 860254527a..19a512ac66 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 f7255e5591..e9773dbbb9 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 598835a000..1422a08407 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 0222b393da..a1b3d06b7c 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 859fc074c3..885d761c53 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 f7579c0a08..a0ce4f5a69 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 705160a2bb..8043236e01 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 f1e374f954..3f632af226 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 1b5849f356..7598fd9573 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 81bdb29418..8133666a67 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 041/106] 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 9c80528e34..e2ff90d7bf 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 = "$.source"; - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); public static void main(String[] args) throws Exception { From b0dc92786f83c428498ab4c64102ca53d39fb54b Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Mon, 4 Jan 2021 17:01:35 +0100 Subject: [PATCH 042/106] defined a single oozie workflow for the generation of doiboost --- .../SparkGenerateDOIBoostActionSet.scala | 3 +- .../doiboost/generate_doiboost_as_params.json | 3 +- .../dhp/doiboost/oozie_app/config-default.xml | 42 +++ .../dhp/doiboost/oozie_app/workflow.xml | 326 ++++++++++++++++++ 4 files changed, 372 insertions(+), 2 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala index 7a6cd3faaa..da9da22b64 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala @@ -39,6 +39,7 @@ object SparkGenerateDOIBoostActionSet { val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath") val dbOrganizationPath = parser.get("dbOrganizationPath") val workingDirPath = parser.get("targetPath") + val sequenceFilePath = parser.get("sFilePath") spark.read.load(dbDatasetPath).as[OafDataset] .map(d =>DoiBoostMappingUtil.fixResult(d)) @@ -65,7 +66,7 @@ object SparkGenerateDOIBoostActionSet { val d: Dataset[(String, String)] =spark.read.load(s"$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 6eb1ec6f16..0cf9955c94 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 0000000000..508202e301 --- /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 0000000000..d779725129 --- /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 043/106] 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 19a512ac66..11f9828db4 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 02dc4979af..780e65c1e9 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 ea08f47d43..1ff63dd0ec 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 d779725129..c116d07b1d 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 044/106] 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 c116d07b1d..bc859d0e05 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${outputPath} --masteryarn-cluster From 7834a357683cf3a340794e03945825dd780f0c19 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Mon, 4 Jan 2021 17:54:57 +0100 Subject: [PATCH 045/106] avoid to save intermediate dataset before generation of Sequence file --- .../SparkGenerateDOIBoostActionSet.scala | 26 +++++++++++-------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala index da9da22b64..78477ae4d9 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala @@ -41,30 +41,34 @@ object SparkGenerateDOIBoostActionSet { val workingDirPath = parser.get("targetPath") val sequenceFilePath = parser.get("sFilePath") - spark.read.load(dbDatasetPath).as[OafDataset] + val asDataset = spark.read.load(dbDatasetPath).as[OafDataset] .map(d =>DoiBoostMappingUtil.fixResult(d)) .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING)) - .write.mode(SaveMode.Overwrite).save(s"$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 046/106] 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 e2ff90d7bf..3186f828ce 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 047/106] [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 f69a05da1c..cda4983b72 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 e31ccf399b..dcebbbcac8 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 87a138d525..0920d516a4 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 bc859d0e05..9464c1a615 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 048/106] [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 0cf9955c94..93d24a8910 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 049/106] [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 9464c1a615..3f5805b629 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 050/106] [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 443c182308..0026ee9aa9 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 50bda898c0..dfe48542cb 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 051/106] [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 dfe48542cb..2cd37d9ea0 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 052/106] [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 0000000000..d5b2ced7cb --- /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 0000000000..0bebe2fb0e --- /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 0000000000..6909a96344 --- /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 0000000000..493e944177 --- /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 0000000000..7cc21b44da --- /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 053/106] [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 0000000000..7663a454b9 --- /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 0000000000..31771a40ad --- /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 0000000000..5311a6614a --- /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 0000000000..7200d2896d --- /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 0000000000..a4f3fa8b82 --- /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 054/106] [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 83fe47c758..7c5b722d21 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 055/106] 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 08c74a291b..e061c0d3b7 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 83fe47c758..7c5b722d21 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 a2e2587b31..3e0626aed2 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 056/106] 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 7c5b722d21..dba3c9f73b 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 057/106] 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 5ca865e8fc..951afb6c5e 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 e9644122f3..1e060d824f 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 d8b8dd8079..04985a6ab9 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 058/106] 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 951afb6c5e..416ee5024f 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 cfee360c57..9e128d49e5 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 d5c53ea360..c44aead5e9 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 d3cbe0034f..929c316004 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 792a2354a4..e1d2e7d245 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 762bfbb903..106528666c 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 39fa76e43d..01778ad74f 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 8e502f7366..82c3619e10 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 55ab497f07..bd6135d413 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 4d06f6f133..18e8c00b2a 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 b53d7e39b9..9655303620 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 1e060d824f..ec694f5d36 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 eb9add00de..a575328e8d 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 0cfc1adcbb..8c2879b38d 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 166372a7f4..0c23181274 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 e988366c8c..1952b5d9c9 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 724acc4dce..d6ac27fc51 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 d15565d0d7..c4ccf4af68 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 d3c7113ec0..cf44506038 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 0000000000..2584b78fcc --- /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 adee1888a1..0d942cd59f 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 14e33b0916..1a1df418b8 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 bab8081932..a482ee2dc6 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 ac1dbf7867..079709ad89 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 4921bc03e2..441249661e 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 5eea894c8e..63e9b12637 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 879c0d3490..c73b3fb524 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${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json index 10ba926abf..12cd6a391c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json @@ -1,8 +1,8 @@ [ { "paramName": "o", - "paramLongName": "workingPath", - "paramDescription": "the path where the temporary data will be stored", + "paramLongName": "outputDir", + "paramDescription": "the path where the data will be stored", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index dba3c9f73b..83fe47c758 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the opendoar IDs whitelist (comma separated) - workingPath + outputDir the path where the the generated data will be stored @@ -87,7 +87,7 @@ --conf spark.eventLog.dir=${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 15d7d251f6..2388b1c1f4 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 059/106] 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 416ee5024f..d42c692f7b 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 9e128d49e5..457b82517c 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 c44aead5e9..2772f8fd16 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 929c316004..72efc9e6b3 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 e1d2e7d245..29fc72d04b 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 106528666c..006cde48cb 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 ec694f5d36..08c74a291b 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 060/106] 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 457b82517c..1ae241e340 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 1ab56cc346..103751f954 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 1a1df418b8..ea81c90d04 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 a482ee2dc6..e803bb5b90 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 0000000000..2e0ed9aeea --- /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 0000000000..43c26f3a3e --- /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${brokerApiBaseUrl} + + + + + + + + + + \ No newline at end of file From 1391341d0690ed978da64a1d7c232f84cea89166 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 14 Dec 2020 11:11:41 +0100 Subject: [PATCH 061/106] mkdir of output dir --- .../dhp/broker/oa/generate_all/oozie_app/workflow.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index ea81c90d04..250f928f8e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -116,15 +116,15 @@ - + Action failed, error message[${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 062/106] 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 72efc9e6b3..e18a7ef560 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 29fc72d04b..75f4eb066d 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 006cde48cb..380a689e4d 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 250f928f8e..d06eec87e3 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 079709ad89..f7e072d0fb 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 441249661e..0046490bbb 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 63e9b12637..370b484115 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 c73b3fb524..248326d57e 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${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml index 43c26f3a3e..9095004ad5 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml @@ -13,6 +13,26 @@ esIndexHost the elasticsearch host + + esBatchWriteRetryCount + 8 + an ES configuration property + + + esBatchWriteRetryWait + 60s + an ES configuration property + + + esBatchSizeEntries + 200 + an ES configuration property + + + esNodesWanOnly + true + an ES configuration property + maxIndexedEventsForDsAndTopic the max number of events for each couple (ds/topic) @@ -102,6 +122,10 @@ --outputDir${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 063/106] 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 053627a5fb..0856814881 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 064/106] 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 a575328e8d..dc156cbcf9 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 8c2879b38d..9bdf32a642 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 1952b5d9c9..9498c0f337 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 d6ac27fc51..8270500fd4 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 c4ccf4af68..16b4507338 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 04985a6ab9..9ce64f6bde 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 0856814881..ecbfd821ea 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 75c4625ce4..c693be93c5 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 065/106] 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 26ebbb7c03..cb3ea54645 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 bbe6609d75..1f6edf96e7 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 066/106] 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 08c74a291b..e061c0d3b7 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 83fe47c758..7c5b722d21 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${opendoarIds} diff --git a/pom.xml b/pom.xml index a2e2587b31..3e0626aed2 100644 --- a/pom.xml +++ b/pom.xml @@ -704,7 +704,7 @@ 3.3.3 3.4.2 [2.12,3.0) - 3.1.1 + 3.1.6 7.5.0 4.7.2 1.20 From b230d4441192fbb7dde49fe484fe9580d0afd382 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 14 Jan 2021 14:23:44 +0100 Subject: [PATCH 067/106] fixed conflict --- .../dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml index 7c5b722d21..dba3c9f73b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml @@ -6,7 +6,7 @@ the opendoar IDs whitelist (comma separated) - outputDir + workingPath the path where the the generated data will be stored @@ -87,7 +87,7 @@ --conf spark.eventLog.dir=${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 068/106] 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 3b575a5b76..7c5b722d21 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 069/106] 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 a65c4514a3..0000000000 --- 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 5593d4d872..0000000000 --- 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 9b4325508d..0000000000 --- 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 25b30e8adf..0000000000 --- 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 88db1f8191..0000000000 --- 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 a73b299ec5..0000000000 --- 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 b28578e4bf..0000000000 --- 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 ccb3eebd30..0000000000 --- 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 7b07fbc258..0000000000 --- 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 f8d51a8825..0000000000 --- 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 b5c8073787..0000000000 --- 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 3a81e497d7..0000000000 --- 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 b56257ee54..0000000000 --- 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 29dd5648bf..0000000000 --- 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 50b951cbc2..0000000000 --- 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 011c905323..0000000000 --- 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 7a61b1f469..0000000000 --- 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 747b5ce0e4..0000000000 --- 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 8f7fffa9f4..0000000000 --- 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 6d5bdfac0b..0000000000 --- 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 1708a1c648..0000000000 --- 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 06e350c9ee..0000000000 --- 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 405b58bd5b..0000000000 --- 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 988c23b488..0000000000 --- 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 b5c8073787..0000000000 --- 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 8d62a85a9f..0000000000 --- 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 070/106] [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 885d761c53..0cbf7219af 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 071/106] 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 0026ee9aa9..845c4c9825 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 072/106] [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 0cbf7219af..42ce7f90bb 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 073/106] [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 42ce7f90bb..1d0e351258 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 074/106] 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 6d2e28ba8c..9dc0bb44ba 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 2a62e25b2a..ae203b3a78 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 0000000000..53256bed01 --- /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 075/106] 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 9dc0bb44ba..683b376309 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 ae203b3a78..9827dcc991 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 076/106] [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 1d0e351258..7a12a92d66 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 077/106] [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 7a12a92d66..0d69a448e6 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 078/106] [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 0d69a448e6..db7d34ec96 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 079/106] 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 44f28ff565..a78f92d410 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 79fabb603b..20d2f5b76f 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 080/106] 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 9827dcc991..ffe71aa038 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 0000000000..2fd7cfa2db --- /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 081/106] 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 ffe71aa038..853106cd80 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 67c070d1dc..ba47aaf5c8 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 2fd7cfa2db..c363d026c8 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 From 82e6c50f3fe37f69a82b9f273a7ab96b1a9ebe8b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 9 Feb 2021 16:27:04 +0100 Subject: [PATCH 082/106] updated solr fields (authoridtypevalue, resultsubject, resultresourcetypename) --- .../src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml | 4 +++- .../src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml index 1f5cf7b815..70cc287544 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml @@ -61,7 +61,7 @@ - + @@ -72,6 +72,7 @@ + @@ -79,6 +80,7 @@ + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml index b617dbea25..a0ca0aa6fe 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml @@ -39,6 +39,8 @@ Saykally, Jessica N. Keeley, Kristen L. Haris Hatic + Baglioni, Miriam + De Bonis, Michele 2017-06-01 Withania somnifera has been used in traditional medicine for a variety of neural disorders. Recently, chronic neurodegenerative conditions have been @@ -115,7 +117,7 @@ Cell Transplantation - + Cell Transplantation From 09fc7e2f7882277534b9ccf97b6a1d9060ded335 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 10 Feb 2021 11:22:09 +0100 Subject: [PATCH 083/106] serialization of validated flag on relationships --- .../CreateRelatedEntitiesJob_phase2.java | 2 +- .../oa/provision/utils/GraphMappingUtils.java | 3 +- .../oa/provision/utils/TemplateFactory.java | 6 +- .../oa/provision/utils/XmlRecordFactory.java | 3 +- .../dnetlib/dhp/oa/provision/template/rel.st | 3 +- .../oa/provision/XmlRecordFactoryTest.java | 70 +++++++++++ .../eu/dnetlib/dhp/oa/provision/project.json | 109 ++++++++++++++++++ .../eu/dnetlib/dhp/oa/provision/record.xml | 22 ++++ .../dhp/oa/provision/relToProject.json | 31 +++++ .../oa/provision/relToValidatedProject.json | 31 +++++ 10 files changed, 275 insertions(+), 5 deletions(-) create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project.json create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToProject.json create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToValidatedProject.json diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java index f3fbca47de..e2cf58d00f 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java @@ -8,7 +8,6 @@ import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; @@ -28,6 +27,7 @@ import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport; import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java index 74d35bf5ee..d2131ef28f 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java @@ -14,7 +14,8 @@ public class GraphMappingUtils { public static final String SEPARATOR = "_"; - public static Set authorPidTypes = Sets.newHashSet( + public static Set authorPidTypes = Sets + .newHashSet( ModelConstants.ORCID, ModelConstants.ORCID_PENDING, "magidentifier"); public static String removePrefix(final String s) { diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java index 21b526ab1b..173ba326a3 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java @@ -73,7 +73,9 @@ public class TemplateFactory { final Collection fields, final String semanticclass, final String semantischeme, - final DataInfo info) { + final DataInfo info, + final boolean validated, + final String validationDate) { return getTemplate(resources.getRel()) .add("type", type) .add("objIdentifier", escapeXml(removePrefix(objIdentifier))) @@ -86,6 +88,8 @@ public class TemplateFactory { .add( "provenanceaction", info.getProvenanceaction() != null ? info.getProvenanceaction().getClassid() : "") + .add("validated", validated) + .add("validationdate", validationDate) .render(); } 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 9f16e99d8a..b0a21c62b4 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 @@ -1096,7 +1096,8 @@ public class XmlRecordFactory implements Serializable { final HashSet fields = Sets.newHashSet(mapFields(link, contexts)); return templateFactory .getRel( - targetType, rel.getTarget(), fields, rel.getRelClass(), scheme, rel.getDataInfo()); + targetType, rel.getTarget(), fields, rel.getRelClass(), scheme, rel.getDataInfo(), rel.getValidated(), + rel.getValidationDate()); } private List listChildren( diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/rel.st b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/rel.st index af19ba497b..e77a86e1d9 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/rel.st +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/rel.st @@ -1,4 +1,5 @@ - $objIdentifier$ +$if(validated)$$else$$endif$ +$objIdentifier$ $metadata:{ it | $it$ }$ \ No newline at end of file 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 8ae8a55c39..c391a95c9b 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 @@ -5,22 +5,29 @@ 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.