country propagation for results collected from institutional repositories
This commit is contained in:
parent
4955be0197
commit
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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"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<parent>
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<artifactId>dhp-workflows</artifactId>
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<groupId>eu.dnetlib.dhp</groupId>
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<version>1.0.5-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>dhp-bulktag</artifactId>
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</project>
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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"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<parent>
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<artifactId>dhp-workflows</artifactId>
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<groupId>eu.dnetlib.dhp</groupId>
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<version>1.0.5-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>dhp-propagation</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_2.11</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_2.11</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>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-schemas</artifactId>
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<version>${project.version}</version>
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</dependency>
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</dependencies>
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</project>
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package eu.dnetlib.dhp.countrypropagation;
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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.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.Optional;
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import org.apache.spark.api.java.function.Function2;
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import org.apache.spark.api.java.function.PairFunction;
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import org.apache.spark.rdd.RDD;
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import org.apache.spark.sql.*;
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import scala.Tuple2;
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import java.util.*;
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import java.util.stream.Stream;
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public class SparkCountryPropagationJob {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCountryPropagationJob.class.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json")));
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parser.parseArgument(args);
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final SparkSession spark = SparkSession
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.builder()
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.appName(SparkCountryPropagationJob.class.getSimpleName())
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.master(parser.get("master"))
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.enableHiveSupport()
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.getOrCreate();
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final String inputPath = parser.get("sourcePath");
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final String outputPath = parser.get("outputPath");
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List<String> whitelist = new ArrayList<>();
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List<String> allowedtypes = new ArrayList<>();
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// JavaPairRDD<String, TypedRow> results = getResults(sc, inputPath);
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// sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
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// .map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class))
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// .map(oaf -> new TypedRow().setType("dataset").setDeleted(oaf.getDataInfo().getDeletedbyinference()).setOaf(oaf.toString()).setSourceId(oaf.getId()))
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// .mapToPair(toPair())
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// .union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
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// .map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class))
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// .map(oaf -> new TypedRow().setType("otherresearchproduct").setDeleted(oaf.getDataInfo().getDeletedbyinference()).setOaf(oaf.toString()).setSourceId(oaf.getId()))
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// .mapToPair(toPair()))
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// .union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
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// .map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class))
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// .map(oaf -> new TypedRow().setType("software").setDeleted(oaf.getDataInfo().getDeletedbyinference()).setOaf(oaf.toString()).setSourceId(oaf.getId()))
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// .mapToPair(toPair()))
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// .union(sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
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// .map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class))
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// .map(oaf -> new TypedRow().setType("publication").setDeleted(oaf.getDataInfo().getDeletedbyinference()).setOaf(oaf.toString()).setSourceId(oaf.getId()))
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// .mapToPair(toPair()));
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//
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//
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JavaPairRDD<String, TypedRow> organizations = sc.sequenceFile(inputPath + "/organization", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Organization.class))
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.filter(org -> !org.getDataInfo().getDeletedbyinference())
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.map(org -> new TypedRow().setSourceId(org.getId()).setCountry(org.getCountry().getClassid()))
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.mapToPair(toPair());
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JavaPairRDD<String, TypedRow> organization_datasource = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class))
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.filter(r -> !r.getDataInfo().getDeletedbyinference())
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.filter(r -> "datasourceOrganization".equals(r.getRelClass()) && "isProvidedBy".equals(r.getRelType()))
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.map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
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.mapToPair(toPair());
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JavaPairRDD<String, TypedRow> datasources = sc.sequenceFile(inputPath + "/datasource", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Datasource.class))
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.filter(ds -> whitelist.contains(ds.getId()) || allowedtypes.contains(ds.getDatasourcetype().getClassid()))
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.map(ds -> new TypedRow().setSourceId(ds.getId()))
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.mapToPair(toPair());
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JavaRDD<Publication> publications = sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class));
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JavaRDD<Dataset> datasets = sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class));
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JavaRDD<Software> software = sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class));
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JavaRDD<OtherResearchProduct> other = sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class));
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JavaPairRDD<String, TypedRow> datasource_results = publications
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.map(oaf -> getTypedRows(oaf))
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.flatMapToPair(f -> {
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ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
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for (TypedRow t : f) {
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ret.add(new Tuple2<>(t.getSourceId(), t));
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}
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return ret.iterator();
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})
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.union(datasets
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.map(oaf -> getTypedRows(oaf))
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.flatMapToPair(f -> {
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ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
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for (TypedRow t : f) {
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ret.add(new Tuple2<>(t.getSourceId(), t));
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}
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return ret.iterator();
