forked from D-Net/dnet-hadoop
Add collecting software code repository URLs
This commit is contained in:
Serafeim Chatzopoulos
parent
8a6892cc63
commit
9d44418d38
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@ -0,0 +1,104 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<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">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-workflows</artifactId>
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<version>1.2.5-SNAPSHOT</version>
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</parent>
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<artifactId>dhp-swh</artifactId>
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<dependencies>
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<dependency>
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<groupId>org.apache.spark</groupId>
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<artifactId>spark-core_${scala.binary.version}</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.spark</groupId>
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<artifactId>spark-sql_${scala.binary.version}</artifactId>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-common</artifactId>
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<version>${project.version}</version>
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<exclusions>
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<exclusion>
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<groupId>net.sf.saxon</groupId>
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<artifactId>Saxon-HE</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>dom4j</groupId>
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<artifactId>dom4j</artifactId>
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</dependency>
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<dependency>
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<groupId>xml-apis</groupId>
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<artifactId>xml-apis</artifactId>
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</dependency>
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<dependency>
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<groupId>jaxen</groupId>
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<artifactId>jaxen</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.hadoop</groupId>
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<artifactId>hadoop-distcp</artifactId>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-actionmanager-api</artifactId>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-actionmanager-common</artifactId>
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<exclusions>
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<exclusion>
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-openaireplus-mapping-utils</artifactId>
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</exclusion>
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<exclusion>
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<groupId>saxonica</groupId>
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<artifactId>saxon</artifactId>
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</exclusion>
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<exclusion>
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<groupId>saxonica</groupId>
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<artifactId>saxon-dom</artifactId>
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</exclusion>
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<exclusion>
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<groupId>jgrapht</groupId>
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<artifactId>jgrapht</artifactId>
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</exclusion>
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<exclusion>
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<groupId>net.sf.ehcache</groupId>
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<artifactId>ehcache</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.springframework</groupId>
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<artifactId>spring-test</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.*</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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<exclusion>
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<groupId>apache</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpclient</artifactId>
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<version>4.5.13</version>
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</dependency>
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</dependencies>
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</project>
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@ -0,0 +1,211 @@
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package eu.dnetlib.dhp.swh;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Optional;
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import java.util.concurrent.TimeUnit;
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import org.apache.commons.io.IOUtils;
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import org.apache.http.Header;
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import org.apache.http.HttpEntity;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.apache.http.impl.client.CloseableHttpClient;
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import org.apache.http.impl.client.HttpClients;
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import org.apache.http.util.EntityUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FlatMapFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.types.DataTypes;
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import org.apache.spark.sql.types.StructType;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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/**
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* Creates action sets for Crossref affiliation relations inferred by BIP!
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*/
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public class CollectSoftwareRepositoryURLs implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(CollectSoftwareRepositoryURLs.class);
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// public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
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// public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
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// public static final String BIP_INFERENCE_PROVENANCE = "bip:affiliation:crossref";
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private static final String DEFAULT_VISIT_TYPE = "git";
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private static final int CONCURRENT_API_CALLS = 1;
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private static final String SWH_LATEST_VISIT_URL = "https://archive.softwareheritage.org/api/1/origin/%s/visit/latest/";
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public static <I extends Result> void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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CollectSoftwareRepositoryURLs.class
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.getResourceAsStream("/eu/dnetlib/dhp/swh/input_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String hiveDbName = parser.get("hiveDbName");
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log.info("hiveDbName {}: ", hiveDbName);
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final String outputPath = parser.get("softwareCodeRepositoryURLs");
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log.info("softwareCodeRepositoryURLs {}: ", outputPath);
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final String hiveMetastoreUris = parser.get("hiveMetastoreUris");
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log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", hiveMetastoreUris);
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runWithSparkHiveSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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doRun(spark, hiveDbName, outputPath);
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});
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}
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private static <I extends Result> void doRun(SparkSession spark, String hiveDbName, String outputPath) {
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String queryTemplate = "SELECT distinct coderepositoryurl.value " +
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"FROM %s.software " +
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"WHERE coderepositoryurl.value IS NOT NULL";
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String query = String.format(queryTemplate, hiveDbName);
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log.info("Hive query to fetch software code URLs: {}", query);
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Dataset<Row> df = spark.sql(query);
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// write distinct repository URLs
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df
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.write()
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.mode(SaveMode.Overwrite)
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// .option("compression", "gzip")
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.csv(outputPath);
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}
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private static Dataset<Row> readSoftware(SparkSession spark, String inputPath) {
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return spark
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.read()
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.json(inputPath)
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.select(
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new Column("codeRepositoryUrl.value").as("codeRepositoryUrl"),
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new Column("dataInfo.deletedbyinference"),
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new Column("dataInfo.invisible"));
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}
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private static Dataset<Row> filterSoftware(Dataset<Row> softwareDF, Integer limit) {
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Dataset<Row> df = softwareDF
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.where(softwareDF.col("codeRepositoryUrl").isNotNull())
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.where("deletedbyinference = false")
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.where("invisible = false")
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.drop("deletedbyinference")
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.drop("invisible");
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// TODO remove when done
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df = df.limit(limit);
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return df;
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}
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public static Dataset<Row> makeParallelRequests(SparkSession spark, Dataset<Row> softwareDF) {
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// TODO replace with coalesce ?