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.io.SAXReader; +import org.junit.Assert; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; +import com.clearspring.analytics.util.Lists; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; +import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; +import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; +import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Relation; public class XmlRecordFactoryTest { @@ -58,4 +65,67 @@ public class XmlRecordFactoryTest { // TODO add assertions based of values extracted from the XML record } + + @Test + public void testXMLRecordFactoryWithValidatedProject() throws IOException, DocumentException { + + ContextMapper contextMapper = new ContextMapper(); + + XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, + otherDsTypeId); + + Publication p = OBJECT_MAPPER + .readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class); + Project pj = OBJECT_MAPPER + .readValue(IOUtils.toString(getClass().getResourceAsStream("project.json")), Project.class); + Relation rel = OBJECT_MAPPER + .readValue( + (IOUtils.toString(getClass().getResourceAsStream("relToValidatedProject.json"))), Relation.class); + RelatedEntity relatedProject = CreateRelatedEntitiesJob_phase1.asRelatedEntity(pj, Project.class); + List links = Lists.newArrayList(); + RelatedEntityWrapper rew = new RelatedEntityWrapper(rel, relatedProject); + links.add(rew); + JoinedEntity je = new JoinedEntity<>(p); + je.setLinks(links); + + String xml = xmlRecordFactory.build(je); + + assertNotNull(xml); + + Document doc = new SAXReader().read(new StringReader(xml)); + assertNotNull(doc); + System.out.println(doc.asXML()); + Assertions.assertEquals("2021-01-01", doc.valueOf("//validated/@date")); + } + + @Test + public void testXMLRecordFactoryWithNonValidatedProject() throws IOException, DocumentException { + + ContextMapper contextMapper = new ContextMapper(); + + XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, + otherDsTypeId); + + Publication p = OBJECT_MAPPER + .readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class); + Project pj = OBJECT_MAPPER + .readValue(IOUtils.toString(getClass().getResourceAsStream("project.json")), Project.class); + Relation rel = OBJECT_MAPPER + .readValue((IOUtils.toString(getClass().getResourceAsStream("relToProject.json"))), Relation.class); + RelatedEntity relatedProject = CreateRelatedEntitiesJob_phase1.asRelatedEntity(pj, Project.class); + List links = Lists.newArrayList(); + RelatedEntityWrapper rew = new RelatedEntityWrapper(rel, relatedProject); + links.add(rew); + JoinedEntity je = new JoinedEntity<>(p); + je.setLinks(links); + + String xml = xmlRecordFactory.build(je); + + assertNotNull(xml); + + Document doc = new SAXReader().read(new StringReader(xml)); + assertNotNull(doc); + System.out.println(doc.asXML()); + assertEquals("", doc.valueOf("//rel/validated")); + } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project.json new file mode 100644 index 0000000000..b61e55d1a6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project.json @@ -0,0 +1,109 @@ +{ + "id": "40|corda__h2020::79a0e16c122c9a18eb60e4a5e64b620d", + "originalId": [], + "pid": [], + "dateofcollection": "2020-01-01", + "dateoftransformation": "2020-01-01", + "extraInfo": [], + "oaiprovenance": null, + "websiteurl": { + "value": "https://web.site", + "datainfo": null + }, + "code": { + "value": "79a0e", + "datainfo": null + }, + "acronym": { + "value": "79a0e_acronym", + "datainfo": null + }, + "title": { + "value": "79a0e_title", + "datainfo": null + }, + "startdate": { + "value": "2019-02-01", + "datainfo": null + }, + "enddate": { + "value": "2021-01-09", + "datainfo": null + }, + "callidentifier": { + "value": "79a0e_callID", + "datainfo": null + }, + "keywords": { + "value": "", + "datainfo": null + }, + "duration": { + "value": "", + "datainfo": null + }, + "ecsc39": { + "value": "true", + "datainfo": null + }, + "oamandatepublications": { + "value": "true", + "datainfo": null + }, + "ecarticle29_3": { + "value": "false", + "datainfo": null + }, + "optional1": { + "value": "", + "datainfo": null + }, + "optional2": { + "value": "", + "datainfo": null + }, + "jsonextrainfo":{ + "value": "", + "datainfo": null + }, + "contactfullname":{ + "value": "", + "datainfo": null + }, + "contactfax": { + "value": "", + "datainfo": null + }, + "contactphone": { + "value": "", + "datainfo": null + }, + "contactemail": { + "value": "", + "datainfo": null + }, + "summary": { + "value": "79a0e_description", + "datainfo": null + }, + "currency": { + "value": "EUR", + "datainfo": null + }, + "totalcost": 120000, + "fundedamount": 18000, + "h2020topiccode": "", + "h2020topicdescription": "", + "h2020classification": [], + "subjects": [ + { + "value": "", + "qualifier": null, + "datainfo": null + } + ], + "fundingtree": [] + +} + + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml index a0ca0aa6fe..2d60494164 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml @@ -294,6 +294,28 @@ >rcuk________::23feba2a5ca7f6b6016bf3a45180da50 University of Delhi + + true + corda_______::30c6b5ab90f30666de1d112fb93d8c77 + 227878 + + + ec__________::EC::FP7 + ec__________::EC::FP7::SP2 + ec__________::EC::FP7::SP2::ERC + + Complex structure and dynamics of collective motion + COLLMOT + + + + irb_hr______::2330a1d0dac71ffbe15fbcbc807288d4 + 108-1083570-3635 + + + + Pentadecapeptide BPC 157 - further investigations + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToProject.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToProject.json new file mode 100644 index 0000000000..b4d9752559 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToProject.json @@ -0,0 +1,31 @@ +{ +"collectedfrom": [ +{ +"key": "10|opendoar____::eccbc87e4b5ce2fe28308fd9f2a7baf3", +"value": "AMS Acta", +"dataInfo": null +} +], +"dataInfo": { +"invisible": false, +"inferred": false, +"deletedbyinference": false, +"trust": "0.9", +"inferenceprovenance": "", +"provenanceaction": { +"classid": "sysimport:crosswalk:repository", +"classname": "sysimport:crosswalk:repository", +"schemeid": "dnet:provenanceActions", +"schemename": "dnet:provenanceActions" +} +}, +"lastupdatetimestamp": 1606898557407, +"relType": "resultProject", +"subRelType": "outcome", +"relClass": "isProducedBy", +"source": "50|CSC_________::0000ec4dd9df012feaafa77e71a0fb4c", +"target": "40|corda__h2020::79a0e16c122c9a18eb60e4a5e64b620d", +"validated": false, +"validationDate": null, +"properties": [] +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToValidatedProject.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToValidatedProject.json new file mode 100644 index 0000000000..0346d72643 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToValidatedProject.json @@ -0,0 +1,31 @@ +{ +"collectedfrom": [ +{ +"key": "10|opendoar____::eccbc87e4b5ce2fe28308fd9f2a7baf3", +"value": "AMS Acta", +"dataInfo": null +} +], +"dataInfo": { +"invisible": false, +"inferred": false, +"deletedbyinference": false, +"trust": "0.9", +"inferenceprovenance": "", +"provenanceaction": { +"classid": "sysimport:crosswalk:repository", +"classname": "sysimport:crosswalk:repository", +"schemeid": "dnet:provenanceActions", +"schemename": "dnet:provenanceActions" +} +}, +"lastupdatetimestamp": 1606898557407, +"relType": "resultProject", +"subRelType": "outcome", +"relClass": "isProducedBy", +"source": "50|CSC_________::0000ec4dd9df012feaafa77e71a0fb4c", +"target": "40|corda__h2020::79a0e16c122c9a18eb60e4a5e64b620d", +"validated": true, +"validationDate": "2021-01-01", +"properties": [] +} \ No newline at end of file From c4d1feca7451b8e50f0abe8287fb056c32516f17 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 10 Feb 2021 11:22:54 +0100 Subject: [PATCH 084/106] mapper test with validated link to project --- .../src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 1 + .../resources/eu/dnetlib/dhp/oa/graph/raw/oaf_claim_crossref.xml | 1 + 2 files changed, 2 insertions(+) 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 853106cd80..ab956a3782 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 @@ -334,6 +334,7 @@ public class MappersTest { assertValidId(p.getCollectedfrom().get(0).getKey()); System.out.println(p.getTitle().get(0).getValue()); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_claim_crossref.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_claim_crossref.xml index 8f69a5e2d1..93349f3c92 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_claim_crossref.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_claim_crossref.xml @@ -46,6 +46,7 @@ 10.1080/23744235.2020.1774644 Infectious Diseases + corda__h2020::814530 From 986dd969d3e32975f7d49cbbdda2eb6f2adcee8a Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 10 Feb 2021 12:03:54 +0100 Subject: [PATCH 085/106] use the proper import for Lists --- .../eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.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/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index c391a95c9b..27860ca32d 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 @@ -11,14 +11,12 @@ import org.apache.commons.io.IOUtils; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.io.SAXReader; -import org.junit.Assert; import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; -import com.clearspring.analytics.util.Lists; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Lists; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; From 7249cceb5327a6fdd69018c9e7065d5cb703cf16 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 11 Feb 2021 09:27:08 +0100 Subject: [PATCH 086/106] switch of 2 nodes --- .../oa/generate_all/oozie_app/workflow.xml | 56 +++++++++---------- 1 file changed, 28 insertions(+), 28 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 d06eec87e3..0aeb51c3c3 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 @@ -505,6 +505,33 @@ --maxEventsForTopic${maxIndexedEventsForDsAndTopic} --brokerApiBaseUrl${brokerApiBaseUrl} + + + + + + + yarn + cluster + GenerateStatsJob + eu.dnetlib.dhp.broker.oa.GenerateStatsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${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}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --outputDir${outputDir} + --dbUrl${brokerDbUrl} + --dbUser${brokerDbUser} + --dbPassword${brokerDbPassword} + --brokerApiBaseUrl${brokerApiBaseUrl} + @@ -535,37 +562,10 @@ --esNodesWanOnly${esNodesWanOnly} --brokerApiBaseUrl${brokerApiBaseUrl} - - - - - - - yarn - cluster - GenerateStatsJob - eu.dnetlib.dhp.broker.oa.GenerateStatsJob - dhp-broker-events-${projectVersion}.jar - - --executor-cores=${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}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=3840 - - --outputDir${outputDir} - --dbUrl${brokerDbUrl} - --dbUser${brokerDbUser} - --dbPassword${brokerDbPassword} - --brokerApiBaseUrl${brokerApiBaseUrl} - - + \ No newline at end of file From b34b5a39ca05cc3a2f1363aca7171bacb9f739a6 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 11 Feb 2021 09:36:04 +0100 Subject: [PATCH 087/106] index field authoridtypevalue mixes up different author id-type value pairs, dropped in favour of orcidtypevalue --- .../src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml index 70cc287544..f92b63dfde 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml @@ -80,7 +80,7 @@ - + From 8c1600398a1f0c8d51fc84d8ab71ac468da5791b Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 11 Feb 2021 10:54:16 +0100 Subject: [PATCH 088/106] added resumeFrom parameter --- .../broker/oa/generate_all/oozie_app/workflow.xml | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) 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 0aeb51c3c3..ea80c3acf6 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 @@ -136,7 +136,17 @@ - + + + + + ${wf:conf('resumeFrom') eq 'ensure_output_dir'} + ${wf:conf('resumeFrom') eq 'index_event_subset'} + ${wf:conf('resumeFrom') eq 'stats'} + ${wf:conf('resumeFrom') eq 'index_notifications'} + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] From 83d815d0bce32ab98cd385832ea2bcbf7e1a694d Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 11 Feb 2021 10:57:23 +0100 Subject: [PATCH 089/106] only stats --- .../oa/stats/oozie_app/config-default.xml | 18 +++ .../broker/oa/stats/oozie_app/workflow.xml | 114 ++++++++++++++++++ 2 files changed, 132 insertions(+) create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats/oozie_app/config-default.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats/oozie_app/config-default.xml new file mode 100644 index 0000000000..2e0ed9aeea --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats/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/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats/oozie_app/workflow.xml new file mode 100644 index 0000000000..218af4515e --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats/oozie_app/workflow.xml @@ -0,0 +1,114 @@ + + + + + outputDir + the path where the the generated data will be stored + + + 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 + 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 + GenerateStatsJob + eu.dnetlib.dhp.broker.oa.GenerateStatsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${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}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --outputDir${outputDir} + --dbUrl${brokerDbUrl} + --dbUser${brokerDbUser} + --dbPassword${brokerDbPassword} + --brokerApiBaseUrl${brokerApiBaseUrl} + + + + + + + + From 2c4dcc90ba1f0ef2f0baeeaca5468bc88c25f86f Mon Sep 17 00:00:00 2001 From: antleb Date: Sun, 14 Feb 2021 02:54:55 +0200 Subject: [PATCH 090/106] analyzing tables to produce stats --- .../graph/stats/oozie_app/scripts/step10.sql | 5 +++- .../graph/stats/oozie_app/scripts/step11.sql | 3 +++ .../graph/stats/oozie_app/scripts/step12.sql | 13 +++++++++++ .../graph/stats/oozie_app/scripts/step13.sql | 9 ++++++++ .../graph/stats/oozie_app/scripts/step14.sql | 13 +++++++++++ .../graph/stats/oozie_app/scripts/step15.sql | 9 ++++++++ .../graph/stats/oozie_app/scripts/step16.sql | 13 ++++++++++- .../stats/oozie_app/scripts/step16_5.sql | 5 +++- .../stats/oozie_app/scripts/step16_6.sql | 9 +++++++- .../graph/stats/oozie_app/scripts/step2.sql | 23 ++++++++++++++++--- .../graph/stats/oozie_app/scripts/step3.sql | 18 ++++++++++++++- .../graph/stats/oozie_app/scripts/step4.sql | 18 ++++++++++++++- .../graph/stats/oozie_app/scripts/step5.sql | 22 ++++++++++++++---- .../graph/stats/oozie_app/scripts/step6.sql | 15 ++++++++---- .../graph/stats/oozie_app/scripts/step7.sql | 7 ++++-- .../graph/stats/oozie_app/scripts/step8.sql | 9 +++++++- .../graph/stats/oozie_app/scripts/step9.sql | 3 +++ 17 files changed, 174 insertions(+), 20 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql index 46ff295f4d..e2e37d3fca 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql @@ -18,4 +18,7 @@ CREATE OR REPLACE VIEW ${stats_db_name}.concept AS SELECT * FROM ${external_sta -- Creation date of the database ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ -create table ${stats_db_name}.creation_date as select date_format(current_date(), 'dd-MM-yyyy') as date; \ No newline at end of file +create table ${stats_db_name}.creation_date as select date_format(current_date(), 'dd-MM-yyyy') as date; + +ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql index 13e141459d..25f9f09aea 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql @@ -42,3 +42,6 @@ UPDATE ${stats_db_name}.software_tmp SET delayed = 'yes' WHERE software_tmp.id I UPDATE ${stats_db_name}.otherresearchproduct_tmp SET delayed = 'yes' WHERE otherresearchproduct_tmp.id IN (SELECT distinct r.id FROM ${stats_db_name}.result r, ${stats_db_name}.project_results pr, ${stats_db_name}.project_tmp p WHERE r.id=pr.result AND pr.id=p.id AND to_date(r.date)-to_date(p.enddate) > 0); CREATE OR REPLACE VIEW ${stats_db_name}.project_results_publication AS SELECT result_projects.id AS result, result_projects.project AS project_results, result.date as resultdate, project.enddate as projectenddate, result_projects.daysfromend AS daysfromend FROM ${stats_db_name}.result_projects, ${stats_db_name}.result, ${stats_db_name}.project WHERE result_projects.id=result.id AND result.type='publication' AND project.id=result_projects.project; + +ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql index 25439852ee..bf3f1d6153 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql @@ -36,3 +36,16 @@ CREATE OR REPLACE VIEW ${stats_db_name}.result AS SELECT *, bestlicence AS acces -- To see with Antonis if the following is needed and where it should be placed ------------------------------------------------------------------------------- CREATE TABLE ${stats_db_name}.numbers_country AS SELECT org.country AS country, count(distinct rd.datasource) AS datasources, count(distinct r.id) AS publications FROM ${stats_db_name}.result r, ${stats_db_name}.result_datasources rd, ${stats_db_name}.datasource d, ${stats_db_name}.datasource_organizations dor, ${stats_db_name}.organization org WHERE r.id=rd.id AND rd.datasource=d.id AND d.id=dor.id AND dor.organization=org.id AND r.type='publication' AND r.bestlicence='Open Access' GROUP BY org.country; + +ANALYZE TABLE ${stats_db_name}.datasource COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.datasource COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.publication COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.dataset COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.software COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.numbers_country COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.numbers_country COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index 7957703130..4c1ca0203d 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -57,3 +57,12 @@ UNION ALL SELECT * FROM ${stats_db_name}.software_sources UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; + +ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.datast_sources COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql index 4a56b5d686..e05e648b4f 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql @@ -47,3 +47,16 @@ FROM ( SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false) d on o.datasource = d.id; + +ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.datast_licenses COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_licenses COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_licenses COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_licenses COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.organization_pids COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.organization_pids COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.organization_sources COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.organization_sources COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql index 60b37048bd..4940a73daf 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql @@ -34,3 +34,12 @@ union all select * from ${stats_db_name}.software_refereed union all select * from ${stats_db_name}.otherresearchproduct_refereed; + +ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.datast_refereed COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16.sql index 33849b9606..a7e6c74e44 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16.sql @@ -77,4 +77,15 @@ join ${stats_db_name}.result_datasources rd on rd.id=r.id join ${stats_db_name}.datasource d on d.id=rd.datasource join ${stats_db_name}.datasource_organizations dor on dor.id=d.id join ${stats_db_name}.organization o on o.id=dor.organization -where o.country is not null and o.country!=''; \ No newline at end of file +where o.country is not null and o.country!