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Clean workflows

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Dimitris 2021-01-15 16:19:12 +02:00
parent dc9c2f3272
commit 3e8d2a6b2d
26 changed files with 0 additions and 5558 deletions
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18
dhp-workflows/dhp-usage-datasets-stats-update/nb-configuration.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project-shared-configuration>
<!--
This file contains additional configuration written by modules in the NetBeans IDE.
The configuration is intended to be shared among all the users of project and
therefore it is assumed to be part of version control checkout.
Without this configuration present, some functionality in the IDE may be limited or fail altogether.
-->
<properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
<!--
Properties that influence various parts of the IDE, especially code formatting and the like.
You can copy and paste the single properties, into the pom.xml file and the IDE will pick them up.
That way multiple projects can share the same settings (useful for formatting rules for example).
Any value defined here will override the pom.xml file value but is only applicable to the current project.
-->
<netbeans.hint.jdkPlatform>JDK_1.8</netbeans.hint.jdkPlatform>
</properties>
</project-shared-configuration>

112
dhp-workflows/dhp-usage-datasets-stats-update/pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<!-- <parent>
<artifactId>dhp-workflows</artifactId >
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.7-SNAPSHOT</version>
</parent>
<groupId>eu.dnetlib</groupId> -->
<!-- <parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-workflows</artifactId>
<version>1.1.7-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-usage-stats-update</artifactId> -->
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.7-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-usage-datasets-stats-update</artifactId>
<build>
<plugins>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<version>2.1.15</version>
<executions>
<execution>
<goals>
<goal>revision</goal>
</goals>
</execution>
</executions>
<configuration>
<dotGitDirectory>${project.basedir}/../.git</dotGitDirectory>
<!-- more config here as you see fit -->
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.6.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</build>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<cdh.hive.version>0.13.1-cdh5.2.1</cdh.hive.version>
<cdh.hadoop.version>2.5.0-cdh5.2.1</cdh.hadoop.version>
</properties>
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
<version>2.2.0</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
<version>2.4.5</version>
</dependency>
<dependency>
<groupId>com.googlecode.json-simple</groupId>
<artifactId>json-simple</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20180130</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.apache.hive</groupId>
<artifactId>hive-jdbc</artifactId>
<version>${cdh.hive.version}</version>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-common</artifactId>
<version>${cdh.hadoop.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>com.mchange</groupId>
<artifactId>c3p0</artifactId>
<version>0.9.5.2</version>
</dependency>
<dependency>
<groupId>c3p0</groupId>
<artifactId>c3p0</artifactId>
<version>0.9.1.2</version>
<type>jar</type>
</dependency>
</dependencies>
<name>dhp-usage-datasets-stats-update</name>
</project>

1
dhp-workflows/dhp-usage-datasets-stats-update/runworkflow.sh
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mvn clean package -Poozie-package,deploy,run -Dworkflow.source.dir=eu/dnetlib/dhp/oa/graph/datasetsusagestats

131
dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ConnectDB.java
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/*
* 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();
}
}

168
dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DatasetsStatsDB.java
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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 <STRING>,\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();
}
}

102
dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/DownloadReportsListFromDatacite.java
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/*
* 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);
}
}
}
}

69
dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ExecuteWorkflow.java
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/*
* 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();
}
}

408
dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/ReadReportsListFromDatacite.java
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/*
* 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<String> 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<String>
* 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<String> listHdfsDir(String dir) throws Exception {
FileSystem hdfs = FileSystem.get(new Configuration());
RemoteIterator<LocatedFileStatus> Files;
ArrayList<String> 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 (?,?,?,?,?,?,?,?)"
* );
*/

111
dhp-workflows/dhp-usage-datasets-stats-update/src/main/java/eu/dnetlib/oa/graph/datasetsusagestats/export/UsageStatsExporter.java
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@ -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(); }
*/

56
dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/export/datasets_usagestats_parameters.json
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@ -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
}
]

38
dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/config-default.xml
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<configuration>
<property>
<name>jobTracker</name>
<value>${jobTracker}</value>
</property>
<property>
<name>nameNode</name>
<value>${nameNode}</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hiveMetastoreUris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hiveJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1</value>
</property>
<property>
<name>impalaJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-gw.ocean.icm.edu.pl:21050/;auth=noSasl;</value>
</property>
<property>
<name>oozie.wf.workflow.notification.url</name>
<value>{serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
</configuration>