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}))
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.union(software
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.map(oaf -> getTypedRows(oaf))
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.flatMapToPair(f -> {
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ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
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for (TypedRow t : f) {
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ret.add(new Tuple2<>(t.getSourceId(), t));
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}
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return ret.iterator();
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}))
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.union(other
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.map(oaf -> getTypedRows(oaf))
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.flatMapToPair(f -> {
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ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
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for (TypedRow t : f) {
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ret.add(new Tuple2<>(t.getSourceId(), t));
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}
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return ret.iterator();
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}));
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JavaPairRDD<String, OafEntity> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
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JavaPairRDD<String, OafEntity> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
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JavaPairRDD<String, OafEntity> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
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JavaPairRDD<String, OafEntity> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
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JavaPairRDD<String, TypedRow> datasource_country = organizations.join(organization_datasource)
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.map(x -> x._2()._1().setSourceId(x._2()._2().getTargetId())) // (OrganizationId,(TypedRow for Organization, TypedRow for Relation)
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.mapToPair(toPair()); //(DatasourceId, TypedRowforOrganziation)
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JavaPairRDD<String, TypedRow> alloweddatasources_country = datasources.join(datasource_country)
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.mapToPair(ds -> new Tuple2<>(ds._1(), ds._2()._2()));
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JavaPairRDD<String,TypedRow> toupdateresult = alloweddatasources_country.join(datasource_results)
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.map(u -> u._2()._2().setCountry(u._2()._1().getCountry()))
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.mapToPair(toPair())
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.reduceByKey((a, p) -> {
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if (a == null) {
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return p;
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}
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if (p == null) {
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return a;
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}
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HashSet<String> countries = new HashSet();
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countries.addAll(Arrays.asList(a.getCountry().split(";")));
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countries.addAll(Arrays.asList(p.getCountry().split(";")));
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String country = new String();
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for (String c : countries) {
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country += c + ";";
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}
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return a.setCountry(country);
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});
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updateResult(pubs, toupdateresult, outputPath, "publication");
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updateResult(dss, toupdateresult, outputPath, "dataset");
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updateResult(sfw, toupdateresult, outputPath, "software");
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updateResult(orp, toupdateresult, outputPath, "otherresearchproduct");
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//we use leftOuterJoin because we want to rebuild the entire structure
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}
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private static void updateResult(JavaPairRDD<String, OafEntity> results, JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type) {
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results.leftOuterJoin(toupdateresult)
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.map(c -> {
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OafEntity oaf = c._2()._1();
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List<Qualifier> qualifierList = null;
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if (oaf.getClass() == Publication.class) {
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qualifierList = ((Publication) oaf).getCountry();
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}
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if (oaf.getClass() == Dataset.class){
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qualifierList = ((Dataset) oaf).getCountry();
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}
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if (oaf.getClass() == Software.class){
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qualifierList = ((Software) oaf).getCountry();
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}
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if (oaf.getClass() == OtherResearchProduct.class){
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qualifierList = ((OtherResearchProduct) oaf).getCountry();
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}
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if (c._2()._2().isPresent()) {
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HashSet<String> countries = new HashSet<>();
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for (Qualifier country : qualifierList) {
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countries.add(country.getClassid());
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}
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TypedRow t = c._2()._2().get();
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for (String country : t.getCountry().split(";")) {
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if (!countries.contains(country)) {
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Qualifier q = new Qualifier();
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q.setClassid(country);
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qualifierList.add(q);
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}
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}
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if (oaf.getClass() == Publication.class) {
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((Publication) oaf).setCountry(qualifierList);
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return (Publication) oaf;
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}
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if (oaf.getClass() == Dataset.class){
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((Dataset) oaf).setCountry(qualifierList);
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return (Dataset) oaf;
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}
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if (oaf.getClass() == Software.class){
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((Software) oaf).setCountry(qualifierList);
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return (Software) oaf;
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}
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if (oaf.getClass() == OtherResearchProduct.class){
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((OtherResearchProduct) oaf).setCountry(qualifierList);
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return (OtherResearchProduct) oaf;
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}
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}
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return null;
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})
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.map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath+"/"+type);
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}
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private static List<TypedRow> getTypedRows(OafEntity oaf) {
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List<TypedRow> lst = new ArrayList<>();
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Set<String> datasources_provenance = new HashSet<>();
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List<Instance> instanceList = null;
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String type = "";
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if (oaf.getClass() == Publication.class) {
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instanceList = ((Publication) oaf).getInstance();