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Dataset<Row> df = softwareDF.repartition(CONCURRENT_API_CALLS);
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log.info("Number of partitions: {}", df.rdd().getNumPartitions());
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ObjectMapper objectMapper = new ObjectMapper();
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List<Row> collectedRows = df
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.javaRDD()
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// max parallelism should be equal to the number of partitions here
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.mapPartitions((FlatMapFunction<Iterator<Row>, Row>) partition -> {
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List<Row> resultRows = new ArrayList<>();
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while (partition.hasNext()) {
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Row row = partition.next();
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String url = String.format(SWH_LATEST_VISIT_URL, row.getString(0));
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// String snapshotId = null;
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// String type = null;
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// String date = null;
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String responseBody = makeAPICall(url);
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TimeUnit.SECONDS.sleep(1);
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// Thread.sleep(500);
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// if (responseBody != null) {
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// LastVisitResponse visitResponse = objectMapper.readValue(responseBody, LastVisitResponse.class);
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// snapshotId = visitResponse.getSnapshot();
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// type = visitResponse.getType();
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// date = visitResponse.getDate();
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// }
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// resultRows.add(RowFactory.create(url, snapshotId, type, date));
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resultRows.add(RowFactory.create(url, responseBody));
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}
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return resultRows.iterator();
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})
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.collect();
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StructType resultSchema = new StructType()
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.add("codeRepositoryUrl", DataTypes.StringType)
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.add("response", DataTypes.StringType);
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// .add("snapshotId", DataTypes.StringType)
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// .add("type", DataTypes.StringType)
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// .add("date", DataTypes.StringType);
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// create a DataFrame from the collected rows
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return spark.createDataFrame(collectedRows, resultSchema);
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}
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private static String makeAPICall(String url) throws IOException {
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System.out.println(java.time.LocalDateTime.now());
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try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
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HttpGet httpGet = new HttpGet(url);
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httpGet
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.setHeader(
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"Authorization",
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"Bearer eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJhMTMxYTQ1My1hM2IyLTQwMTUtODQ2Ny05MzAyZjk3MTFkOGEifQ.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.XHj1VIZu1dZ4Ej32-oU84mFmaox9cLNjXosNxwZM0Xs");
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try (CloseableHttpResponse response = httpClient.execute(httpGet)) {
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int statusCode = response.getStatusLine().getStatusCode();
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// if (statusCode != 200)
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// return null;
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Header[] headers = response.getHeaders("X-RateLimit-Remaining");
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for (Header header : headers) {
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System.out
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.println(
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"Key : " + header.getName()
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+ " ,Value : " + header.getValue());
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}
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HttpEntity entity = response.getEntity();
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if (entity != null) {
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return EntityUtils.toString(entity);
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}
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}
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}
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return null;
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}
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}
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@ -0,0 +1,40 @@
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package eu.dnetlib.dhp.swh.models;
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import com.cloudera.com.fasterxml.jackson.annotation.JsonProperty;
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import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
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@JsonIgnoreProperties(ignoreUnknown = true)
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public class LastVisitResponse {
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private String type;
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private String date;
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@JsonProperty("snapshot")
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private String snapshotId;
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public String getType() {
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return type;
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}
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public void setType(String type) {
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this.type = type;
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}
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public String getDate() {
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return date;
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}
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public void setDate(String date) {
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this.date = date;
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}
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public String getSnapshot() {
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return snapshotId;
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}
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public void setSnapshot(String snapshotId) {
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this.snapshotId = snapshotId;
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}
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}
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@ -0,0 +1,26 @@
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[
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "when true will stop SparkSession after job execution",
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"paramRequired": false
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},
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{
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"paramName": "ip",