=''; + +ANALYZE TABLE ${stats_db_name}.result_peerreviewed COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.result_peerreviewed COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.result_greenoa COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.result_greenoa COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.result_gold COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.result_gold COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.result_affiliated_country COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.result_affiliated_country COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.result_deposited_country COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.result_deposited_country COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql index f737c1ea61..52b7a58fab 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql @@ -52,4 +52,7 @@ LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id; drop table if exists ${stats_db_name}.result; drop view if exists ${stats_db_name}.result; create table ${stats_db_name}.result stored as parquet as select * from ${stats_db_name}.result_tmp; -drop table ${stats_db_name}.result_tmp; \ No newline at end of file +drop table ${stats_db_name}.result_tmp; + +ANALYZE TABLE ${stats_db_name}.result COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.result COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql index ced7bbc11d..273a121082 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql @@ -29,4 +29,11 @@ select rcount.pid, sum(case when rcount.type='publication' then rcount.count els from rcount group by rcount.pid; -create view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture \ No newline at end of file +create view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture + +ANALYZE TABLE ${stats_db_name}.result_projectcount COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.result_projectcount COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.result_fundercount COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.result_fundercount COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.project_resultcount COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.project_resultcount COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql index ba0db25bec..ccd3994b44 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql @@ -5,8 +5,6 @@ -------------------------------------------------------------- -- Publication temporary table -DROP TABLE IF EXISTS ${stats_db_name}.publication_tmp; - CREATE TABLE ${stats_db_name}.publication_tmp (id STRING, title STRING, publisher STRING, journal STRING, date STRING, year STRING, bestlicence STRING, embargo_end_date STRING, delayed BOOLEAN, authors INT, source STRING, abstract BOOLEAN, type STRING ) clustered by (id) into 100 buckets stored as orc tblproperties('transactional'='true'); INSERT INTO ${stats_db_name}.publication_tmp SELECT substr(p.id, 4) as id, p.title[0].value as title, p.publisher.value as publisher, p.journal.name as journal , @@ -41,4 +39,23 @@ CREATE TABLE ${stats_db_name}.publication_pids AS SELECT substr(p.id, 4) AS id, CREATE TABLE ${stats_db_name}.publication_topics as select substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS TYPE, subjects.subject.value AS topic FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference=false; -- Publication_citations -CREATE TABLE ${stats_db_name}.publication_citations AS SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result FROM ${openaire_db_name}.publication p lateral view explode(p.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") !="" and p.datainfo.deletedbyinference=false; \ No newline at end of file +CREATE TABLE ${stats_db_name}.publication_citations AS SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result FROM ${openaire_db_name}.publication p lateral view explode(p.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") !="" and p.datainfo.deletedbyinference=false; + +ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql index f69715a319..0100efe181 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql @@ -5,7 +5,6 @@ ------------------------------------------------------ -- Dataset temporary table supporting updates -DROP TABLE IF EXISTS ${stats_db_name}.dataset_tmp; CREATE TABLE ${stats_db_name}.dataset_tmp (id STRING, title STRING, publisher STRING, journal STRING, date STRING, year STRING, bestlicence STRING, embargo_end_date STRING, delayed BOOLEAN, authors INT, source STRING, abstract BOOLEAN, type STRING ) clustered by (id) into 100 buckets stored AS orc tblproperties('transactional'='true'); INSERT INTO ${stats_db_name}.dataset_tmp SELECT substr(d.id, 4) AS id, d.title[0].value AS title, d.publisher.value AS publisher, cast(null AS string) AS journal, @@ -34,3 +33,20 @@ CREATE TABLE ${stats_db_name}.dataset_oids AS SELECT substr(p.id, 4) AS id, oids CREATE TABLE ${stats_db_name}.dataset_pids AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference=false; CREATE TABLE ${stats_db_name}.dataset_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference=false; + +ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql index 2c4a625e18..b44bc08c6b 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql @@ -5,7 +5,6 @@ -------------------------------------------------------- -- Software temporary table supporting updates -DROP TABLE IF EXISTS ${stats_db_name}.software_tmp; CREATE TABLE ${stats_db_name}.software_tmp (id STRING, title STRING, publisher STRING, journal STRING, date STRING, year STRING, bestlicence STRING, embargo_end_date STRING, delayed BOOLEAN, authors INT, source STRING, abstract BOOLEAN, type STRING ) clustered by (id) INTO 100 buckets stored AS orc tblproperties('transactional'='true'); INSERT INTO ${stats_db_name}.software_tmp SELECT substr(s.id, 4) as id, s.title[0].value AS title, s.publisher.value AS publisher, CAST(NULL AS string) AS journal, @@ -34,3 +33,20 @@ CREATE TABLE ${stats_db_name}.software_oids AS SELECT substr(p.id, 4) AS id, oid CREATE TABLE ${stats_db_name}.software_pids AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference=false; CREATE TABLE ${stats_db_name}.software_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference=false; + +ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql index 1fa5df8cb6..a8b099d8db 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql @@ -5,7 +5,6 @@ -------------------------------------------------------------------------------- -- Otherresearchproduct temporary table supporting updates -DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_tmp; CREATE TABLE ${stats_db_name}.otherresearchproduct_tmp ( id STRING, title STRING, publisher STRING, journal STRING, date STRING, year STRING, bestlicence STRING, embargo_end_date STRING, delayed BOOLEAN, authors INT, source STRING, abstract BOOLEAN, type STRING ) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties('transactional'='true'); INSERT INTO ${stats_db_name}.otherresearchproduct_tmp SELECT substr(o.id, 4) AS id, o.title[0].value AS title, o.publisher.value AS publisher, CAST(NULL AS string) AS journal, @@ -23,9 +22,7 @@ CREATE TABLE ${stats_db_name}.otherresearchproduct_classifications AS SELECT sub CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts AS SELECT substr(p.id, 4) AS id, contexts.context.id AS concept FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.context) contexts AS context where p.datainfo.deletedbyinference=false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources AS SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource -from ${openaire_db_name}.otherresearchproduct p lateral view explode(p.instance) instances as instance where p.datainfo.deletedbyinference=false) p LEFT OUTER JOIN -(SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false) d on p.datasource = d.id; +CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources AS SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource from ${openaire_db_name}.otherresearchproduct p lateral view explode(p.instance) instances as instance where p.datainfo.deletedbyinference=false) p LEFT OUTER JOIN(SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false) d on p.datasource = d.id; CREATE TABLE ${stats_db_name}.otherresearchproduct_languages AS SELECT substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.otherresearchproduct p where p.datainfo.deletedbyinference=false; @@ -34,3 +31,20 @@ CREATE TABLE ${stats_db_name}.otherresearchproduct_oids AS SELECT substr(p.id, 4 CREATE TABLE ${stats_db_name}.otherresearchproduct_pids AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference=false; CREATE TABLE ${stats_db_name}.otherresearchproduct_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference=false; + +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index b4745535df..0091caad1f 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -6,21 +6,17 @@ ------------------------------------------------------ ------------------------------------------------------ -- Project_oids Table -DROP TABLE IF EXISTS ${stats_db_name}.project_oids; CREATE TABLE ${stats_db_name}.project_oids AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.project p LATERAL VIEW explode(p.originalid) oids AS ids; -- Project_organizations Table -DROP TABLE IF EXISTS ${stats_db_name}.project_organizations; CREATE TABLE ${stats_db_name}.project_organizations AS SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization from ${openaire_db_name}.relation r WHERE r.reltype='projectOrganization' and r.datainfo.deletedbyinference=false; -- Project_results Table -DROP TABLE IF EXISTS ${stats_db_name}.project_results; CREATE TABLE ${stats_db_name}.project_results AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result FROM ${openaire_db_name}.relation r WHERE r.reltype='resultProject' and r.datainfo.deletedbyinference=false; -- Project table ---------------- -- Creating and populating temporary Project table -DROP TABLE IF EXISTS ${stats_db_name}.project_tmp; CREATE TABLE ${stats_db_name}.project_tmp (id STRING, acronym STRING, title STRING, funder STRING, funding_lvl0 STRING, funding_lvl1 STRING, funding_lvl2 STRING, ec39 STRING, type STRING, startdate STRING, enddate STRING, start_year INT, end_year INT, duration INT, haspubs STRING, numpubs INT, daysforlastpub INT, delayedpubs INT, callidentifier STRING, code STRING) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties('transactional'='true'); INSERT INTO ${stats_db_name}.project_tmp SELECT substr(p.id, 4) AS id, p.acronym.value AS acronym, p.title.value AS title, xpath_string(p.fundingtree[0].value, '//funder/name') AS funder, xpath_string(p.fundingtree[0].value, '//funding_level_0/name') AS funding_lvl0, xpath_string(p.fundingtree[0].value, '//funding_level_1/name') AS funding_lvl1, xpath_string(p.fundingtree[0].value, '//funding_level_2/name') AS funding_lvl2, p.ecsc39.value AS ec39, p.contracttype.classname AS type, p.startdate.value AS startdate, p.enddate.value AS enddate, year(p.startdate.value) AS start_year, year(p.enddate.value) AS end_year, CAST(MONTHS_BETWEEN(p.enddate.value, p.startdate.value) AS INT) AS duration, 'no' AS haspubs, 0 AS numpubs, 0 AS daysforlastpub, 0 AS delayedpubs, p.callidentifier.value AS callidentifier, p.code.value AS code FROM ${openaire_db_name}.project p WHERE p.datainfo.deletedbyinference=false; @@ -28,3 +24,14 @@ INSERT INTO ${stats_db_name}.project_tmp SELECT substr(p.id, 4) AS id, p.acronym create table ${stats_db_name}.funder as select distinct xpath_string(fund, '//funder/id') as id, xpath_string(fund, '//funder/name') as name, xpath_string(fund, '//funder/shortname') as shortname from ${openaire_db_name}.project p lateral view explode(p.fundingtree.value) fundingtree as fund + +ANALYZE TABLE ${stats_db_name}.project_oids COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.project_oids COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.project_organizations COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.project_organizations COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.project_results COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.project_results COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.project_tmp COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.project_tmp COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.funder COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.funder COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index 36a4a8a49f..8506657a67 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -24,8 +24,11 @@ CREATE OR REPLACE VIEW ${stats_db_name}.result_pids AS SELECT * FROM ${stats_db_ CREATE OR REPLACE VIEW ${stats_db_name}.result_topics AS SELECT * FROM ${stats_db_name}.publication_topics UNION ALL SELECT * FROM ${stats_db_name}.software_topics UNION ALL SELECT * FROM ${stats_db_name}.dataset_topics UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_topics; -DROP TABLE IF EXISTS ${stats_db_name}.result_organization; CREATE TABLE ${stats_db_name}.result_organization AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype='resultOrganization' and r.datainfo.deletedbyinference=false; -DROP TABLE IF EXISTS ${stats_db_name}.result_projects; CREATE TABLE ${stats_db_name}.result_projects AS select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend FROM ${stats_db_name}.result r JOIN ${stats_db_name}.project_results pr ON r.id=pr.result JOIN ${stats_db_name}.project_tmp p ON p.id=pr.id; + +ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index 197047c8b9..e74ecc7683 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -55,4 +55,11 @@ create table if not exists ${stats_db_name}.datasource_sources AS select substr( CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS SELECT datasource AS id, id AS result FROM ${stats_db_name}.result_datasources; - +ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS FOR COLUMNS; +ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql index a918e4de48..4fb9919c99 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql @@ -10,3 +10,6 @@ FROM ${openaire_db_name}.organization o WHERE o.datainfo.deletedbyinference=FALS CREATE OR REPLACE VIEW ${stats_db_name}.organization_datasources AS SELECT organization AS id, id AS datasource FROM ${stats_db_name}.datasource_organizations; CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects AS SELECT id AS project, organization as id FROM ${stats_db_name}.project_organizations; + +ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file From 1c029b9fc075ee77386fb187033740ec7d501406 Mon Sep 17 00:00:00 2001 From: antleb Date: Sun, 14 Feb 2021 03:14:24 +0200 Subject: [PATCH 091/106] fixed formatting --- .../graph/stats/oozie_app/scripts/step10.sql | 42 ++++-- .../graph/stats/oozie_app/scripts/step11.sql | 129 ++++++++++++++---- .../graph/stats/oozie_app/scripts/step12.sql | 54 ++++++-- .../graph/stats/oozie_app/scripts/step2.sql | 98 +++++++++---- .../graph/stats/oozie_app/scripts/step3.sql | 96 ++++++++++--- .../graph/stats/oozie_app/scripts/step4.sql | 96 ++++++++++--- .../graph/stats/oozie_app/scripts/step5.sql | 83 +++++++++-- .../graph/stats/oozie_app/scripts/step6.sql | 77 +++++++++-- .../graph/stats/oozie_app/scripts/step7.sql | 129 ++++++++++++++++-- .../graph/stats/oozie_app/scripts/step8.sql | 112 ++++++++++----- .../graph/stats/oozie_app/scripts/step9.sql | 18 ++- 11 files changed, 744 insertions(+), 190 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql index e2e37d3fca..d5ae0a5c8c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql @@ -3,14 +3,37 @@ -- Tables/views from external tables/views (Fundref, Country, CountyGDP, roarmap, rndexpediture) ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ -CREATE OR REPLACE VIEW ${stats_db_name}.fundref AS SELECT * FROM ${external_stats_db_name}.fundref; -CREATE OR REPLACE VIEW ${stats_db_name}.country AS SELECT * FROM ${external_stats_db_name}.country; -CREATE OR REPLACE VIEW ${stats_db_name}.countrygdp AS SELECT * FROM ${external_stats_db_name}.countrygdp; -CREATE OR REPLACE VIEW ${stats_db_name}.roarmap AS SELECT * FROM ${external_stats_db_name}.roarmap; -CREATE OR REPLACE VIEW ${stats_db_name}.rndexpediture AS SELECT * FROM ${external_stats_db_name}.rndexpediture; -CREATE OR REPLACE VIEW ${stats_db_name}.context AS SELECT * FROM ${external_stats_db_name}.context; -CREATE OR REPLACE VIEW ${stats_db_name}.category AS SELECT * FROM ${external_stats_db_name}.category; -CREATE OR REPLACE VIEW ${stats_db_name}.concept AS SELECT * FROM ${external_stats_db_name}.concept; +CREATE OR REPLACE VIEW ${stats_db_name}.fundref AS +SELECT * +FROM ${external_stats_db_name}.fundref; + +CREATE OR REPLACE VIEW ${stats_db_name}.country AS +SELECT * +FROM ${external_stats_db_name}.country; + +CREATE OR REPLACE VIEW ${stats_db_name}.countrygdp AS +SELECT * +FROM ${external_stats_db_name}.countrygdp; + +CREATE OR REPLACE VIEW ${stats_db_name}.roarmap AS +SELECT * +FROM ${external_stats_db_name}.roarmap; + +CREATE OR REPLACE VIEW ${stats_db_name}.rndexpediture AS +SELECT * +FROM ${external_stats_db_name}.rndexpediture; + +CREATE OR REPLACE VIEW ${stats_db_name}.context AS +SELECT * +FROM ${external_stats_db_name}.context; + +CREATE OR REPLACE VIEW ${stats_db_name}.category AS +SELECT * +FROM ${external_stats_db_name}.category; + +CREATE OR REPLACE VIEW ${stats_db_name}.concept AS +SELECT * +FROM ${external_stats_db_name}.concept; ------------------------------------------------------------------------------------------------ @@ -18,7 +41,8 @@ CREATE OR REPLACE VIEW ${stats_db_name}.concept AS SELECT * FROM ${external_sta -- Creation date of the database ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ -create table ${stats_db_name}.creation_date as select date_format(current_date(), 'dd-MM-yyyy') as date; +create table ${stats_db_name}.creation_date as +select date_format(current_date(), 'dd-MM-yyyy') as date; ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql index 25f9f09aea..db5fdb1c38 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql @@ -5,43 +5,114 @@ ---------------------------------------------------------------- --Datasource temporary table updates -UPDATE ${stats_db_name}.datasource_tmp SET harvested='true' WHERE datasource_tmp.id IN (SELECT DISTINCT d.id FROM ${stats_db_name}.datasource_tmp d, ${stats_db_name}.result_datasources rd WHERE d.id=rd.datasource); +UPDATE ${stats_db_name}.datasource_tmp +SET harvested='true' +WHERE datasource_tmp.id IN (SELECT DISTINCT d.id + FROM ${stats_db_name}.datasource_tmp d, + ${stats_db_name}.result_datasources rd + WHERE d.id = rd.datasource); -- Project temporary table update and final project table creation with final updates that can not be applied to ORC tables -UPDATE ${stats_db_name}.project_tmp SET haspubs='yes' WHERE project_tmp.id IN (SELECT pr.id FROM ${stats_db_name}.project_results pr, ${stats_db_name}.result r WHERE pr.result=r.id AND r.type='publication'); +UPDATE ${stats_db_name}.project_tmp +SET haspubs='yes' +WHERE project_tmp.id IN (SELECT pr.id + FROM ${stats_db_name}.project_results pr, + ${stats_db_name}.result r + WHERE pr.result = r.id + AND r.type = 'publication'); -DROP TABLE IF EXISTS ${stats_db_name}.project; CREATE TABLE ${stats_db_name}.project stored as parquet as -SELECT p.id , p.acronym, p.title, p.funder, p.funding_lvl0, p.funding_lvl1, p.funding_lvl2, p.ec39, p.type, p.startdate, p.enddate, p.start_year, p.end_year, p.duration, -CASE WHEN prr1.id IS NULL THEN 'no' ELSE 'yes' END AS haspubs, -CASE WHEN prr1.id IS NULL THEN 0 ELSE prr1.np END AS numpubs, -CASE WHEN prr2.id IS NULL THEN 0 ELSE prr2.daysForlastPub END AS daysforlastpub, -CASE WHEN prr2.id IS NULL THEN 0 ELSE prr2.dp END AS delayedpubs, -p.callidentifier, p.code -FROM ${stats_db_name}.project_tmp p -LEFT JOIN (SELECT pr.id, count(distinct pr.result) AS np - FROM ${stats_db_name}.project_results pr INNER JOIN ${stats_db_name}.result r ON pr.result=r.id - WHERE r.type='publication' - GROUP BY pr.id) AS prr1 on prr1.id = p.id -LEFT JOIN (SELECT pp.id, max(datediff(to_date(r.date), to_date(pp.enddate)) ) AS daysForlastPub , count(distinct r.id) AS dp - FROM ${stats_db_name}.project_tmp pp, ${stats_db_name}.project_results pr, ${stats_db_name}.result r - WHERE pp.id=pr.id AND pr.result=r.id AND r.type='publication' AND datediff(to_date(r.date), to_date(pp.enddate)) > 0 - GROUP BY pp.id) AS prr2 - ON prr2.id = p.id; - --- Publication temporary table updates -UPDATE ${stats_db_name}.publication_tmp SET delayed = 'yes' WHERE publication_tmp.id IN (SELECT distinct r.id FROM stats_wf_db_obs.result r, ${stats_db_name}.project_results pr, ${stats_db_name}.project_tmp p WHERE r.id=pr.result AND pr.id=p.id AND to_date(r.date)-to_date(p.enddate) > 0); +SELECT p.id, + p.acronym, + p.title, + p.funder, + p.funding_lvl0, + p.funding_lvl1, + p.funding_lvl2, + p.ec39, + p.type, + p.startdate, + p.enddate, + p.start_year, + p.end_year, + p.duration, + CASE WHEN prr1.id IS NULL THEN 'no' ELSE 'yes' END AS haspubs, + CASE WHEN prr1.id IS NULL THEN 0 ELSE prr1.np END AS numpubs, + CASE WHEN prr2.id IS NULL THEN 0 ELSE prr2.daysForlastPub END AS daysforlastpub, + CASE WHEN prr2.id IS NULL THEN 0 ELSE prr2.dp END AS delayedpubs, + p.callidentifier, + p.code +FROM ${stats_db_name}.project_tmp p + LEFT JOIN (SELECT pr.id, count(distinct pr.result) AS np + FROM ${stats_db_name}.project_results pr + INNER JOIN ${stats_db_name}.result r ON pr.result = r.id + WHERE r.type = 'publication' + GROUP BY pr.id) AS prr1 on prr1.id = p.id + LEFT JOIN (SELECT pp.id, + max(datediff(to_date(r.date), to_date(pp.enddate))) AS daysForlastPub, + count(distinct r.id) AS dp + FROM ${stats_db_name}.project_tmp pp, + ${stats_db_name}.project_results pr, + ${stats_db_name}.result r + WHERE pp.id = pr.id + AND pr.result = r.id + AND r.type = 'publication' + AND datediff(to_date(r.date), to_date(pp.enddate)) > 0 + GROUP BY pp.id) AS prr2 + ON prr2.id = p.id; --- Dataset temporary table updates -UPDATE ${stats_db_name}.dataset_tmp SET delayed = 'yes' WHERE dataset_tmp.id IN (SELECT distinct r.id FROM stats_wf_db_obs.result r, ${stats_db_name}.project_results pr, ${stats_db_name}.project_tmp p WHERE r.id=pr.result AND pr.id=p.id AND to_date(r.date)-to_date(p.enddate) > 0); +UPDATE ${stats_db_name}.publication_tmp +SET delayed = 'yes' +WHERE publication_tmp.id IN (SELECT distinct r.id + FROM stats_wf_db_obs.result r, + ${stats_db_name}.project_results pr, + ${stats_db_name}.project_tmp p + WHERE r.id = pr.result + AND pr.id = p.id + AND to_date(r.date) - to_date(p.enddate) > 0); --- Software temporary table updates -UPDATE ${stats_db_name}.software_tmp SET delayed = 'yes' WHERE software_tmp.id IN (SELECT distinct r.id FROM ${stats_db_name}.result r, ${stats_db_name}.project_results pr, ${stats_db_name}.project_tmp p WHERE r.id=pr.result AND pr.id=p.id AND