forked from D-Net/dnet-hadoop
146 lines
4.8 KiB
Java
146 lines
4.8 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.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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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.Datasource;
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import eu.dnetlib.dhp.schema.oaf.Organization;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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public class PrepareResultInstRepoAssociation {
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private static final Logger log = LoggerFactory.getLogger(PrepareResultInstRepoAssociation.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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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PrepareResultInstRepoAssociation.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_prepareresultorg_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 datasourceOrganizationPath = parser.get("datasourceOrganizationPath");
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log.info("datasourceOrganizationPath {}: ", datasourceOrganizationPath);
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final String alreadyLinkedPath = parser.get("alreadyLinkedPath");
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log.info("alreadyLinkedPath {}: ", alreadyLinkedPath);
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List<String> blacklist = Optional
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.ofNullable(parser.get("blacklist"))
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.map(v -> Arrays.asList(v.split(";")))
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.orElse(new ArrayList<>());
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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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readNeededResources(spark, inputPath);
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removeOutputDir(spark, datasourceOrganizationPath);
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prepareDatasourceOrganization(spark, datasourceOrganizationPath, blacklist);
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removeOutputDir(spark, alreadyLinkedPath);
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prepareAlreadyLinkedAssociation(spark, alreadyLinkedPath);
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});
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}
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private static void readNeededResources(SparkSession spark, String inputPath) {
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Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class);
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datasource.createOrReplaceTempView("datasource");
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Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class);
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relation.createOrReplaceTempView("relation");
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Dataset<Organization> organization = readPath(spark, inputPath + "/organization", Organization.class);
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organization.createOrReplaceTempView("organization");
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}
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private static void prepareDatasourceOrganization(
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SparkSession spark, String datasourceOrganizationPath, List<String> blacklist) {
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String blacklisted = "";
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if (blacklist.size() > 0) {
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blacklisted = " AND d.id != '" + blacklist.get(0) + "'";
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for (int i = 1; i < blacklist.size(); i++) {
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blacklisted += " AND d.id != '" + blacklist.get(i) + "'";
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}
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}
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String query = "SELECT source datasourceId, target organizationId "
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+ "FROM ( SELECT id "
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+ "FROM datasource "
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+ "WHERE datasourcetype.classid = '"
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+ INSTITUTIONAL_REPO_TYPE
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+ "' "
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+ "AND datainfo.deletedbyinference = false " + blacklisted + " ) d "
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+ "JOIN ( SELECT source, target "
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+ "FROM relation "
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+ "WHERE lower(relclass) = '"
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+ ModelConstants.IS_PROVIDED_BY.toLowerCase()
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+ "' "
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+ "AND datainfo.deletedbyinference = false ) rel "
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+ "ON d.id = rel.source ";
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spark
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.sql(query)
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.as(Encoders.bean(DatasourceOrganization.class))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(datasourceOrganizationPath);
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}
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private static void prepareAlreadyLinkedAssociation(
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SparkSession spark, String alreadyLinkedPath) {
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String query = "Select source resultId, collect_set(target) organizationSet "
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+ "from relation "
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+ "where datainfo.deletedbyinference = false "
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+ "and lower(relClass) = '"
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+ ModelConstants.HAS_AUTHOR_INSTITUTION.toLowerCase()
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+ "' "
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+ "group by source";
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spark
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.sql(query)
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.as(Encoders.bean(ResultOrganizationSet.class))
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// TODO retry to stick with datasets
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.toJavaRDD()
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.map(r -> OBJECT_MAPPER.writeValueAsString(r))
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.saveAsTextFile(alreadyLinkedPath, GzipCodec.class);
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}
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}
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