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dhp-workflows/dhp-usage-datasets-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/datasetsusagestats/oozie_app/workflow.xml
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<workflow-app name="Usage Graph Stats" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>hiveMetastoreUris</name>
<description>Hive server metastore URIs</description>
</property>
<property>
<name>hiveJdbcUrl</name>
<description>Hive server jdbc url</description>
</property>
<property>
<name>impalaJdbcUrl</name>
<description>Impala server jdbc url</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>hive.metastore.uris</name>
<value>${hiveMetastoreUris}</value>
</property>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
</configuration>
</global>
<start to="Step1"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name='Step1'>
<java>
<main-class>eu.dnetlib.oa.graph.datasetsusagestats.export.ExecuteWorkflow</main-class>
<arg>--dataciteBaseURL</arg>
<arg>${dataciteBaseURL}</arg>
<arg>--dataciteReportPath</arg>
<arg>${dataciteReportPath}</arg>
<arg>--dbHiveUrl</arg>
<arg>${hiveJdbcUrl}</arg>
<arg>--dbImpalaUrl</arg>
<arg>${impalaJdbcUrl}</arg>
<arg>--datasetUsageStatsDBSchema</arg>
<arg>${datasetUsageStatsDBSchema}</arg>
<arg>--statsDBSchema</arg>
<arg>${statsDBSchema}</arg>
<arg>--recreateDbAndTables</arg>
<arg>${recreateDbAndTables}</arg>
<arg>--datasetsEmptyDirs</arg>
<arg>${datasetsEmptyDirs}</arg>
<arg>--finalTablesVisibleToImpala</arg>
<arg>${finalTablesVisibleToImpala}</arg>
<capture-output/>
</java>
<ok to="End" />
<error to="Kill" />
</action>
<end name="End"/>
</workflow-app>

78
dhp-workflows/dhp-usage-stats-update/pom.xml
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@ -1,78 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<!-- <parent>
<artifactId>dhp-workflows</artifactId >
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.7-SNAPSHOT</version>
</parent>
<groupId>eu.dnetlib</groupId> -->
<!-- <parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-workflows</artifactId>
<version>1.1.7-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-usage-stats-update</artifactId> -->
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.7-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-usage-stats-update</artifactId>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<cdh.hive.version>0.13.1-cdh5.2.1</cdh.hive.version>
<cdh.hadoop.version>2.5.0-cdh5.2.1</cdh.hadoop.version>
</properties>
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
<version>2.2.0</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
<version>2.4.5</version>
</dependency>
<dependency>
<groupId>com.googlecode.json-simple</groupId>
<artifactId>json-simple</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20180130</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.apache.hive</groupId>
<artifactId>hive-jdbc</artifactId>
<version>${cdh.hive.version}</version>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-common</artifactId>
<version>${cdh.hadoop.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>c3p0</groupId>
<artifactId>c3p0</artifactId>
<version>0.9.1.2</version>
<type>jar</type>
</dependency>
</dependencies>
</project>

125
dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ConnectDB.java
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@ -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();
}
}

197
dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ExecuteWorkflow.java
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@ -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;
}
}

419
dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/IrusStats.java
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@ -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<String> opendoarsToVisit = new ArrayList<String>();
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;
}
}
}

265
dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaDownloadLogs.java
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@ -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<Integer> siteIdsToVisit = new ArrayList<Integer>();
// 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();
}
}
}
}

436
dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/LaReferenciaStats.java
View File

@ -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<p2.timestamp AND ((unix_timestamp(p2.timestamp)-unix_timestamp(p1.timestamp))/60)<30 " +
"AND lareferencialogtmp.source=p1.source AND lareferencialogtmp.id_visit=p1.id_visit " +
"AND lareferencialogtmp.action=p1.action AND lareferencialogtmp.entity_id=p1.entity_id " +
"AND lareferencialogtmp.timestamp=p1.timestamp)";
stmt.executeUpdate(sql);
stmt.close();
logger.info("Cleaned download double clicks");
stmt = ConnectDB.getHiveConnection().createStatement();
logger.info("Cleaning action double clicks");
// clean view double clicks
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='action' AND p1.timestamp!=p2.timestamp " +
"AND p1.timestamp<p2.timestamp AND ((unix_timestamp(p2.timestamp)-unix_timestamp(p1.timestamp))/60)<10 " +
"AND lareferencialogtmp.source=p1.source AND lareferencialogtmp.id_visit=p1.id_visit " +
"AND lareferencialogtmp.action=p1.action AND lareferencialogtmp.entity_id=p1.entity_id " +
"AND lareferencialogtmp.timestamp=p1.timestamp)";
stmt.executeUpdate(sql);
stmt.close();
logger.info("Cleaned action double clicks");
// 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();
ConnectDB.getHiveConnection().setAutoCommit(false);
logger.info("Updating lareferencialog");
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);
stmt.close();
ConnectDB.getHiveConnection().close();
}
private ArrayList<String> listHdfsDir(String dir) throws Exception {
FileSystem hdfs = FileSystem.get(new Configuration());
RemoteIterator<LocatedFileStatus> Files;
ArrayList<String> 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;
}
}

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dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikDownloadLogs.java
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@ -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<Integer> piwikIdToVisit = new ArrayList<Integer>();
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();
}
}

1262
dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/PiwikStatsDB.java
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54
dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/ReadCounterRobotsList.java
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@ -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;
}
}

575
dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/SarcStats.java
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@ -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<String[]> issnAndUrls = new ArrayList<String[]>();
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<String> jkeys = new HashSet<String>(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 "";
}
}

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dhp-workflows/dhp-usage-stats-update/src/main/java/eu/dnetlib/oa/graph/usagestats/export/UsageStatsExporter.java
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@ -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();
}
}

231
dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/export/usagestats_parameters.json
View File