to_date(r.date)-to_date(p.enddate) > 0); +UPDATE ${stats_db_name}.dataset_tmp +SET delayed = 'yes' +WHERE dataset_tmp.id IN (SELECT distinct r.id + FROM stats_wf_db_obs.result r, + ${stats_db_name}.project_results pr, + ${stats_db_name}.project_tmp p + WHERE r.id = pr.result + AND pr.id = p.id + AND to_date(r.date) - to_date(p.enddate) > 0); --- Oherresearchproduct temporary table updates -UPDATE ${stats_db_name}.otherresearchproduct_tmp SET delayed = 'yes' WHERE otherresearchproduct_tmp.id IN (SELECT distinct r.id FROM ${stats_db_name}.result r, ${stats_db_name}.project_results pr, ${stats_db_name}.project_tmp p WHERE r.id=pr.result AND pr.id=p.id AND to_date(r.date)-to_date(p.enddate) > 0); +UPDATE ${stats_db_name}.software_tmp +SET delayed = 'yes' +WHERE software_tmp.id IN (SELECT distinct r.id + FROM ${stats_db_name}.result r, + ${stats_db_name}.project_results pr, + ${stats_db_name}.project_tmp p + WHERE r.id = pr.result + AND pr.id = p.id + AND to_date(r.date) - to_date(p.enddate) > 0); -CREATE OR REPLACE VIEW ${stats_db_name}.project_results_publication AS SELECT result_projects.id AS result, result_projects.project AS project_results, result.date as resultdate, project.enddate as projectenddate, result_projects.daysfromend AS daysfromend FROM ${stats_db_name}.result_projects, ${stats_db_name}.result, ${stats_db_name}.project WHERE result_projects.id=result.id AND result.type='publication' AND project.id=result_projects.project; +UPDATE ${stats_db_name}.otherresearchproduct_tmp +SET delayed = 'yes' +WHERE otherresearchproduct_tmp.id IN (SELECT distinct r.id + FROM ${stats_db_name}.result r, + ${stats_db_name}.project_results pr, + ${stats_db_name}.project_tmp p + WHERE r.id = pr.result + AND pr.id = p.id + AND to_date(r.date) - to_date(p.enddate) > 0); + +CREATE OR REPLACE VIEW ${stats_db_name}.project_results_publication AS +SELECT result_projects.id AS result, + result_projects.project AS project_results, + result.date as resultdate, + project.enddate as projectenddate, + result_projects.daysfromend AS daysfromend +FROM ${stats_db_name}.result_projects, + ${stats_db_name}.result, + ${stats_db_name}.project +WHERE result_projects.id = result.id + AND result.type = 'publication' + AND project.id = result_projects.project; ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql index bf3f1d6153..779547a841 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql @@ -1,21 +1,25 @@ ------------------------------------------------------------------------------------------------------ -- Creating parquet tables from the updated temporary tables and removing unnecessary temporary tables ------------------------------------------------------------------------------------------------------ +CREATE TABLE ${stats_db_name}.datasource stored AS parquet AS +SELECT * +FROM ${stats_db_name}.datasource_tmp; -DROP TABLE IF EXISTS ${stats_db_name}.datasource; -CREATE TABLE ${stats_db_name}.datasource stored AS parquet AS SELECT * FROM ${stats_db_name}.datasource_tmp; +CREATE TABLE ${stats_db_name}.publication stored AS parquet AS +SELECT * +FROM ${stats_db_name}.publication_tmp; -DROP TABLE IF EXISTS ${stats_db_name}.publication; -CREATE TABLE ${stats_db_name}.publication stored AS parquet AS SELECT * FROM ${stats_db_name}.publication_tmp; +CREATE TABLE ${stats_db_name}.dataset stored AS parquet AS +SELECT * +FROM ${stats_db_name}.dataset_tmp; -DROP TABLE IF EXISTS ${stats_db_name}.dataset; -CREATE TABLE ${stats_db_name}.dataset stored AS parquet AS SELECT * FROM ${stats_db_name}.dataset_tmp; +CREATE TABLE ${stats_db_name}.software stored AS parquet AS +SELECT * +FROM ${stats_db_name}.software_tmp; -DROP TABLE IF EXISTS ${stats_db_name}.software; -CREATE TABLE ${stats_db_name}.software stored AS parquet AS SELECT * FROM ${stats_db_name}.software_tmp; - -DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct; -CREATE TABLE ${stats_db_name}.otherresearchproduct stored AS parquet AS SELECT * FROM ${stats_db_name}.otherresearchproduct_tmp; +CREATE TABLE ${stats_db_name}.otherresearchproduct stored AS parquet AS +SELECT * +FROM ${stats_db_name}.otherresearchproduct_tmp; DROP TABLE ${stats_db_name}.project_tmp; DROP TABLE ${stats_db_name}.datasource_tmp; @@ -29,13 +33,37 @@ DROP TABLE ${stats_db_name}.otherresearchproduct_tmp; --------------------------------------------- -- Result -CREATE OR REPLACE VIEW ${stats_db_name}.result AS SELECT *, bestlicence AS access_mode FROM ${stats_db_name}.publication UNION ALL SELECT *, bestlicence as access_mode FROM ${stats_db_name}.software UNION ALL SELECT *, bestlicence AS access_mode FROM ${stats_db_name}.dataset UNION ALL SELECT *, bestlicence AS access_mode FROM ${stats_db_name}.otherresearchproduct; +CREATE OR REPLACE VIEW ${stats_db_name}.result AS +SELECT *, bestlicence AS access_mode +FROM ${stats_db_name}.publication +UNION ALL +SELECT *, bestlicence as access_mode +FROM ${stats_db_name}.software +UNION ALL +SELECT *, bestlicence AS access_mode +FROM ${stats_db_name}.dataset +UNION ALL +SELECT *, bestlicence AS access_mode +FROM ${stats_db_name}.otherresearchproduct; ------------------------------------------------------------------------------- -- To see with Antonis if the following is needed and where it should be placed ------------------------------------------------------------------------------- -CREATE TABLE ${stats_db_name}.numbers_country AS SELECT org.country AS country, count(distinct rd.datasource) AS datasources, count(distinct r.id) AS publications FROM ${stats_db_name}.result r, ${stats_db_name}.result_datasources rd, ${stats_db_name}.datasource d, ${stats_db_name}.datasource_organizations dor, ${stats_db_name}.organization org WHERE r.id=rd.id AND rd.datasource=d.id AND d.id=dor.id AND dor.organization=org.id AND r.type='publication' AND r.bestlicence='Open Access' GROUP BY org.country; +CREATE TABLE ${stats_db_name}.numbers_country AS +SELECT org.country AS country, count(distinct rd.datasource) AS datasources, count(distinct r.id) AS publications +FROM ${stats_db_name}.result r, + ${stats_db_name}.result_datasources rd, + ${stats_db_name}.datasource d, + ${stats_db_name}.datasource_organizations dor, + ${stats_db_name}.organization org +WHERE r.id = rd.id + AND rd.datasource = d.id + AND d.id = dor.id + AND dor.organization = org.id + AND r.type = 'publication' + AND r.bestlicence = 'Open Access' +GROUP BY org.country; ANALYZE TABLE ${stats_db_name}.datasource COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.datasource COMPUTE STATISTICS FOR COLUMNS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql index ccd3994b44..d2700f415c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql @@ -5,41 +5,93 @@ -------------------------------------------------------------- -- Publication temporary table -CREATE TABLE ${stats_db_name}.publication_tmp (id STRING, title STRING, publisher STRING, journal STRING, date STRING, year STRING, bestlicence STRING, embargo_end_date STRING, delayed BOOLEAN, authors INT, source STRING, abstract BOOLEAN, type STRING ) clustered by (id) into 100 buckets stored as orc tblproperties('transactional'='true'); +CREATE TABLE ${stats_db_name}.publication_tmp +( + id STRING, + title STRING, + publisher STRING, + journal STRING, + date STRING, + year STRING, + bestlicence STRING, + embargo_end_date STRING, + delayed BOOLEAN, + authors INT, + source STRING, + abstract BOOLEAN, + type STRING +) + clustered by (id) into 100 buckets stored as orc tblproperties ('transactional' = 'true'); -INSERT INTO ${stats_db_name}.publication_tmp SELECT substr(p.id, 4) as id, p.title[0].value as title, p.publisher.value as publisher, p.journal.name as journal , -p.dateofacceptance.value as date, date_format(p.dateofacceptance.value,'yyyy') as year, p.bestaccessright.classname as bestlicence, -p.embargoenddate.value as embargo_end_date, false as delayed, size(p.author) as authors , concat_ws('\u003B',p.source.value) as source, -case when size(p.description) > 0 then true else false end as abstract, -'publication' as type +INSERT INTO ${stats_db_name}.publication_tmp +SELECT substr(p.id, 4) as id, + p.title[0].value as title, + p.publisher.value as publisher, + p.journal.name as journal, + p.dateofacceptance.value as date, + date_format(p.dateofacceptance.value, 'yyyy') as year, + p.bestaccessright.classname as bestlicence, + p.embargoenddate.value as embargo_end_date, + false as delayed, + size(p.author) as authors, + concat_ws('\u003B', p.source.value) as source, + case when size(p.description) > 0 then true else false end as abstract, + 'publication' as type from ${openaire_db_name}.publication p -where p.datainfo.deletedbyinference=false; +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.publication_classifications AS SELECT substr(p.id, 4) as id, instancetype.classname as type from ${openaire_db_name}.publication p LATERAL VIEW explode(p.instance.instancetype) instances as instancetype where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.publication_classifications AS +SELECT substr(p.id, 4) as id, instancetype.classname as type +from ${openaire_db_name}.publication p + LATERAL VIEW explode(p.instance.instancetype) instances as instancetype +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.publication_concepts AS SELECT substr(p.id, 4) as id, contexts.context.id as concept from ${openaire_db_name}.publication p LATERAL VIEW explode(p.context) contexts as context where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.publication_concepts AS +SELECT substr(p.id, 4) as id, contexts.context.id as concept +from ${openaire_db_name}.publication p + LATERAL VIEW explode(p.context) contexts as context +where p.datainfo.deletedbyinference = false; CREATE TABLE ${stats_db_name}.publication_datasources as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource - FROM ( - SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) as datasource - from ${openaire_db_name}.publication p lateral view explode(p.instance) instances as instance - where p.datainfo.deletedbyinference=false ) p - LEFT OUTER JOIN ( - SELECT substr(d.id, 4) id - from ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference=false ) d on p.datasource = d.id; +FROM ( + SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) as datasource + from ${openaire_db_name}.publication p lateral view explode(p.instance) instances as instance + where p.datainfo.deletedbyinference = false) p + LEFT OUTER JOIN ( + SELECT substr(d.id, 4) id + from ${openaire_db_name}.datasource d + WHERE d.datainfo.deletedbyinference = false) d on p.datasource = d.id; -CREATE TABLE ${stats_db_name}.publication_languages AS select substr(p.id, 4) as id, p.language.classname as language FROM ${openaire_db_name}.publication p where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.publication_languages AS +select substr(p.id, 4) as id, p.language.classname as language +FROM ${openaire_db_name}.publication p +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.publication_oids AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.publication_oids AS +SELECT substr(p.id, 4) AS id, oids.ids AS oid +FROM ${openaire_db_name}.publication p + LATERAL VIEW explode(p.originalid) oids AS ids +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.publication_pids AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value as pid FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.publication_pids AS +SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value as pid +FROM ${openaire_db_name}.publication p + LATERAL VIEW explode(p.pid) pids AS ppid +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.publication_topics as select substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS TYPE, subjects.subject.value AS topic FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.publication_topics as +select substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS TYPE, subjects.subject.value AS topic +FROM ${openaire_db_name}.publication p + LATERAL VIEW explode(p.subject) subjects AS subject +where p.datainfo.deletedbyinference = false; --- Publication_citations -CREATE TABLE ${stats_db_name}.publication_citations AS SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result FROM ${openaire_db_name}.publication p lateral view explode(p.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") !="" and p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.publication_citations AS +SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result +FROM ${openaire_db_name}.publication p + lateral view explode(p.extrainfo) citations AS citation +WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" + and p.datainfo.deletedbyinference = false; ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS FOR COLUMNS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql index 0100efe181..977d321322 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql @@ -5,34 +5,94 @@ ------------------------------------------------------ -- Dataset temporary table supporting updates -CREATE TABLE ${stats_db_name}.dataset_tmp (id STRING, title STRING, publisher STRING, journal STRING, date STRING, year STRING, bestlicence STRING, embargo_end_date STRING, delayed BOOLEAN, authors INT, source STRING, abstract BOOLEAN, type STRING ) clustered by (id) into 100 buckets stored AS orc tblproperties('transactional'='true'); +CREATE TABLE ${stats_db_name}.dataset_tmp +( + id STRING, + title STRING, + publisher STRING, + journal STRING, + date STRING, + year STRING, + bestlicence STRING, + embargo_end_date STRING, + delayed BOOLEAN, + authors INT, + source STRING, + abstract BOOLEAN, + type STRING +) + clustered by (id) into 100 buckets stored AS orc tblproperties ('transactional' = 'true'); -INSERT INTO ${stats_db_name}.dataset_tmp SELECT substr(d.id, 4) AS id, d.title[0].value AS title, d.publisher.value AS publisher, cast(null AS string) AS journal, -d.dateofacceptance.value as date, date_format(d.dateofacceptance.value,'yyyy') AS year, d.bestaccessright.classname AS bestlicence, -d.embargoenddate.value AS embargo_end_date, false AS delayed, size(d.author) AS authors , concat_ws('\u003B',d.source.value) AS source, - CASE WHEN SIZE(d.description) > 0 THEN TRUE ELSE FALSE end AS abstract, -'dataset' AS type +INSERT INTO ${stats_db_name}.dataset_tmp +SELECT substr(d.id, 4) AS id, + d.title[0].value AS title, + d.publisher.value AS publisher, + cast(null AS string) AS journal, + d.dateofacceptance.value as date, + date_format(d.dateofacceptance.value, 'yyyy') AS year, + d.bestaccessright.classname AS bestlicence, + d.embargoenddate.value AS embargo_end_date, + false AS delayed, + size(d.author) AS authors, + concat_ws('\u003B', d.source.value) AS source, + CASE WHEN SIZE(d.description) > 0 THEN TRUE ELSE FALSE end AS abstract, + 'dataset' AS type FROM ${openaire_db_name}.dataset d -WHERE d.datainfo.deletedbyinference=FALSE; +WHERE d.datainfo.deletedbyinference = FALSE; --- Dataset_citations -CREATE TABLE ${stats_db_name}.dataset_citations AS SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result FROM ${openaire_db_name}.dataset d LATERAL VIEW explode(d.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") !="" and d.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.dataset_citations AS +SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result +FROM ${openaire_db_name}.dataset d + LATERAL VIEW explode(d.extrainfo) citations AS citation +WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" + and d.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.dataset_classifications AS SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.dataset_classifications AS +SELECT substr(p.id, 4) AS id, instancetype.classname AS type +FROM ${openaire_db_name}.dataset p + LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.dataset_concepts AS SELECT substr(p.id, 4) as id, contexts.context.id as concept from ${openaire_db_name}.dataset p LATERAL VIEW explode(p.context) contexts as context where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.dataset_concepts AS +SELECT substr(p.id, 4) as id, contexts.context.id as concept +from ${openaire_db_name}.dataset p + LATERAL VIEW explode(p.context) contexts as context +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.dataset_datasources AS SELECT p.id, case when d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource FROM (SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) AS datasource -FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance) instances AS instance where p.datainfo.deletedbyinference=false) p LEFT OUTER JOIN -(SELECT substr(d.id, 4) id FROM ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false) d ON p.datasource = d.id; +CREATE TABLE ${stats_db_name}.dataset_datasources AS +SELECT p.id, case when d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource +FROM ( + SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) AS datasource + FROM ${openaire_db_name}.dataset p + LATERAL VIEW explode(p.instance) instances AS instance + where p.datainfo.deletedbyinference = false) p + LEFT OUTER JOIN ( + SELECT substr(d.id, 4) id + FROM ${openaire_db_name}.datasource d + WHERE d.datainfo.deletedbyinference = false) d ON p.datasource = d.id; -CREATE TABLE ${stats_db_name}.dataset_languages AS SELECT substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.dataset p where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.dataset_languages AS +SELECT substr(p.id, 4) AS id, p.language.classname AS language +FROM ${openaire_db_name}.dataset p +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.dataset_oids AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.dataset_oids AS +SELECT substr(p.id, 4) AS id, oids.ids AS oid +FROM ${openaire_db_name}.dataset p + LATERAL VIEW explode(p.originalid) oids AS ids +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.dataset_pids AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.dataset_pids AS +SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid +FROM ${openaire_db_name}.dataset p + LATERAL VIEW explode(p.pid) pids AS ppid +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.dataset_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.dataset_topics AS +SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic +FROM ${openaire_db_name}.dataset p + LATERAL VIEW explode(p.subject) subjects AS subject +where p.datainfo.deletedbyinference = false; ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS FOR COLUMNS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql index b44bc08c6b..ace084d231 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql @@ -5,34 +5,94 @@ -------------------------------------------------------- -- Software temporary table supporting updates -CREATE TABLE ${stats_db_name}.software_tmp (id STRING, title STRING, publisher STRING, journal STRING, date STRING, year STRING, bestlicence STRING, embargo_end_date STRING, delayed BOOLEAN, authors INT, source STRING, abstract BOOLEAN, type STRING ) clustered by (id) INTO 100 buckets stored AS orc tblproperties('transactional'='true'); +CREATE TABLE ${stats_db_name}.software_tmp +( + id STRING, + title STRING, + publisher STRING, + journal STRING, + date STRING, + year STRING, + bestlicence STRING, + embargo_end_date STRING, + delayed BOOLEAN, + authors INT, + source STRING, + abstract BOOLEAN, + type STRING +) + clustered by (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); -INSERT INTO ${stats_db_name}.software_tmp SELECT substr(s.id, 4) as id, s.title[0].value AS title, s.publisher.value AS publisher, CAST(NULL AS string) AS journal, -s.dateofacceptance.value AS DATE, date_format(s.dateofacceptance.value,'yyyy') AS YEAR, s.bestaccessright.classname AS bestlicence, -s.embargoenddate.value AS embargo_end_date, FALSE AS delayed, SIZE(s.author) AS authors , concat_ws('\u003B',s.source.value) AS source, - CASE WHEN SIZE(s.description) > 0 THEN TRUE ELSE FALSE END AS abstract, -'software' as type +INSERT INTO ${stats_db_name}.software_tmp +SELECT substr(s.id, 4) as id, + s.title[0].value AS title, + s.publisher.value AS publisher, + CAST(NULL AS string) AS journal, + s.dateofacceptance.value AS DATE, + date_format(s.dateofacceptance.value, 'yyyy') AS YEAR, + s.bestaccessright.classname AS bestlicence, + s.embargoenddate.value AS embargo_end_date, + FALSE AS delayed, + SIZE(s.author) AS authors, + concat_ws('\u003B', s.source.value) AS source, + CASE WHEN SIZE(s.description) > 0 THEN TRUE ELSE FALSE END AS abstract, + 'software' as type from ${openaire_db_name}.software s -where s.datainfo.deletedbyinference=false; +where s.datainfo.deletedbyinference = false; --- Software_citations -CREATE TABLE ${stats_db_name}.software_citations AS SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS RESULT FROM ${openaire_db_name}.software s LATERAL VIEW explode(s.extrainfo) citations as citation where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") !="" and s.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.software_citations AS +SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS RESULT +FROM ${openaire_db_name}.software s + LATERAL VIEW explode(s.extrainfo) citations as citation +where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" + and s.