forked from D-Net/dnet-hadoop
class to compute some information needed for the actual propagation
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package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
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package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
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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.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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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.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 static eu.dnetlib.dhp.PropagationConstant.RELATION_RESULT_ORGANIZATION_REL_CLASS;
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import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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public class PrepareResultInstRepoAssociation {
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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.toString(PrepareResultInstRepoAssociation.class
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.getResourceAsStream("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_prepareresultorg_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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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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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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runWithSparkHiveSession(conf, isSparkSessionManaged,
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spark -> {
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prepareAssociations(spark, inputPath, datasourceOrganizationPath, alreadyLinkedPath);
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});
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}
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private static void prepareAssociations(SparkSession spark, String inputPath, String datasourceOrganizationPath,
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String alreadyLinkedPath){
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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org.apache.spark.sql.Dataset<Datasource> datasource = spark.createDataset(sc.textFile(inputPath + "/datasource")
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.map(item -> new ObjectMapper().readValue(item, Datasource.class)).rdd(), Encoders.bean(Datasource.class));
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org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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org.apache.spark.sql.Dataset<Organization> organization = spark.createDataset(sc.textFile(inputPath + "/organization")
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.map(item -> new ObjectMapper().readValue(item, Organization.class)).rdd(), Encoders.bean(Organization.class));
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datasource.createOrReplaceTempView("datasource");
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relation.createOrReplaceTempView("relation");
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organization.createOrReplaceTempView("organization");
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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 = 'pubsrepository::institutional' " +
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"AND datainfo.deletedbyinference = false ) d " +
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"JOIN ( SELECT source, target " +
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"FROM relation " +
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"WHERE relclass = 'provides' " +
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"AND datainfo.deletedbyinference = false ) rel " +
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"ON d.id = rel.source ";
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spark.sql(query)
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.as(Encoders.bean(DatasourceOrganization.class))
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.toJSON()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression","gzip")
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.text(datasourceOrganizationPath);
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query = "Select source, collect_set(target) organizationSet " +
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"from relation " +
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"where datainfo.deletedbyinference = false " +
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"and relClass = '" + RELATION_RESULT_ORGANIZATION_REL_CLASS +"' " +
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"group by source";
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spark.sql(query)
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.as(Encoders.bean(ResultOrganizationSet.class))
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.toJSON()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression","gzip")
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.text(alreadyLinkedPath);
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}
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}
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}
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