192 lines
6.0 KiB
Java
192 lines
6.0 KiB
Java
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package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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import java.util.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.FlatMapFunction;
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import org.apache.spark.broadcast.Broadcast;
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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.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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import scala.Tuple2;
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public class SparkResultToOrganizationFromIstRepoJob {
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private static final Logger log = LoggerFactory.getLogger(SparkResultToOrganizationFromIstRepoJob.class);
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private static final String RESULT_ORGANIZATIONSET_QUERY = "SELECT id resultId, collect_set(organizationId) organizationSet "
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+ "FROM ( SELECT id, organizationId "
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+ "FROM rels "
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+ "JOIN cfhb "
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+ " ON cf = datasourceId "
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+ "UNION ALL "
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+ "SELECT id , organizationId "
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+ "FROM rels "
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+ "JOIN cfhb "
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+ " ON hb = datasourceId ) tmp "
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+ "GROUP BY id";
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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SparkResultToOrganizationFromIstRepoJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_propagationresulaffiliationfrominstrepo_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final String datasourceorganization = parser.get("datasourceOrganizationPath");
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log.info("datasourceOrganizationPath: {}", datasourceorganization);
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final String alreadylinked = parser.get("alreadyLinkedPath");
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log.info("alreadyLinkedPath: {}", alreadylinked);
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final Boolean saveGraph = Optional
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.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("saveGraph: {}", saveGraph);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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runWithSparkHiveSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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// removeOutputDir(spark, outputPath);
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if (saveGraph) {
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execPropagation(
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spark,
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datasourceorganization,
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alreadylinked,
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inputPath,
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outputPath,
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resultClazz);
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}
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});
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}
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private static void execPropagation(
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SparkSession spark,
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String datasourceorganization,
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String alreadyLinkedPath,
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String inputPath,
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String outputPath,
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Class<? extends Result> clazz) {
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Dataset<DatasourceOrganization> ds_org = readPath(spark, datasourceorganization, DatasourceOrganization.class);
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Dataset<ResultOrganizationSet> potentialUpdates = getPotentialRelations(spark, inputPath, clazz, ds_org);
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Dataset<ResultOrganizationSet> alreadyLinked = readPath(spark, alreadyLinkedPath, ResultOrganizationSet.class);
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potentialUpdates
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.joinWith(
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alreadyLinked,
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potentialUpdates.col("resultId").equalTo(alreadyLinked.col("resultId")),
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"left_outer")
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.flatMap(createRelationFn(), Encoders.bean(Relation.class))
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.write()
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.mode(SaveMode.Append)
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.option("compression", "gzip")
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.json(outputPath);
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}
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private static FlatMapFunction<Tuple2<ResultOrganizationSet, ResultOrganizationSet>, Relation> createRelationFn() {
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return (FlatMapFunction<Tuple2<ResultOrganizationSet, ResultOrganizationSet>, Relation>) value -> {
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List<Relation> new_relations = new ArrayList<>();
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ResultOrganizationSet potential_update = value._1();
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Optional<ResultOrganizationSet> already_linked = Optional.ofNullable(value._2());
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List<String> organization_list = potential_update.getOrganizationSet();
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if (already_linked.isPresent()) {
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already_linked
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.get()
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.getOrganizationSet()
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.stream()
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.forEach(
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rId -> {
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organization_list.remove(rId);
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});
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}
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String resultId = potential_update.getResultId();
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organization_list
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.stream()
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.forEach(
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orgId -> {
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new_relations
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.add(
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getRelation(
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orgId,
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resultId,
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ModelConstants.IS_AUTHOR_INSTITUTION_OF,
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ModelConstants.RESULT_ORGANIZATION,
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ModelConstants.AFFILIATION,
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PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID,
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PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
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new_relations
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.add(
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getRelation(
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resultId,
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orgId,
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ModelConstants.HAS_AUTHOR_INSTITUTION,
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ModelConstants.RESULT_ORGANIZATION,
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ModelConstants.AFFILIATION,
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PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID,
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PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
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});
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return new_relations.iterator();
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};
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}
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private static <R extends Result> Dataset<ResultOrganizationSet> getPotentialRelations(
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SparkSession spark,
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String inputPath,
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Class<R> resultClazz,
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Dataset<DatasourceOrganization> ds_org) {
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Dataset<R> result = readPath(spark, inputPath, resultClazz);
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result.createOrReplaceTempView("result");
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createCfHbforResult(spark);
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ds_org.createOrReplaceTempView("rels");
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return spark
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.sql(RESULT_ORGANIZATIONSET_QUERY)
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.as(Encoders.bean(ResultOrganizationSet.class));
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}
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}
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