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.software_classifications AS SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.software_classifications AS +SELECT substr(p.id, 4) AS id, instancetype.classname AS type +FROM ${openaire_db_name}.software p + LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.software_concepts AS SELECT substr(p.id, 4) AS id, contexts.context.id AS concept FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.context) contexts AS context where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.software_concepts AS +SELECT substr(p.id, 4) AS id, contexts.context.id AS concept +FROM ${openaire_db_name}.software p + LATERAL VIEW explode(p.context) contexts AS context +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.software_datasources AS SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource end as datasource FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource -FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.instance) instances AS instance where p.datainfo.deletedbyinference=false) p LEFT OUTER JOIN -(SELECT substr(d.id, 4) id FROM ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false) d ON p.datasource = d.id; +CREATE TABLE ${stats_db_name}.software_datasources AS +SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource end as datasource +FROM ( + SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource + FROM ${openaire_db_name}.software p + LATERAL VIEW explode(p.instance) instances AS instance + where p.datainfo.deletedbyinference = false) p + LEFT OUTER JOIN ( + SELECT substr(d.id, 4) id + FROM ${openaire_db_name}.datasource d + WHERE d.datainfo.deletedbyinference = false) d ON p.datasource = d.id; -CREATE TABLE ${stats_db_name}.software_languages AS select substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.software p where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.software_languages AS +select substr(p.id, 4) AS id, p.language.classname AS language +FROM ${openaire_db_name}.software p +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.software_oids AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.software_oids AS +SELECT substr(p.id, 4) AS id, oids.ids AS oid +FROM ${openaire_db_name}.software p + LATERAL VIEW explode(p.originalid) oids AS ids +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.software_pids AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.software_pids AS +SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid +FROM ${openaire_db_name}.software p + LATERAL VIEW explode(p.pid) pids AS ppid +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.software_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.software_topics AS +SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic +FROM ${openaire_db_name}.software p + LATERAL VIEW explode(p.subject) subjects AS subject +where p.datainfo.deletedbyinference = false; ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS FOR COLUMNS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql index a8b099d8db..0fd8e7189d 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql @@ -5,32 +5,85 @@ -------------------------------------------------------------------------------- -- Otherresearchproduct temporary table supporting updates -CREATE TABLE ${stats_db_name}.otherresearchproduct_tmp ( id STRING, title STRING, publisher STRING, journal STRING, date STRING, year STRING, bestlicence STRING, embargo_end_date STRING, delayed BOOLEAN, authors INT, source STRING, abstract BOOLEAN, type STRING ) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties('transactional'='true'); +CREATE TABLE ${stats_db_name}.otherresearchproduct_tmp +( + id STRING, + title STRING, + publisher STRING, + journal STRING, + date STRING, + year STRING, + bestlicence STRING, + embargo_end_date STRING, + delayed BOOLEAN, + authors INT, + source STRING, + abstract BOOLEAN, + type STRING +) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); -INSERT INTO ${stats_db_name}.otherresearchproduct_tmp SELECT substr(o.id, 4) AS id, o.title[0].value AS title, o.publisher.value AS publisher, CAST(NULL AS string) AS journal, -o.dateofacceptance.value AS DATE, date_format(o.dateofacceptance.value,'yyyy') AS year, o.bestaccessright.classname AS bestlicence, -o.embargoenddate.value as embargo_end_date, FALSE AS delayed, SIZE(o.author) AS authors , concat_ws('\u003B',o.source.value) AS source, -CASE WHEN SIZE(o.description) > 0 THEN TRUE ELSE FALSE END AS abstract, -'other' AS type +INSERT INTO ${stats_db_name}.otherresearchproduct_tmp +SELECT substr(o.id, 4) AS id, + o.title[0].value AS title, + o.publisher.value AS publisher, + CAST(NULL AS string) AS journal, + o.dateofacceptance.value AS DATE, + date_format(o.dateofacceptance.value, 'yyyy') AS year, + o.bestaccessright.classname AS bestlicence, + o.embargoenddate.value as embargo_end_date, + FALSE AS delayed, + SIZE(o.author) AS authors, + concat_ws('\u003B', o.source.value) AS source, + CASE WHEN SIZE(o.description) > 0 THEN TRUE ELSE FALSE END AS abstract, + 'other' AS type FROM ${openaire_db_name}.otherresearchproduct o -WHERE o.datainfo.deletedbyinference=FALSE; +WHERE o.datainfo.deletedbyinference = FALSE; -- Otherresearchproduct_citations -CREATE TABLE ${stats_db_name}.otherresearchproduct_citations AS SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS RESULT FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") !="" and o.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.otherresearchproduct_citations AS +SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS RESULT +FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation +WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" + and o.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_classifications AS SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.otherresearchproduct_classifications AS +SELECT substr(p.id, 4) AS id, instancetype.classname AS type +FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts AS SELECT substr(p.id, 4) AS id, contexts.context.id AS concept FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.context) contexts AS context where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts AS +SELECT substr(p.id, 4) AS id, contexts.context.id AS concept +FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.context) contexts AS context +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources AS SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource from ${openaire_db_name}.otherresearchproduct p lateral view explode(p.instance) instances as instance where p.datainfo.deletedbyinference=false) p LEFT OUTER JOIN(SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false) d on p.datasource = d.id; +CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources AS +SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource +FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource + from ${openaire_db_name}.otherresearchproduct p lateral view explode(p.instance) instances as instance + where p.datainfo.deletedbyinference = false) p + LEFT OUTER JOIN(SELECT substr(d.id, 4) id + from ${openaire_db_name}.datasource d + WHERE d.datainfo.deletedbyinference = false) d on p.datasource = d.id; -CREATE TABLE ${stats_db_name}.otherresearchproduct_languages AS SELECT substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.otherresearchproduct p where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.otherresearchproduct_languages AS +SELECT substr(p.id, 4) AS id, p.language.classname AS language +FROM ${openaire_db_name}.otherresearchproduct p +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_oids AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.otherresearchproduct_oids AS +SELECT substr(p.id, 4) AS id, oids.ids AS oid +FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.originalid) oids AS ids +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_pids AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.otherresearchproduct_pids AS +SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid +FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.pid) pids AS ppid +where p.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.otherresearchproduct_topics AS +SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic +FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject +where p.datainfo.deletedbyinference = false; ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS FOR COLUMNS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index 0091caad1f..383d3f6fd7 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -1,28 +1,75 @@ --- noinspection SqlNoDataSourceInspectionForFile - ------------------------------------------------------ ------------------------------------------------------ -- Project table/view and Project related tables/views ------------------------------------------------------ ------------------------------------------------------ --- Project_oids Table -CREATE TABLE ${stats_db_name}.project_oids AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.project p LATERAL VIEW explode(p.originalid) oids AS ids; +CREATE TABLE ${stats_db_name}.project_oids AS +SELECT substr(p.id, 4) AS id, oids.ids AS oid +FROM ${openaire_db_name}.project p LATERAL VIEW explode(p.originalid) oids AS ids; +CREATE TABLE ${stats_db_name}.project_organizations AS +SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization +from ${openaire_db_name}.relation r +WHERE r.reltype = 'projectOrganization' + and r.datainfo.deletedbyinference = false; --- Project_organizations Table -CREATE TABLE ${stats_db_name}.project_organizations AS SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization from ${openaire_db_name}.relation r WHERE r.reltype='projectOrganization' and r.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.project_results AS +SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result +FROM ${openaire_db_name}.relation r +WHERE r.reltype = 'resultProject' + and r.datainfo.deletedbyinference = false; --- Project_results Table -CREATE TABLE ${stats_db_name}.project_results AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result FROM ${openaire_db_name}.relation r WHERE r.reltype='resultProject' and r.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.project_tmp +( + id STRING, + acronym STRING, + title STRING, + funder STRING, + funding_lvl0 STRING, + funding_lvl1 STRING, + funding_lvl2 STRING, + ec39 STRING, + type STRING, + startdate STRING, + enddate STRING, + start_year INT, + end_year INT, + duration INT, + haspubs STRING, + numpubs INT, + daysforlastpub INT, + delayedpubs INT, + callidentifier STRING, + code STRING +) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); --- Project table ----------------- --- Creating and populating temporary Project table -CREATE TABLE ${stats_db_name}.project_tmp (id STRING, acronym STRING, title STRING, funder STRING, funding_lvl0 STRING, funding_lvl1 STRING, funding_lvl2 STRING, ec39 STRING, type STRING, startdate STRING, enddate STRING, start_year INT, end_year INT, duration INT, haspubs STRING, numpubs INT, daysforlastpub INT, delayedpubs INT, callidentifier STRING, code STRING) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties('transactional'='true'); - -INSERT INTO ${stats_db_name}.project_tmp SELECT substr(p.id, 4) AS id, p.acronym.value AS acronym, p.title.value AS title, xpath_string(p.fundingtree[0].value, '//funder/name') AS funder, xpath_string(p.fundingtree[0].value, '//funding_level_0/name') AS funding_lvl0, xpath_string(p.fundingtree[0].value, '//funding_level_1/name') AS funding_lvl1, xpath_string(p.fundingtree[0].value, '//funding_level_2/name') AS funding_lvl2, p.ecsc39.value AS ec39, p.contracttype.classname AS type, p.startdate.value AS startdate, p.enddate.value AS enddate, year(p.startdate.value) AS start_year, year(p.enddate.value) AS end_year, CAST(MONTHS_BETWEEN(p.enddate.value, p.startdate.value) AS INT) AS duration, 'no' AS haspubs, 0 AS numpubs, 0 AS daysforlastpub, 0 AS delayedpubs, p.callidentifier.value AS callidentifier, p.code.value AS code FROM ${openaire_db_name}.project p WHERE p.datainfo.deletedbyinference=false; +INSERT INTO ${stats_db_name}.project_tmp +SELECT substr(p.id, 4) AS id, + p.acronym.value AS acronym, + p.title.value AS title, + xpath_string(p.fundingtree[0].value, '//funder/name') AS funder, + xpath_string(p.fundingtree[0].value, '//funding_level_0/name') AS funding_lvl0, + xpath_string(p.fundingtree[0].value, '//funding_level_1/name') AS funding_lvl1, + xpath_string(p.fundingtree[0].value, '//funding_level_2/name') AS funding_lvl2, + p.ecsc39.value AS ec39, + p.contracttype.classname AS type, + p.startdate.value AS startdate, + p.enddate.value AS enddate, + year(p.startdate.value) AS start_year, + year(p.enddate.value) AS end_year, + CAST(MONTHS_BETWEEN(p.enddate.value, p.startdate.value) AS INT) AS duration, + 'no' AS haspubs, + 0 AS numpubs, + 0 AS daysforlastpub, + 0 AS delayedpubs, + p.callidentifier.value AS callidentifier, + p.code.value AS code +FROM ${openaire_db_name}.project p +WHERE p.datainfo.deletedbyinference = false; create table ${stats_db_name}.funder as -select distinct xpath_string(fund, '//funder/id') as id, xpath_string(fund, '//funder/name') as name, xpath_string(fund, '//funder/shortname') as shortname +select distinct xpath_string(fund, '//funder/id') as id, + xpath_string(fund, '//funder/name') as name, + xpath_string(fund, '//funder/shortname') as shortname from ${openaire_db_name}.project p lateral view explode(p.fundingtree.value) fundingtree as fund ANALYZE TABLE ${stats_db_name}.project_oids COMPUTE STATISTICS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index 8506657a67..d330bde468 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -5,28 +5,135 @@ ---------------------------------------------------- -- Views on temporary tables that should be re-created in the end -CREATE OR REPLACE VIEW ${stats_db_name}.result as SELECT *, bestlicence AS access_mode FROM ${stats_db_name}.publication_tmp UNION ALL SELECT *,bestlicence AS access_mode FROM ${stats_db_name}.software_tmp UNION ALL SELECT *,bestlicence AS access_mode FROM ${stats_db_name}.dataset_tmp UNION ALL SELECT *,bestlicence AS access_mode FROM ${stats_db_name}.otherresearchproduct_tmp; +CREATE OR REPLACE VIEW ${stats_db_name}.result as +SELECT *, bestlicence AS access_mode +FROM ${stats_db_name}.publication_tmp +UNION ALL +SELECT *, bestlicence AS access_mode +FROM ${stats_db_name}.software_tmp +UNION ALL +SELECT *, bestlicence AS access_mode +FROM ${stats_db_name}.dataset_tmp +UNION ALL +SELECT *, bestlicence AS access_mode +FROM ${stats_db_name}.otherresearchproduct_tmp; -- Views on final tables -CREATE OR REPLACE VIEW ${stats_db_name}.result_datasources AS SELECT * FROM ${stats_db_name}.publication_datasources UNION ALL SELECT * FROM ${stats_db_name}.software_datasources UNION ALL SELECT * FROM ${stats_db_name}.dataset_datasources UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_datasources; +CREATE OR REPLACE VIEW ${stats_db_name}.result_datasources AS +SELECT * +FROM ${stats_db_name}.publication_datasources +UNION ALL +SELECT * +FROM ${stats_db_name}.software_datasources +UNION ALL +SELECT * +FROM ${stats_db_name}.dataset_datasources +UNION ALL +SELECT * +FROM ${stats_db_name}.otherresearchproduct_datasources; -CREATE OR REPLACE VIEW ${stats_db_name}.result_citations AS SELECT * FROM ${stats_db_name}.publication_citations UNION ALL SELECT * FROM ${stats_db_name}.software_citations UNION ALL SELECT * FROM ${stats_db_name}.dataset_citations UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_citations; +CREATE OR REPLACE VIEW ${stats_db_name}.result_citations AS +SELECT * +FROM ${stats_db_name}.publication_citations +UNION ALL +SELECT * +FROM ${stats_db_name}.software_citations +UNION ALL +SELECT * +FROM ${stats_db_name}.dataset_citations +UNION ALL +SELECT * +FROM ${stats_db_name}.otherresearchproduct_citations; -CREATE OR REPLACE VIEW ${stats_db_name}.result_classifications AS SELECT * FROM ${stats_db_name}.publication_classifications UNION ALL SELECT * FROM ${stats_db_name}.software_classifications UNION ALL SELECT * FROM ${stats_db_name}.dataset_classifications UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_classifications; +CREATE OR REPLACE VIEW ${stats_db_name}.result_classifications AS +SELECT * +FROM ${stats_db_name}.publication_classifications +UNION ALL +SELECT * +FROM ${stats_db_name}.software_classifications +UNION ALL +SELECT * +FROM ${stats_db_name}.dataset_classifications +UNION ALL +SELECT * +FROM ${stats_db_name}.otherresearchproduct_classifications; -CREATE OR REPLACE VIEW ${stats_db_name}.result_concepts AS SELECT * FROM ${stats_db_name}.publication_concepts UNION ALL SELECT * FROM ${stats_db_name}.software_concepts UNION ALL SELECT * FROM ${stats_db_name}.dataset_concepts UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_concepts; +CREATE OR REPLACE VIEW ${stats_db_name}.result_concepts AS +SELECT * +FROM ${stats_db_name}.publication_concepts +UNION ALL +SELECT * +FROM ${stats_db_name}.software_concepts +UNION ALL +SELECT * +FROM ${stats_db_name}.dataset_concepts +UNION ALL +SELECT * +FROM ${stats_db_name}.otherresearchproduct_concepts; -CREATE OR REPLACE VIEW ${stats_db_name}.result_languages AS SELECT * FROM ${stats_db_name}.publication_languages UNION ALL SELECT * FROM ${stats_db_name}.software_languages UNION ALL SELECT * FROM ${stats_db_name}.dataset_languages UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_languages; +CREATE OR REPLACE VIEW ${stats_db_name}.result_languages AS +SELECT * +FROM ${stats_db_name}.publication_languages +UNION ALL +SELECT * +FROM ${stats_db_name}.software_languages +UNION ALL +SELECT * +FROM ${stats_db_name}.dataset_languages +UNION ALL +SELECT * +FROM ${stats_db_name}.otherresearchproduct_languages; -CREATE OR REPLACE VIEW ${stats_db_name}.result_oids AS SELECT * FROM ${stats_db_name}.publication_oids UNION ALL SELECT * FROM ${stats_db_name}.software_oids UNION ALL SELECT * FROM ${stats_db_name}.dataset_oids UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_oids; +CREATE OR REPLACE VIEW ${stats_db_name}.result_oids AS +SELECT * +FROM ${stats_db_name}.publication_oids +UNION ALL +SELECT * +FROM ${stats_db_name}.software_oids +UNION ALL +SELECT * +FROM ${stats_db_name}.dataset_oids +UNION ALL +SELECT * +FROM ${stats_db_name}.otherresearchproduct_oids; -CREATE OR REPLACE VIEW ${stats_db_name}.result_pids AS SELECT * FROM ${stats_db_name}.publication_pids UNION ALL SELECT * FROM ${stats_db_name}.software_pids UNION ALL SELECT * FROM ${stats_db_name}.dataset_pids UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_pids; +CREATE OR REPLACE VIEW ${stats_db_name}.result_pids AS +SELECT * +FROM ${stats_db_name}.publication_pids +UNION ALL +SELECT * +FROM ${stats_db_name}.software_pids +UNION ALL +SELECT * +FROM ${stats_db_name}.dataset_pids +UNION ALL +SELECT * +FROM ${stats_db_name}.otherresearchproduct_pids; -CREATE OR REPLACE VIEW ${stats_db_name}.result_topics AS SELECT * FROM ${stats_db_name}.publication_topics UNION ALL SELECT * FROM ${stats_db_name}.software_topics UNION ALL SELECT * FROM ${stats_db_name}.dataset_topics UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_topics; +CREATE OR REPLACE VIEW ${stats_db_name}.result_topics AS +SELECT * +FROM ${stats_db_name}.publication_topics +UNION ALL +SELECT * +FROM ${stats_db_name}.software_topics +UNION ALL +SELECT * +FROM ${stats_db_name}.dataset_topics +UNION ALL +SELECT * +FROM ${stats_db_name}.otherresearchproduct_topics; -CREATE TABLE ${stats_db_name}.result_organization AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype='resultOrganization' and r.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.result_organization AS +SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization +FROM ${openaire_db_name}.relation r +WHERE r.reltype = 'resultOrganization' + and r.datainfo.deletedbyinference = false; -CREATE TABLE ${stats_db_name}.result_projects AS select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend FROM ${stats_db_name}.result r JOIN ${stats_db_name}.project_results pr ON r.id=pr.result JOIN ${stats_db_name}.project_tmp p ON p.id=pr.id; +CREATE TABLE ${stats_db_name}.result_projects AS +select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend +FROM ${stats_db_name}.result r + JOIN ${stats_db_name}.project_results pr ON r.id = pr.result + JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS FOR COLUMNS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index e74ecc7683..73ea0c0849 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -5,55 +5,99 @@ -- Datasource table/view and Datasource related tables/views ------------------------------------------------------------ ------------------------------------------------------------ - --- Datasource table creation & update -------------------------------------- --- Creating and populating temporary datasource table -DROP TABLE IF EXISTS ${stats_db_name}.datasource_tmp; -CREATE TABLE ${stats_db_name}.datasource_tmp(`id` string, `name` STRING, `type` STRING, `dateofvalidation` STRING, `yearofvalidation` string, `harvested` BOOLEAN, `piwik_id` INT, `latitude` STRING, `longitude`STRING, `websiteurl` STRING, `compatibility` STRING) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties('transactional'='true'); +CREATE TABLE ${stats_db_name}.datasource_tmp +( + `id` string, + `name` STRING, + `type` STRING, + `dateofvalidation` STRING, + `yearofvalidation` string, + `harvested` BOOLEAN, + `piwik_id` INT, + `latitude` STRING, + `longitude` STRING, + `websiteurl` STRING, + `compatibility` STRING +) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); -- Insert statement that takes into account the piwik_id of the openAIRE graph -INSERT INTO ${stats_db_name}.datasource_tmp -SELECT substr(d1.id, 4) AS id, officialname.value AS name, -datasourcetype.classname AS type, dateofvalidation.value AS dateofvalidation, date_format(d1.dateofvalidation.value,'yyyy') AS yearofvalidation, -FALSE AS harvested, -CASE WHEN d2.piwik_id IS NULL THEN 0 ELSE d2.piwik_id END AS piwik_id, -d1.latitude.value AS latitude, d1.longitude.value AS longitude, -d1.websiteurl.value AS websiteurl, d1.openairecompatibility.classid AS compatibility +INSERT INTO ${stats_db_name}.datasource_tmp +SELECT substr(d1.id, 4) AS id, + officialname.value AS name, + datasourcetype.classname AS type, + dateofvalidation.value AS dateofvalidation, + date_format(d1.dateofvalidation.value, 'yyyy') AS yearofvalidation, + FALSE AS harvested, + CASE WHEN d2.piwik_id IS NULL THEN 0 ELSE d2.piwik_id END AS piwik_id, + d1.latitude.value AS latitude, + d1.longitude.value AS longitude, + d1.websiteurl.value AS websiteurl, + d1.openairecompatibility.classid AS compatibility FROM ${openaire_db_name}.datasource d1 -LEFT OUTER JOIN -(SELECT id, split(originalidd, '\\:')[1] as piwik_id -FROM ${openaire_db_name}.datasource -LATERAL VIEW EXPLODE(originalid) temp AS originalidd -WHERE originalidd like "piwik:%") AS d2 -ON d1.id = d2.id -WHERE d1.datainfo.deletedbyinference=FALSE; + LEFT OUTER JOIN + (SELECT id, split(originalidd, '\\:')[1] as piwik_id + FROM ${openaire_db_name}.datasource + LATERAL VIEW EXPLODE(originalid) temp AS originalidd + WHERE originalidd like "piwik:%") AS d2 + ON d1.id = d2.id +WHERE d1.datainfo.deletedbyinference = FALSE; -- Updating temporary table with everything that is not based on results -> This is done with the following "dual" table. -- Creating a temporary dual table that will be removed after the following insert -CREATE TABLE ${stats_db_name}.dual(dummy CHAR(1)); -INSERT INTO ${stats_db_name}.dual VALUES('X'); -INSERT INTO ${stats_db_name}.datasource_tmp (`id`, `name`, `type`, `dateofvalidation`, `yearofvalidation`, `harvested`, `piwik_id`, `latitude`, `longitude`, `websiteurl`, `compatibility`) -SELECT 'other', 'Other', 'Repository', NULL, NULL, false, 0, NULL, NULL, NULL, 'unknown' FROM ${stats_db_name}.dual WHERE 'other' not in (SELECT id FROM ${stats_db_name}.datasource_tmp WHERE name='Unknown Repository'); +CREATE TABLE ${stats_db_name}.dual +( + dummy CHAR(1) +); +INSERT INTO ${stats_db_name}.dual +VALUES ('X'); +INSERT INTO ${stats_db_name}.datasource_tmp (`id`, `name`, `type`, `dateofvalidation`, `yearofvalidation`, `harvested`, + `piwik_id`, `latitude`, `longitude`, `websiteurl`, `compatibility`) +SELECT 'other', + 'Other', + 'Repository', + NULL, + NULL, + false, + 0, + NULL, + NULL, + NULL, + 'unknown' +FROM ${stats_db_name}.dual +WHERE 'other' not in (SELECT id FROM ${stats_db_name}.datasource_tmp WHERE name = 'Unknown Repository'); DROP TABLE ${stats_db_name}.dual; -UPDATE ${stats_db_name}.datasource_tmp SET name='Other' WHERE name='Unknown Repository'; -UPDATE ${stats_db_name}.datasource_tmp SET yearofvalidation=null WHERE yearofvalidation='-1'; +UPDATE ${stats_db_name}.datasource_tmp +SET name='Other' +WHERE name = 'Unknown Repository'; +UPDATE ${stats_db_name}.datasource_tmp +SET yearofvalidation=null +WHERE yearofvalidation = '-1'; -DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages; -CREATE TABLE ${stats_db_name}.datasource_languages AS SELECT substr(d.id, 4) AS id, langs.languages AS language FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs AS languages; +CREATE TABLE ${stats_db_name}.datasource_languages AS +SELECT substr(d.id, 4) AS id, langs.languages AS language +FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs AS languages; -DROP TABLE IF EXISTS ${stats_db_name}.datasource_oids; -CREATE TABLE ${stats_db_name}.datasource_oids AS SELECT substr(d.