@ -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
}
]

38
dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/config-default.xml
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@ -1,38 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>${jobTracker}</value>
</property>
<property>
<name>nameNode</name>
<value>${nameNode}</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hiveMetastoreUris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hiveJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1</value>
</property>
<property>
<name>impalaJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-gw.ocean.icm.edu.pl:21050/;auth=noSasl;</value>
</property>
<property>
<name>oozie.wf.workflow.notification.url</name>
<value>{serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
</configuration>

90
dhp-workflows/dhp-usage-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagestats/oozie_app/workflow.xml
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@ -1,90 +0,0 @@
<workflow-app name="Usage Graph Stats" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>hiveMetastoreUris</name>
<description>Hive server metastore URIs</description>
</property>
<property>
<name>hiveJdbcUrl</name>
<description>Hive server jdbc url</description>
</property>
<property>
<name>impalaJdbcUrl</name>
<description>Impala server jdbc url</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>hive.metastore.uris</name>
<value>${hiveMetastoreUris}</value>
</property>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
</configuration>
</global>
<start to="Step1"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name='Step1'>
<java>
<main-class>eu.dnetlib.oa.graph.usagestats.export.ExecuteWorkflow</main-class>
<arg>--matomoAuthToken</arg><arg>${matomoAuthToken}</arg>
<arg>--matomoBaseURL</arg><arg>${matomoBaseURL}</arg>
<arg>--repoLogPath</arg><arg>${repoLogPath}</arg>
<arg>--portalLogPath</arg><arg>${portalLogPath}</arg>
<arg>--portalMatomoID</arg><arg>${portalMatomoID}</arg>
<arg>--irusUKBaseURL</arg><arg>${irusUKBaseURL}</arg>
<arg>--irusUKReportPath</arg><arg>${irusUKReportPath}</arg>
<arg>--sarcsReportPathArray</arg><arg>${sarcsReportPathArray}</arg>
<arg>--sarcsReportPathNonArray</arg><arg>${sarcsReportPathNonArray}</arg>
<arg>--lareferenciaLogPath</arg><arg>${lareferenciaLogPath}</arg>
<arg>--lareferenciaBaseURL</arg><arg>${lareferenciaBaseURL}</arg>
<arg>--lareferenciaAuthToken</arg><arg>${lareferenciaAuthToken}</arg>
<arg>--dbHiveUrl</arg><arg>${hiveJdbcUrl}</arg>
<arg>--dbImpalaUrl</arg><arg>${impalaJdbcUrl}</arg>
<arg>--usageStatsDBSchema</arg><arg>${usageStatsDBSchema}</arg>
<arg>--statsDBSchema</arg><arg>${statsDBSchema}</arg>
<arg>--recreateDbAndTables</arg><arg>${recreateDbAndTables}</arg>
<arg>--piwikEmptyDirs</arg><arg>${piwikEmptyDirs}</arg>
<arg>--downloadPiwikLogs</arg><arg>${downloadPiwikLogs}</arg>
<arg>--processPiwikLogs</arg><arg>${processPiwikLogs}</arg>
<arg>--startingLogPeriod</arg><arg>${startingLogPeriod}</arg>
<arg>--endingLogPeriod</arg><arg>${endingLogPeriod}</arg>
<arg>--numberOfPiwikIdsToDownload</arg><arg>${numberOfPiwikIdsToDownload}</arg>
<arg>--numberOfSiteIdsToDownload</arg><arg>${numberOfSiteIdsToDownload}</arg>
<arg>--laReferenciaEmptyDirs</arg><arg>${laReferenciaEmptyDirs}</arg>
<arg>--downloadLaReferenciaLogs</arg><arg>${downloadLaReferenciaLogs}</arg>
<arg>--processLaReferenciaLogs</arg><arg>${processLaReferenciaLogs}</arg>
<arg>--irusCreateTablesEmptyDirs</arg><arg>${irusCreateTablesEmptyDirs}</arg>
<arg>--irusDownloadReports</arg><arg>${irusDownloadReports}</arg>
<arg>--irusProcessStats</arg><arg>${irusProcessStats}</arg>
<arg>--irusNumberOfOpendoarsToDownload</arg><arg>${irusNumberOfOpendoarsToDownload}</arg>
<arg>--sarcCreateTablesEmptyDirs</arg><arg>${sarcCreateTablesEmptyDirs}</arg>
<arg>--sarcDownloadReports</arg><arg>${sarcDownloadReports}</arg>
<arg>--sarcProcessStats</arg><arg>${sarcProcessStats}</arg>
<arg>--sarcNumberOfIssnToDownload</arg><arg>${sarcNumberOfIssnToDownload}</arg>
<arg>--finalizeStats</arg><arg>${finalizeStats}</arg>
<arg>--finalTablesVisibleToImpala</arg><arg>${finalTablesVisibleToImpala}</arg>
<arg>--numberOfDownloadThreads</arg><arg>${numberOfDownloadThreads}</arg>
<capture-output/>
</java>
<ok to="End" />
<error to="Kill" />
</action>
<end name="End"/>
</workflow-app>