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type = "publication";
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}
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if (oaf.getClass() == Dataset.class){
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instanceList = ((Dataset)oaf).getInstance();
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type = "dataset";
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}
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if (oaf.getClass() == Software.class){
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instanceList = ((Software)oaf).getInstance();
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type = "software";
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}
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if (oaf.getClass() == OtherResearchProduct.class){
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instanceList = ((OtherResearchProduct)oaf).getInstance();
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type = "otherresearchproduct";
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}
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for (Instance i : instanceList) {
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datasources_provenance.add(i.getCollectedfrom().getKey());
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datasources_provenance.add(i.getHostedby().getKey());
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}
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for (String dsId : datasources_provenance) {
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lst.add(new TypedRow().setSourceId(dsId).setTargetId(oaf.getId()).setType(type));
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}
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return lst;
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}
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private static JavaPairRDD<String, TypedRow> getResults(JavaSparkContext sc , String inputPath){
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return
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sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class))
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.filter(ds -> !ds.getDataInfo().getDeletedbyinference())
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.map(oaf -> new TypedRow().setType("dataset").setSourceId(oaf.getId()))
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.mapToPair(toPair())
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.union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class))
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.filter(o -> !o.getDataInfo().getDeletedbyinference())
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.map(oaf -> new TypedRow().setType("otherresearchproduct").setSourceId(oaf.getId()))
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.mapToPair(toPair()))
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.union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class))
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.filter(s -> !s.getDataInfo().getDeletedbyinference())
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.map(oaf -> new TypedRow().setType("software").setSourceId(oaf.getId()))
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.mapToPair(toPair()))
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.union(sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class))
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.filter(p -> !p.getDataInfo().getDeletedbyinference())
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.map(oaf -> new TypedRow().setType("publication").setSourceId(oaf.getId()))
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.mapToPair(toPair()));
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}
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private static PairFunction<TypedRow, String, TypedRow> toPair() {
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return e -> new Tuple2<>( e.getSourceId(), e);
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};
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}
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@ -0,0 +1,70 @@
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package eu.dnetlib.dhp.countrypropagation;
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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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public class TypedRow implements Serializable {
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private String sourceId;
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private String targetId;
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private String type;
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private String country;
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public List<String> getAccumulator() {
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return accumulator;
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}
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public TypedRow setAccumulator(List<String> accumulator) {
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this.accumulator = accumulator;
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return this;
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}
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private List<String> accumulator;
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public void add(String a){
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if (accumulator == null){
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accumulator = new ArrayList<>();
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}
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accumulator.add(a);
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}
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public Iterator<String> getAccumulatorIterator(){
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return accumulator.iterator();
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}
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public String getCountry() {
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return country;
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}
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public TypedRow setCountry(String country) {
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this.country = country;
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return this;
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}
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public String getSourceId() {
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return sourceId;
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}
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public TypedRow setSourceId(String sourceId) {
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this.sourceId = sourceId;
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return this;
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}
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public String getTargetId() {
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return targetId;
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}
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public TypedRow setTargetId(String targetId) {
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this.targetId = targetId;
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return this;
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}
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public String getType() {
|
||||
return type;
|
||||
}
|
||||
public TypedRow setType(String type) {
|
||||
this.type = type;
|
||||
return this;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,3 @@
|
|||
sourcePath=/tmp/db_openaireplus_services.export_dhp.2020.02.03
|
||||
sparkDriverMemory=15G
|
||||
sparkExecutorMemory=15G
|
||||
|
|
@ -0,0 +1,5 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
|
||||
{"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the path of the sequential file to write", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>yarnRM</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://nameservice1</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>
|
||||
</configuration>
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
<workflow-app name="import_infospace_graph" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
<description>the source path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>outputPath</name>
|
||||
<description>the output path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="MapGraphIntoDataFrame"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="CountryPropagation">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>CountryPropagation</name>
|
||||
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob</class>
|
||||
<jar>dhp-graph-countrypropagation-${projectVersion}.jar</jar>
|
||||
<spark-opts>--executor-memory ${sparkExecutorMemory}
|
||||
--executor-cores ${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
|
||||
--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
|
||||
--conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
|
||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -18,6 +18,8 @@
|
|||
<module>dhp-distcp</module>
|
||||
<module>dhp-graph-mapper</module>
|
||||
<module>dhp-dedup</module>
|
||||
<module>dhp-bulktag</module>
|
||||
<module>dhp-propagation</module>
|
||||
</modules>
|
||||
|
||||
<pluginRepositories>
|
||||
|
|
|
|||
Loading…
Reference in New Issue