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids; +CREATE TABLE ${stats_db_name}.datasource_oids AS +SELECT substr(d.id, 4) AS id, oids.ids AS oid +FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids; -DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations; -CREATE TABLE ${stats_db_name}.datasource_organizations AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype='datasourceOrganization' and r.datainfo.deletedbyinference=false; +CREATE TABLE ${stats_db_name}.datasource_organizations AS +SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization +FROM ${openaire_db_name}.relation r +WHERE r.reltype = 'datasourceOrganization' + and r.datainfo.deletedbyinference = false; -- datasource sources: -- where the datasource info have been collected from. -create table if not exists ${stats_db_name}.datasource_sources AS select substr(d.id,4) as id, substr(cf.key, 4) as datasource from ${openaire_db_name}.datasource d lateral view explode(d.collectedfrom) cfrom as cf where d.datainfo.deletedbyinference=false; +create table if not exists ${stats_db_name}.datasource_sources AS +select substr(d.id, 4) as id, substr(cf.key, 4) as datasource +from ${openaire_db_name}.datasource d lateral view explode(d.collectedfrom) cfrom as cf +where d.datainfo.deletedbyinference = false; -CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS SELECT datasource AS id, id AS result FROM ${stats_db_name}.result_datasources; +CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS +SELECT datasource AS id, id AS result +FROM ${stats_db_name}.result_datasources; ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS FOR COLUMNS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql index 4fb9919c99..9a581900ab 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql @@ -3,13 +3,21 @@ -- Organization table/view and Organization related tables/views ---------------------------------------------------------------- ---------------------------------------------------------------- -DROP TABLE IF EXISTS ${stats_db_name}.organization; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization AS SELECT substr(o.id, 4) as id, o.legalname.value as name, o.legalshortname.value as legalshortname, o.country.classid as country -FROM ${openaire_db_name}.organization o WHERE o.datainfo.deletedbyinference=FALSE; +CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization AS +SELECT substr(o.id, 4) as id, + o.legalname.value as name, + o.legalshortname.value as legalshortname, + o.country.classid as country +FROM ${openaire_db_name}.organization o +WHERE o.datainfo.deletedbyinference = FALSE; -CREATE OR REPLACE VIEW ${stats_db_name}.organization_datasources AS SELECT organization AS id, id AS datasource FROM ${stats_db_name}.datasource_organizations; +CREATE OR REPLACE VIEW ${stats_db_name}.organization_datasources AS +SELECT organization AS id, id AS datasource +FROM ${stats_db_name}.datasource_organizations; -CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects AS SELECT id AS project, organization as id FROM ${stats_db_name}.project_organizations; +CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects AS +SELECT id AS project, organization as id +FROM ${stats_db_name}.project_organizations; ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file From 32e81c2d8973687767c85e57007f2e00a9021d29 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Tue, 16 Feb 2021 11:01:42 +0100 Subject: [PATCH 092/106] non validated rel has null value in validated field --- .../eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java | 2 ++ .../resources/eu/dnetlib/dhp/oa/provision/relToProject.json | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) 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 b0a21c62b4..af6081c5db 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 @@ -1094,6 +1094,8 @@ public class XmlRecordFactory implements Serializable { String.format("missing scheme for: <%s - %s>", type.toString(), targetType)); } final HashSet fields = Sets.newHashSet(mapFields(link, contexts)); + if (rel.getValidated() == null) + rel.setValidated(false); return templateFactory .getRel( targetType, rel.getTarget(), fields, rel.getRelClass(), scheme, rel.getDataInfo(), rel.getValidated(), diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToProject.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToProject.json index b4d9752559..9e2824e521 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToProject.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relToProject.json @@ -25,7 +25,7 @@ "relClass": "isProducedBy", "source": "50|CSC_________::0000ec4dd9df012feaafa77e71a0fb4c", "target": "40|corda__h2020::79a0e16c122c9a18eb60e4a5e64b620d", -"validated": false, +"validated": null, "validationDate": null, "properties": [] } \ No newline at end of file From 6f9864c564757362387f9bc34eb00a463cba0d6f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 16 Feb 2021 11:49:23 +0100 Subject: [PATCH 093/106] manage merging of Relatation validation attributes --- .../dhp/schema/common/ModelSupport.java | 24 ++++++++++ .../eu/dnetlib/dhp/schema/oaf/Relation.java | 12 ++++- .../eu/dnetlib/dhp/schema/oaf/MergeTest.java | 45 +++++++++++++++++++ 3 files changed, 80 insertions(+), 1 deletion(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java index b5bca2e93e..0c7903137d 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java @@ -3,6 +3,9 @@ package eu.dnetlib.dhp.schema.common; import static com.google.common.base.Preconditions.checkArgument; +import java.text.ParseException; +import java.text.SimpleDateFormat; +import java.util.Date; import java.util.Map; import java.util.Objects; import java.util.Optional; @@ -473,4 +476,25 @@ public class ModelSupport { private static String idFnForOafEntity(T t) { return ((OafEntity) t).getId(); } + + public static final String ISO8601FORMAT = "yyyy-MM-dd'T'HH:mm:ssZ"; + + public static String oldest(String dateA, String dateB) throws ParseException { + + if (StringUtils.isBlank(dateA)) { + return dateB; + } + if (StringUtils.isBlank(dateB)) { + return dateA; + } + if (StringUtils.isNotBlank(dateA) && StringUtils.isNotBlank(dateB)) { + + final Date a = new SimpleDateFormat(ISO8601FORMAT).parse(dateA); + final Date b = new SimpleDateFormat(ISO8601FORMAT).parse(dateB); + + return a.before(b) ? dateA : dateB; + } else { + return null; + } + } } 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 0de34dbecc..8825d71378 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 @@ -1,8 +1,11 @@ package eu.dnetlib.dhp.schema.oaf; +import eu.dnetlib.dhp.schema.common.ModelSupport; + import static com.google.common.base.Preconditions.checkArgument; +import java.text.ParseException; import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -106,7 +109,7 @@ public class Relation extends Oaf { } public Boolean getValidated() { - return validated; + return Objects.nonNull(validated) && validated; } public void setValidated(Boolean validated) { @@ -130,6 +133,13 @@ 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"); + setValidated(getValidated() || r.getValidated()); + try { + setValidationDate(ModelSupport.oldest(getValidationDate(), r.getValidationDate())); + } catch (ParseException e) { + throw new IllegalArgumentException(String.format("invalid validation date format in relation [s:%s, t:%s]: %s", getSource(), getTarget(), getValidationDate())); + } + super.mergeFrom(r); } diff --git a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java index f91646f2c5..6ee5b9d859 100644 --- a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java +++ b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java @@ -63,6 +63,51 @@ public class MergeTest { assertEquals(3, a.getSubject().size()); } + @Test + public void mergeRelationTest() { + + Relation a = createRel(null, null); + Relation b = createRel(null, null); + a.mergeFrom(b); + assertEquals(a, b); + + a = createRel(true, null); + b = createRel(null, null); + a.mergeFrom(b); + assertEquals(true, a.getValidated()); + + a = createRel(true, null); + b = createRel(false, null); + a.mergeFrom(b); + assertEquals(true, a.getValidated()); + + a = createRel(true, null); + b = createRel(true, "2016-04-05T12:41:19.202Z"); + a.mergeFrom(b); + assertEquals("2016-04-05T12:41:19.202Z", a.getValidationDate()); + } + + @Test + public void mergeRelationTestParseException() { + assertThrows(IllegalArgumentException.class, () -> { + Relation a = createRel(true, "2016-04-05"); + Relation b = createRel(true, "2016-04-05"); + a.mergeFrom(b); + }); + } + + private Relation createRel(Boolean validated, String validationDate) { + Relation rel = new Relation(); + rel.setSource("1"); + rel.setTarget("2"); + rel.setRelType("reltype"); + rel.setSubRelType("subreltype"); + rel.setRelClass("relclass"); + rel.setValidated(validated); + rel.setValidationDate(validationDate); + return rel; + } + private KeyValue setKV(final String key, final String value) { KeyValue k = new KeyValue(); From cd1b794409bef745b6b4595024c68b1e5a88817a Mon Sep 17 00:00:00 2001 From: antleb Date: Wed, 17 Feb 2021 02:11:55 +0200 Subject: [PATCH 094/106] added the monitor db wf --- .../dhp/oa/graph/stats/oozie_app/monitor.sh | 24 ++++ .../scripts/step21-createMonitorDB.sql | 121 ++++++++++++++++++ .../dhp/oa/graph/stats/oozie_app/workflow.xml | 22 ++++ 3 files changed, 167 insertions(+) create mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh create mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createMonitorDB.sql diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh new file mode 100644 index 0000000000..19989882fb --- /dev/null +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh @@ -0,0 +1,24 @@ +export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs +export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami) +if ! [ -L $link_folder ] +then + rm -Rf "$link_folder" + ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder} +fi + +export SOURCE=$1 +export TARGET=$2 +export SHADOW=$3 +export SCRIPT_PATH=$4 + +echo "Getting file from " $4 +hdfs dfs -copyToLocal $4 + +echo "Creating monitor database" +cat step21-createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f - +echo "Impala shell finished" + +echo "Updating shadow monitor database" +impala-shell -d $3 -q "show tables" --delimited | sed 's/^/drop view if exists $3./' | sed 's/$/;/' | impala-shell -f - +impala-shell -d $2 -q "show tables" --delimited | sed 's/\(.*\)/create view $3.\1 as select * from $2.\1;/' | impala-shell -f - +echo "Shadow db ready!" diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createMonitorDB.sql new file mode 100644 index 0000000000..9477ada12f --- /dev/null +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createMonitorDB.sql @@ -0,0 +1,121 @@ +drop database if exists TARGET cascade; +create database if not exists TARGET; + +create view if not exists TARGET.category as select * from SOURCE.category; +create view if not exists TARGET.concept as select * from SOURCE.concept; +create view if not exists TARGET.context as select * from SOURCE.context; +create view if not exists TARGET.country as select * from SOURCE.country; +create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp; +create view if not exists TARGET.creation_date as select * from SOURCE.creation_date; +create view if not exists TARGET.funder as select * from SOURCE.funder; +create view if not exists TARGET.fundref as select * from SOURCE.fundref; +create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture; +--create view if not exists TARGET.roarmap as select * from SOURCE.roarmap; + +create table TARGET.result as + select distinct * from ( + select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on rp.project=p.id where rp.id=r.id) + union all + select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id) ) foo; +compute stats TARGET.result; + +create table TARGET.result_affiliated_country as select * from SOURCE.result_affiliated_country rac where exists (select 1 from TARGET.result r where r.id=rac.id); +compute stats TARGET.result_affiliated_country; + +create table TARGET.result_citations as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_citations; + +create table TARGET.result_classifications as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_classifications; + +create table TARGET.result_concepts as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_concepts; + +create table TARGET.result_datasources as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_datasources; + +create table TARGET.result_deposited_country as select * from SOURCE.result_deposited_country orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_deposited_country; + +create table TARGET.result_fundercount as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_fundercount; + +create table TARGET.result_gold as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_gold; + +create table TARGET.result_greenoa as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_greenoa; + +create table TARGET.result_languages as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_languages; + +create table TARGET.result_licences as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_licences; + +create table TARGET.result_oids as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_oids; + +create table TARGET.result_organization as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_organization; + +create table TARGET.result_peerreviewed as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_peerreviewed; + +create table TARGET.result_pids as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_pids; + +create table TARGET.result_projectcount as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_projectcount; + +create table TARGET.result_projects as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_projects; + +create table TARGET.result_refereed as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_refereed; + +create table TARGET.result_sources as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_sources; + +create table TARGET.result_topics as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_topics; + +-- datasources +create view if not exists TARGET.datasource as select * from SOURCE.datasource; +create view if not exists TARGET.datasource_oids as select * from SOURCE.datasource_oids; +create view if not exists TARGET.datasource_organizations as select * from SOURCE.datasource_organizations; +create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources; + +create table TARGET.datasource_results as select id as result, datasource as id from TARGET.result_datasources; +compute stats TARGET.datasource_results; + +-- organizations +create view if not exists TARGET.organization as select * from SOURCE.organization; +create view if not exists TARGET.organization_datasources as select * from SOURCE.organization_datasources; +create view if not exists TARGET.organization_pids as select * from SOURCE.organization_pids; +create view if not exists TARGET.organization_projects as select * from SOURCE.organization_projects; +create view if not exists TARGET.organization_sources as select * from SOURCE.organization_sources; + +-- projects +create view if not exists TARGET.project as select * from SOURCE.project; +create view if not exists TARGET.project_oids as select * from SOURCE.project_oids; +create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations; +create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount; + +create table TARGET.project_results as select id as result, project as id from TARGET.result_projects; +compute stats TARGET.project_results; + +--denorm +alter table TARGET.result rename to TARGET.res_tmp; + +create table TARGET.result_denorm as + select distinct r.*, rp.project, p.acronym as pacronym, p.title as ptitle, p.funder as pfunder, p.funding_lvl0 as pfunding_lvl0, rd.datasource, d.name as dname, d.type as dtype + from TARGET.res_tmp r + join TARGET.result_projects rp on rp.id=r.id + join TARGET.result_datasources rd on rd.id=r.id + join TARGET.project p on p.id=rp.project + join TARGET.datasource d on d.id=rd.datasource; +compute stats TARGET.result_denorm; + +alter table TARGET.result_denorm rename to TARGET.result; +drop table TARGET.res_tmp; +--- done! \ No newline at end of file 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 ceaa47794c..3a283f1774 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 @@ -17,6 +17,14 @@ stats_db_shadow_name the name of the shadow schema + + monitor_db_name + the target monitor db name + + + monitor_db_shadow_name + the name of the shadow monitor db + stats_tool_api_url The url of the API of the stats tool. Is used to trigger the cache update. @@ -303,6 +311,20 @@ ${stats_tool_api_url} updateCache.sh + + + + + + + ${jobTracker} + ${nameNode} + monitor.sh + ${stats-db-name} + ${monitor-db-name} + ${wf:appPath()}/scripts/step21-createMonitorDB.sql + monitor.sh + From 00d516360fb5153328c8c4d8e8bc3f8a20247e4c Mon Sep 17 00:00:00 2001 From: antleb Date: Wed, 17 Feb 2021 16:41:10 +0200 Subject: [PATCH 095/106] added missing ; --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql | 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/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index 383d3f6fd7..ade686cf6d 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -70,7 +70,7 @@ create table ${stats_db_name}.funder as select distinct xpath_string(fund, '//funder/id') as id, xpath_string(fund, '//funder/name') as name, xpath_string(fund, '//funder/shortname') as shortname -from ${openaire_db_name}.project p lateral view explode(p.fundingtree.value) fundingtree as fund +from ${openaire_db_name}.project p lateral view explode(p.fundingtree.value) fundingtree as fund; ANALYZE TABLE ${stats_db_name}.project_oids COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.project_oids COMPUTE STATISTICS FOR COLUMNS; From a445c1ac3d6abbde53834c031809029e93669ea8 Mon Sep 17 00:00:00 2001 From: antleb Date: Wed, 17 Feb 2021 16:45:09 +0200 Subject: [PATCH 096/106] fixed variable names in monitor script --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh | 4 ++-- .../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh index 19989882fb..c5700c8fcb 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh @@ -19,6 +19,6 @@ cat step21-createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala echo "Impala shell finished" echo "Updating shadow monitor database" -impala-shell -d $3 -q "show tables" --delimited | sed 's/^/drop view if exists $3./' | sed 's/$/;/' | impala-shell -f - -impala-shell -d $2 -q "show tables" --delimited | sed 's/\(.*\)/create view $3.\1 as select * from $2.\1;/' | impala-shell -f - +impala-shell -d $SHADOW -q "show tables" --delimited | sed 's/^/drop view if exists $SHADOW./' | sed 's/$/;/' | impala-shell -f - +impala-shell -d $TARGET -q "show tables" --delimited | sed 's/\(.*\)/create view $SHADOW.\1 as select * from $TARGET.