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"paramLongName": "softwareCodeRepositoryURLs",
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"paramDescription": "the URL where to store software repository URLs",
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"paramRequired": true
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},
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{
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"paramName": "db",
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"paramLongName": "hiveDbName",
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"paramDescription": "the target hive database name",
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"paramRequired": true
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},
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{
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"paramName": "hmu",
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"paramLongName": "hiveMetastoreUris",
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"paramDescription": "the hive metastore uris",
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"paramRequired": true
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}
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]
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@ -0,0 +1,25 @@
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# hive
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hiveDbName=openaire_prod_20230914
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hiveMetastoreUris=thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083
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# oozie
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oozie.action.sharelib.for.spark=spark2
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oozie.use.system.libpath=true
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oozie.wf.application.path=${oozieTopWfApplicationPath}
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oozie.wf.application.path=${oozieTopWfApplicationPath}
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oozieActionShareLibForSpark2=spark2
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# spark
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spark2EventLogDir=/user/spark/spark2ApplicationHistory
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spark2ExtraListeners=com.cloudera.spark.lineage.NavigatorAppListener
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spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListener
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spark2YarnHistoryServerAddress=http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089
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sparkSqlWarehouseDir=/user/hive/warehouse
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# misc
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wfAppPath=${oozieTopWfApplicationPath}
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resourceManager=http://iis-cdh5-test-m2.ocean.icm.edu.pl:8088/cluster
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# custom params
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softwareCodeRepositoryURLs=${workingDir}/code_repo_urls.csv
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resume=collect-software-repository-urls
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@ -0,0 +1,101 @@
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<workflow-app name="Software-Heritage-Integration-Workflow" xmlns="uri:oozie:workflow:0.5">
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<!-- <parameters>-->
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<!-- <property>-->
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<!-- <name>apiDescription</name>-->
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<!-- <description>A json encoding of the API Description class</description>-->
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<!-- </property>-->
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<!-- <property>-->
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<!-- <name>dataSourceInfo</name>-->
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<!-- <description>A json encoding of the Datasource Info</description>-->
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<!-- </property>-->
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<!-- <property>-->
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<!-- <name>identifierPath</name>-->
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<!-- <description>An xpath to retrieve the metadata identifier for the generation of DNet Identifier </description>-->
|
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<!-- </property>-->
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<!-- <property>-->
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<!-- <name>metadataEncoding</name>-->
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<!-- <description> The type of the metadata XML/JSON</description>-->
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<!-- </property>-->
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<!-- <property>-->
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<!-- <name>timestamp</name>-->
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<!-- <description>The timestamp of the collection date</description>-->
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<!-- </property>-->
|
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<!-- <property>-->
|
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<!-- <name>workflowId</name>-->
|
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<!-- <description>The identifier of the workflow</description>-->
|
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<!-- </property>-->
|
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<!-- <property>-->
|
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<!-- <name>mdStoreID</name>-->
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<!-- <description>The identifier of the mdStore</description>-->
|
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<!-- </property>-->
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<!-- <property>-->
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<!-- <name>mdStoreManagerURI</name>-->
|
||||
<!-- <description>The URI of the MDStore Manager</description>-->
|
||||
<!-- </property>-->
|
||||
|
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<!-- <property>-->
|
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<!-- <name>dnetMessageManagerURL</name>-->
|
||||
<!-- <description>The URI of the Dnet Message Manager</description>-->
|
||||
<!-- </property>-->
|
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<!-- <property>-->
|
||||
<!-- <name>collectionMode</name>-->
|
||||
<!-- <description>Should be REFRESH or INCREMENTAL</description>-->
|
||||
<!-- </property>-->
|
||||
|
||||
<!-- <property>-->
|
||||
<!-- <name>collection_java_xmx</name>-->
|
||||
<!-- <value>-Xmx200m</value>-->
|
||||
<!-- <description>Used to configure the heap size for the map JVM process. Should be 80% of mapreduce.map.memory.mb.</description>-->
|
||||
<!-- </property>-->
|
||||
|
||||
|
||||
<!-- </parameters>-->
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
</global>
|
||||
|
||||
<start to="startFrom"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<decision name="startFrom">
|
||||
<switch>
|
||||
<case to="collect-software-repository-urls">${wf:conf('startFrom') eq 'collect-software-repository-urls'}</case>
|
||||
<default to="collect-software-repository-urls"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<action name="collect-software-repository-urls">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Collect software repository URLs</name>
|
||||
<class>eu.dnetlib.dhp.swh.CollectSoftwareRepositoryURLs</class>
|
||||
<jar>dhp-swh-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
|
||||
<arg>--softwareCodeRepositoryURLs</arg><arg>${softwareCodeRepositoryURLs}</arg>
|
||||
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
|
||||
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
|
||||
</workflow-app>
|
||||
|
|
@ -39,6 +39,7 @@
|
|||
<module>dhp-broker-events</module>
|
||||
<module>dhp-doiboost</module>
|
||||
<module>dhp-impact-indicators</module>
|
||||
<module>dhp-swh</module>
|
||||
</modules>
|
||||
|
||||
<pluginRepositories>
|
||||
|
|
|
|||
Loading…
Reference in New Issue