\1;/' | impala-shell -f - echo "Shadow db ready!" diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql index 273a121082..8b55e83b53 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql @@ -29,7 +29,7 @@ select rcount.pid, sum(case when rcount.type='publication' then rcount.count els from rcount group by rcount.pid; -create view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture +create view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture; ANALYZE TABLE ${stats_db_name}.result_projectcount COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.result_projectcount COMPUTE STATISTICS FOR COLUMNS; From a8836e2f5f2d1950399283f0792df7bed88bf976 Mon Sep 17 00:00:00 2001 From: antleb Date: Wed, 17 Feb 2021 19:27:07 +0200 Subject: [PATCH 097/106] fixed typo --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql | 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/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index 4c1ca0203d..41d2000e7d 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -60,7 +60,7 @@ SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.datast_sources COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS FOR COLUMNS; ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS FOR COLUMNS; From 8ef66452d5d711f3eae9336654feee5320ab0242 Mon Sep 17 00:00:00 2001 From: antleb Date: Wed, 17 Feb 2021 22:24:44 +0200 Subject: [PATCH 098/106] fixed typo --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql | 2 +- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql index e05e648b4f..c46012c026 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql @@ -50,7 +50,7 @@ FROM ( ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.datast_licenses COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_licenses COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.dataset_licenses COMPUTE STATISTICS FOR COLUMNS; ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS FOR COLUMNS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql index 4940a73daf..ee9e04e971 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql @@ -37,7 +37,7 @@ select * from ${stats_db_name}.otherresearchproduct_refereed; ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.datast_refereed COMPUTE STATISTICS; +ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS FOR COLUMNS; ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS; ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS FOR COLUMNS; From 10a29a4b9abb7a2a4fdf8a98e5e5403a6daa5fb9 Mon Sep 17 00:00:00 2001 From: antleb Date: Thu, 18 Feb 2021 15:05:59 +0200 Subject: [PATCH 099/106] fixes in monitor step --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index 3a283f1774..c418ffd6cf 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -58,7 +58,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -322,6 +322,7 @@ monitor.sh ${stats-db-name} ${monitor-db-name} + ${monitor_db_shadow_name} ${wf:appPath()}/scripts/step21-createMonitorDB.sql monitor.sh From bcbfc052b1e5c3f8c74d5c80c140d8eb2133d7e1 Mon Sep 17 00:00:00 2001 From: antleb Date: Thu, 18 Feb 2021 16:32:54 +0200 Subject: [PATCH 100/106] fixed last errors in step 21 --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh | 5 +++-- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml | 6 +++--- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh index c5700c8fcb..b638311e3f 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh @@ -19,6 +19,7 @@ cat step21-createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala echo "Impala shell finished" echo "Updating shadow monitor database" -impala-shell -d $SHADOW -q "show tables" --delimited | sed 's/^/drop view if exists $SHADOW./' | sed 's/$/;/' | impala-shell -f - -impala-shell -d $TARGET -q "show tables" --delimited | sed 's/\(.*\)/create view $SHADOW.\1 as select * from $TARGET.\1;/' | impala-shell -f - +impala-shell -q "create database if not exists ${SHADOW}" +impala-shell -d $SHADOW -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -f - +impala-shell -d $TARGET -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${TARGET}.\1;/" | impala-shell -f - echo "Shadow db ready!" diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index c418ffd6cf..c3cf15d8a0 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -58,7 +58,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -320,8 +320,8 @@ ${jobTracker} ${nameNode} monitor.sh - ${stats-db-name} - ${monitor-db-name} + ${stats_db_name} + ${monitor_db_name} ${monitor_db_shadow_name} ${wf:appPath()}/scripts/step21-createMonitorDB.sql monitor.sh From b8e96c8ae77b3e02e835332f682693181fbc3664 Mon Sep 17 00:00:00 2001 From: antleb Date: Thu, 18 Feb 2021 16:42:22 +0200 Subject: [PATCH 101/106] moved cache update to the end --- .../dhp/oa/graph/stats/oozie_app/monitor.sh | 8 ++--- ...nitorDB.sql => step20-createMonitorDB.sql} | 0 .../dhp/oa/graph/stats/oozie_app/workflow.xml | 30 +++++++++---------- 3 files changed, 19 insertions(+), 19 deletions(-) rename dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/{step21-createMonitorDB.sql => step20-createMonitorDB.sql} (100%) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh index b638311e3f..c5bda6d391 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh @@ -15,11 +15,11 @@ echo "Getting file from " $4 hdfs dfs -copyToLocal $4 echo "Creating monitor database" -cat step21-createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f - +cat step20-createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f - echo "Impala shell finished" echo "Updating shadow monitor database" impala-shell -q "create database if not exists ${SHADOW}" -impala-shell -d $SHADOW -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -f - -impala-shell -d $TARGET -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${TARGET}.\1;/" | impala-shell -f - -echo "Shadow db ready!" +impala-shell -d ${SHADOW} -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -f - +impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${TARGET}.\1;/" | impala-shell -f - +echo "Shadow db ready!" \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql similarity index 100% rename from dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createMonitorDB.sql rename to dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql 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 c3cf15d8a0..2f195d6d39 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 @@ -299,23 +299,11 @@ ${wf:appPath()}/scripts/step19.sql impala-shell.sh - + - - - ${jobTracker} - ${nameNode} - updateCache.sh - ${stats_tool_api_url} - updateCache.sh - - - - - - + ${jobTracker} ${nameNode} @@ -323,9 +311,21 @@ ${stats_db_name} ${monitor_db_name} ${monitor_db_shadow_name} - ${wf:appPath()}/scripts/step21-createMonitorDB.sql + ${wf:appPath()}/scripts/step20-createMonitorDB.sql monitor.sh + + + + + + + ${jobTracker} + ${nameNode} + updateCache.sh + ${stats_tool_api_url} + updateCache.sh + From 33c85d4e667af80bfe5bbf1642b40a008e082609 Mon Sep 17 00:00:00 2001 From: antleb Date: Thu, 18 Feb 2021 17:23:34 +0200 Subject: [PATCH 102/106] moved stats computation in impala instead of hive --- .../oa/graph/stats/oozie_app/finalizedb.sh | 17 ++ .../oa/graph/stats/oozie_app/impala-shell.sh | 18 -- .../graph/stats/oozie_app/scripts/step10.sql | 6 +- .../graph/stats/oozie_app/scripts/step11.sql | 4 +- .../graph/stats/oozie_app/scripts/step12.sql | 24 +- .../graph/stats/oozie_app/scripts/step13.sql | 18 +- .../graph/stats/oozie_app/scripts/step14.sql | 24 +- .../graph/stats/oozie_app/scripts/step15.sql | 18 +- .../graph/stats/oozie_app/scripts/step16.sql | 20 +- .../stats/oozie_app/scripts/step16_5.sql | 6 +- .../stats/oozie_app/scripts/step16_6.sql | 14 +- .../graph/stats/oozie_app/scripts/step17.sql | 207 ------------------ .../graph/stats/oozie_app/scripts/step18.sql | 8 - .../graph/stats/oozie_app/scripts/step19.sql | 8 - .../graph/stats/oozie_app/scripts/step2.sql | 36 +-- .../graph/stats/oozie_app/scripts/step3.sql | 34 +-- .../graph/stats/oozie_app/scripts/step4.sql | 34 +-- .../graph/stats/oozie_app/scripts/step5.sql | 32 +-- .../graph/stats/oozie_app/scripts/step6.sql | 20 +- .../graph/stats/oozie_app/scripts/step7.sql | 8 +- .../graph/stats/oozie_app/scripts/step8.sql | 16 +- .../graph/stats/oozie_app/scripts/step9.sql | 4 +- .../dhp/oa/graph/stats/oozie_app/workflow.xml | 32 +-- 23 files changed, 179 insertions(+), 429 deletions(-) create mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh delete mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh delete mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step17.sql delete mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step18.sql delete mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step19.sql diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh new file mode 100644 index 0000000000..915faab70d --- /dev/null +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh @@ -0,0 +1,17 @@ +export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs +export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami) +if ! [ -L $link_folder ] +then + rm -Rf "$link_folder" + ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder} +fi + +export SOURCE=$1 +export SHADOW=$2 + +echo "Updating shadow database" +impala-shell -q "invalidate metadata ${SOURCE}" +impala-shell -q "create database if not exists ${SHADOW}" +impala-shell -d ${SHADOW} -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -f - +impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -f - +echo "Shadow db ready!" \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh deleted file mode 100644 index 70112dc7be..0000000000 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh +++ /dev/null @@ -1,18 +0,0 @@ -export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs -export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami) -if ! [ -L $link_folder ] -then - rm -Rf "$link_folder" - ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder} -fi - -echo "Getting file from " $3 -hdfs dfs -copyToLocal $3 - -echo "Running impala shell make the new database visible" -impala-shell -q "INVALIDATE METADATA;" - -echo "Running impala shell to compute new table stats" -impala-shell -d $1 -f $2 -echo "Impala shell finished" -rm $2 diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql index d5ae0a5c8c..6c96317e6c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql @@ -43,6 +43,6 @@ FROM ${external_stats_db_name}.concept; ------------------------------------------------------------------------------------------------ create table ${stats_db_name}.creation_date as select date_format(current_date(), 'dd-MM-yyyy') as date; - -ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- +-- ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql index db5fdb1c38..d26169fd6e 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql @@ -114,5 +114,5 @@ WHERE result_projects.id = result.id AND result.type = 'publication' AND project.id = result_projects.project; -ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql index 779547a841..51d3a73c9e 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql @@ -65,15 +65,15 @@ WHERE r.id = rd.id AND r.bestlicence = 'Open Access' GROUP BY org.country; -ANALYZE TABLE ${stats_db_name}.datasource COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.datasource COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.publication COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.dataset COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.software COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.numbers_country COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.numbers_country COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- ANALYZE TABLE ${stats_db_name}.datasource COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.datasource COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.publication COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.dataset COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.software COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.numbers_country COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.numbers_country COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index 41d2000e7d..d79396b3bc 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -57,12 +57,12 @@ UNION ALL SELECT * FROM ${stats_db_name}.software_sources UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; - -ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- +-- ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql index c46012c026..00a6913bc5 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql @@ -48,15 +48,15 @@ FROM ( from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false) d on o.datasource = d.id; -ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.dataset_licenses COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset_licenses COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_licenses COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_licenses COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.organization_pids COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.organization_pids COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.organization_sources COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.organization_sources COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.dataset_licenses COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset_licenses COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_licenses COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_licenses COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.organization_pids COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.organization_pids COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.organization_sources COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.organization_sources COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql index ee9e04e971..8f364d7478 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql @@ -34,12 +34,12 @@ union all select * from ${stats_db_name}.software_refereed union all select * from ${stats_db_name}.otherresearchproduct_refereed; - -ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- +-- ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16.sql index a7e6c74e44..833deff734 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16.sql @@ -79,13 +79,13 @@ join ${stats_db_name}.datasource_organizations dor on dor.id=d.id join ${stats_db_name}.organization o on o.id=dor.organization where o.country is not null and o.country!=''; -ANALYZE TABLE ${stats_db_name}.result_peerreviewed COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.result_peerreviewed COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.result_greenoa COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.result_greenoa COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.result_gold COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.result_gold COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.result_affiliated_country COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.result_affiliated_country COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.result_deposited_country COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.result_deposited_country COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- ANALYZE TABLE ${stats_db_name}.result_peerreviewed COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.result_peerreviewed COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.result_greenoa COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.result_greenoa COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.result_gold COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.result_gold COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.result_affiliated_country COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.result_affiliated_country COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.result_deposited_country COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.result_deposited_country COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql index 52b7a58fab..2bdc263ef5 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql @@ -53,6 +53,6 @@ drop table if exists ${stats_db_name}.result; drop view if exists ${stats_db_name}.result; create table ${stats_db_name}.result stored as parquet as select * from ${stats_db_name}.result_tmp; drop table ${stats_db_name}.result_tmp; - -ANALYZE TABLE ${stats_db_name}.result COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.result COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- +-- ANALYZE TABLE ${stats_db_name}.result COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.result COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql index 8b55e83b53..528aaff528 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_6.sql @@ -30,10 +30,10 @@ from rcount group by rcount.pid; create view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture; - -ANALYZE TABLE ${stats_db_name}.result_projectcount COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.result_projectcount COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.result_fundercount COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.result_fundercount COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.project_resultcount COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.project_resultcount COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- +-- ANALYZE TABLE ${stats_db_name}.result_projectcount COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.result_projectcount COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.result_fundercount COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.result_fundercount COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.project_resultcount COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.project_resultcount COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step17.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step17.sql deleted file mode 100644 index 5c102d014a..0000000000 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step17.sql +++ /dev/null @@ -1,207 +0,0 @@ ------------------------------------------------------- ------------------------------------------------------- --- Shadow schema table exchange ------------------------------------------------------- ------------------------------------------------------- - --- Dropping old views -DROP VIEW IF EXISTS ${stats_db_shadow_name}.category; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.concept; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.context; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.country; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.countrygdp; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.creation_date; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset_citations; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset_classifications; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset_concepts; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset_datasources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset_languages; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset_licenses; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset_oids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset_pids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset_refereed; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset_sources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.dataset_topics; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.datasource; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.datasource_languages; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.datasource_oids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.datasource_organizations; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.datasource_results; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.datasource_sources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.funder; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.fundref; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.numbers_country; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.organization; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.organization_datasources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.organization_pids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.organization_projects; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.organization_sources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct_citations; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct_classifications; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct_concepts; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct_datasources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct_languages; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct_licenses; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct_oids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct_pids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct_refereed; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct_sources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.otherresearchproduct_topics; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.project; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.project_oids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.project_organizations; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.project_results; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.project_resultcount; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.project_results_publication; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication_citations; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication_classifications; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication_concepts; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication_datasources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication_languages; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication_licenses; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication_oids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication_pids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication_refereed; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication_sources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.publication_topics; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_affiliated_country; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_citations; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_classifications; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_concepts; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_datasources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_deposited_country; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_fundercount; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_gold; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_greenoa; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_languages; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_licenses; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_oids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_organization; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_peerreviewed; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_pids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_projectcount; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_projects; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_refereed; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_sources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.result_topics; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.rndexpediture; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.roarmap; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software_citations; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software_classifications; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software_concepts; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software_datasources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software_languages; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software_licenses; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software_oids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software_pids; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software_refereed; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software_sources; -DROP VIEW IF EXISTS ${stats_db_shadow_name}.software_topics; - - --- Creating the shadow database, in case it doesn't exist -CREATE database IF NOT EXISTS ${stats_db_shadow_name}; - --- Creating new views -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.category AS SELECT * FROM ${stats_db_name}.category; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.concept AS SELECT * FROM ${stats_db_name}.concept; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.context AS SELECT * FROM ${stats_db_name}.context; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.country AS SELECT * FROM ${stats_db_name}.country; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.countrygdp AS SELECT * FROM ${stats_db_name}.countrygdp; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.creation_date AS SELECT * FROM ${stats_db_name}.creation_date; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset AS SELECT * FROM ${stats_db_name}.dataset; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset_citations AS SELECT * FROM ${stats_db_name}.dataset_citations; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset_classifications AS SELECT * FROM ${stats_db_name}.dataset_classifications; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset_concepts AS SELECT * FROM ${stats_db_name}.dataset_concepts; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset_datasources AS SELECT * FROM ${stats_db_name}.dataset_datasources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset_languages AS SELECT * FROM ${stats_db_name}.dataset_languages; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset_licenses AS SELECT * FROM ${stats_db_name}.dataset_licenses; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset_oids AS SELECT * FROM ${stats_db_name}.dataset_oids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset_pids AS SELECT * FROM ${stats_db_name}.dataset_pids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset_refereed AS SELECT * FROM ${stats_db_name}.dataset_refereed; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset_sources AS SELECT * FROM ${stats_db_name}.dataset_sources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.dataset_topics AS SELECT * FROM ${stats_db_name}.dataset_topics; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.datasource AS SELECT * FROM ${stats_db_name}.datasource; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.datasource_languages AS SELECT * FROM ${stats_db_name}.datasource_languages; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.datasource_oids AS SELECT * FROM ${stats_db_name}.datasource_oids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.datasource_organizations AS SELECT * FROM ${stats_db_name}.datasource_organizations; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.datasource_results AS SELECT * FROM ${stats_db_name}.datasource_results; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.datasource_sources AS SELECT * FROM ${stats_db_name}.datasource_sources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.funder AS SELECT * FROM ${stats_db_name}.funder; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.fundref AS SELECT * FROM ${stats_db_name}.fundref; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.numbers_country AS SELECT * FROM ${stats_db_name}.numbers_country; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.organization AS SELECT * FROM ${stats_db_name}.organization; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.organization_datasources AS SELECT * FROM ${stats_db_name}.organization_datasources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.organization_pids AS SELECT * FROM ${stats_db_name}.organization_pids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.organization_projects AS SELECT * FROM ${stats_db_name}.organization_projects; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.organization_sources AS SELECT * FROM ${stats_db_name}.organization_sources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct AS SELECT * FROM ${stats_db_name}.otherresearchproduct; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct_citations AS SELECT * FROM ${stats_db_name}.otherresearchproduct_citations; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct_classifications AS SELECT * FROM ${stats_db_name}.otherresearchproduct_classifications; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct_concepts AS SELECT * FROM ${stats_db_name}.otherresearchproduct_concepts; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct_datasources AS SELECT * FROM ${stats_db_name}.otherresearchproduct_datasources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct_languages AS SELECT * FROM ${stats_db_name}.otherresearchproduct_languages; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct_licenses AS SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct_oids AS SELECT * FROM ${stats_db_name}.otherresearchproduct_oids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct_pids AS SELECT * FROM ${stats_db_name}.otherresearchproduct_pids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct_refereed AS SELECT * FROM ${stats_db_name}.otherresearchproduct_refereed; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct_sources AS SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.otherresearchproduct_topics AS SELECT * FROM ${stats_db_name}.otherresearchproduct_topics; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.project AS SELECT * FROM ${stats_db_name}.project; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.project_oids AS SELECT * FROM ${stats_db_name}.project_oids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.project_organizations AS SELECT * FROM ${stats_db_name}.project_organizations; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.project_results AS SELECT * FROM ${stats_db_name}.project_results; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.project_resultcount AS SELECT * FROM ${stats_db_name}.project_resultcount; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.project_results_publication AS SELECT * FROM ${stats_db_name}.project_results_publication; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication AS SELECT * FROM ${stats_db_name}.publication; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication_citations AS SELECT * FROM ${stats_db_name}.publication_citations; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication_classifications AS SELECT * FROM ${stats_db_name}.publication_classifications; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication_concepts AS SELECT * FROM ${stats_db_name}.publication_concepts; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication_datasources AS SELECT * FROM ${stats_db_name}.publication_datasources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication_languages AS SELECT * FROM ${stats_db_name}.publication_languages; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication_licenses AS SELECT * FROM ${stats_db_name}.publication_licenses; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication_oids AS SELECT * FROM ${stats_db_name}.publication_oids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication_pids AS SELECT * FROM ${stats_db_name}.publication_pids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication_refereed AS SELECT * FROM ${stats_db_name}.publication_refereed; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication_sources AS SELECT * FROM ${stats_db_name}.publication_sources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.publication_topics AS SELECT * FROM ${stats_db_name}.publication_topics; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result AS SELECT * FROM ${stats_db_name}.result; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_affiliated_country AS SELECT * FROM ${stats_db_name}.result_affiliated_country; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_citations AS SELECT * FROM ${stats_db_name}.result_citations; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_classifications AS SELECT * FROM ${stats_db_name}.result_classifications; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_concepts AS SELECT * FROM ${stats_db_name}.result_concepts; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_datasources AS SELECT * FROM ${stats_db_name}.result_datasources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_deposited_country AS SELECT * FROM ${stats_db_name}.result_deposited_country; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_fundercount AS SELECT * FROM ${stats_db_name}.result_fundercount; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_gold AS SELECT * FROM ${stats_db_name}.result_gold; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_greenoa AS SELECT * FROM ${stats_db_name}.result_greenoa; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_languages AS SELECT * FROM ${stats_db_name}.result_languages; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_licenses AS SELECT * FROM ${stats_db_name}.result_licenses; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_oids AS SELECT * FROM ${stats_db_name}.result_oids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_organization AS SELECT * FROM ${stats_db_name}.result_organization; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_peerreviewed AS SELECT * FROM ${stats_db_name}.result_peerreviewed; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_pids AS SELECT * FROM ${stats_db_name}.result_pids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_projectcount AS SELECT * FROM ${stats_db_name}.result_projectcount; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_projects AS SELECT * FROM ${stats_db_name}.result_projects; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_refereed AS SELECT * FROM ${stats_db_name}.result_refereed; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_sources AS SELECT * FROM ${stats_db_name}.result_sources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.result_topics AS SELECT * FROM ${stats_db_name}.result_topics; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.rndexpediture AS SELECT * FROM ${stats_db_name}.rndexpediture; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.roarmap AS SELECT * FROM ${stats_db_name}.roarmap; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software AS SELECT * FROM ${stats_db_name}.software; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software_citations AS SELECT * FROM ${stats_db_name}.software_citations; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software_classifications AS SELECT * FROM ${stats_db_name}.software_classifications; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software_concepts AS SELECT * FROM ${stats_db_name}.software_concepts; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software_datasources AS SELECT * FROM ${stats_db_name}.software_datasources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software_languages AS SELECT * FROM ${stats_db_name}.software_languages; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software_licenses AS SELECT * FROM ${stats_db_name}.software_licenses; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software_oids AS SELECT * FROM ${stats_db_name}.software_oids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software_pids AS SELECT * FROM ${stats_db_name}.software_pids; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software_refereed AS SELECT * FROM ${stats_db_name}.software_refereed; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software_sources AS SELECT * FROM ${stats_db_name}.software_sources; -CREATE VIEW IF NOT EXISTS ${stats_db_shadow_name}.software_topics AS SELECT * FROM ${stats_db_name}.software_topics; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step18.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step18.sql deleted file mode 100644 index 34e48a18a3..0000000000 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step18.sql +++ /dev/null @@ -1,8 +0,0 @@ ------------------------------------------------------- ------------------------------------------------------- --- Impala table statistics - Needed to make the tables --- visible for impala ------------------------------------------------------- ------------------------------------------------------- - -INVALIDATE METADATA ${stats_db_name}; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step19.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step19.sql deleted file mode 100644 index 34e48a18a3..0000000000 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step19.sql +++ /dev/null @@ -1,8 +0,0 @@ ------------------------------------------------------- ------------------------------------------------------- --- Impala table statistics - Needed to make the tables --- visible for impala ------------------------------------------------------- ------------------------------------------------------- - -INVALIDATE METADATA ${stats_db_name}; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql index d2700f415c..62a1585608 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql @@ -93,21 +93,21 @@ FROM ${openaire_db_name}.publication p WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" and p.datainfo.deletedbyinference = false; -ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql index 977d321322..dcd5ad858f 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql @@ -93,20 +93,20 @@ SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subj FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference = false; - -ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- +-- ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql index ace084d231..fd5390e663 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql @@ -93,20 +93,20 @@ SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subj FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference = false; - -ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- +-- ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql index 0fd8e7189d..b359b596f3 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql @@ -85,19 +85,19 @@ SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subj FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference = false; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index ade686cf6d..23ef03bc93 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -72,13 +72,13 @@ select distinct xpath_string(fund, '//funder/id') as id, xpath_string(fund, '//funder/shortname') as shortname from ${openaire_db_name}.project p lateral view explode(p.fundingtree.value) fundingtree as fund; -ANALYZE TABLE ${stats_db_name}.project_oids COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.project_oids COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.project_organizations COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.project_organizations COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.project_results COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.project_results COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.project_tmp COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.project_tmp COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.funder COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.funder COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- ANALYZE TABLE ${stats_db_name}.project_oids COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.project_oids COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.project_organizations COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.project_organizations COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.project_results COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.project_results COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.project_tmp COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.project_tmp COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.funder COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.funder COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index d330bde468..ae540b9b23 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -135,7 +135,7 @@ FROM ${stats_db_name}.result r JOIN ${stats_db_name}.project_results pr ON r.id = pr.result JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; -ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index 73ea0c0849..de0fedd7e2 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -99,11 +99,11 @@ CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS SELECT datasource AS id, id AS result FROM ${stats_db_name}.result_datasources; -ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS FOR COLUMNS; -ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS FOR COLUMNS; +-- ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql index 9a581900ab..a1cb461855 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql @@ -19,5 +19,5 @@ CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects AS SELECT id AS project, organization as id FROM ${stats_db_name}.project_organizations; -ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS; -ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +-- ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS; +-- ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index 2f195d6d39..95c151c09a 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -260,31 +260,6 @@ stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} - - - - - - - ${hive_jdbc_url} - - stats_db_name=${stats_db_name} - stats_db_shadow_name=${stats_db_shadow_name} - - - - - - - - ${jobTracker} - ${nameNode} - impala-shell.sh - ${stats_db_name} - step18.sql - ${wf:appPath()}/scripts/step18.sql - impala-shell.sh - @@ -293,11 +268,10 @@ ${jobTracker} ${nameNode} - impala-shell.sh + finalizedb.sh + stats_db_name ${stats_db_shadow_name} - step19.sql - ${wf:appPath()}/scripts/step19.sql - impala-shell.sh + finalizedb.sh From c5502eba8f79b5526a750afbf8de82979a305232 Mon Sep 17 00:00:00 2001 From: antleb Date: Fri, 19 Feb 2021 02:54:39 +0200 Subject: [PATCH 103/106] actually moved stats computation in impala instead of hive... --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh index 915faab70d..3a4a28aff6 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh @@ -11,6 +11,7 @@ export SHADOW=$2 echo "Updating shadow database" impala-shell -q "invalidate metadata ${SOURCE}" +impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/^\(.*\)/compute stats ${SOURCE}.\1;/" | impala-shell -c -f - impala-shell -q "create database if not exists ${SHADOW}" impala-shell -d ${SHADOW} -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -f - impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -f - From 3681afbe048d45b6aac4c800da45c7e2ae9387cc Mon Sep 17 00:00:00 2001 From: antleb Date: Fri, 19 Feb 2021 03:04:27 +0200 Subject: [PATCH 104/106] typo --- .../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 95c151c09a..9c16f149db 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 @@ -269,7 +269,7 @@ ${jobTracker} ${nameNode} finalizedb.sh - stats_db_name + ${stats_db_name} ${stats_db_shadow_name} finalizedb.sh From d90767c73385434872aee398e64dbf96a9e57eab Mon Sep 17 00:00:00 2001 From: antleb Date: Fri, 19 Feb 2021 03:18:47 +0200 Subject: [PATCH 105/106] correctly invalidating metadata --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh index 3a4a28aff6..57acb2ee7d 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizedb.sh @@ -10,9 +10,9 @@ export SOURCE=$1 export SHADOW=$2 echo "Updating shadow database" -impala-shell -q "invalidate metadata ${SOURCE}" +impala-shell -d ${SOURCE} -q "invalidate metadata" impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/^\(.*\)/compute stats ${SOURCE}.\1;/" | impala-shell -c -f - impala-shell -q "create database if not exists ${SHADOW}" -impala-shell -d ${SHADOW} -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -f - -impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -f - +impala-shell -d ${SHADOW} -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -c -f - +impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -c -f - echo "Shadow db ready!" \ No newline at end of file From 27796343ca960c7ecb60e48e70a42742bf6247c7 Mon Sep 17 00:00:00 2001 From: antleb Date: Wed, 3 Mar 2021 01:37:47 +0200 Subject: [PATCH 106/106] crude sleep. hardcoded value --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh | 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/updateCache.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh index 36e74a5561..dc19f84b4b 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh @@ -1,4 +1,4 @@ #!/usr/bin/env bash curl --request GET $1/cache/updateCache - +sleep 20h \ No newline at end of file