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class to compute some information needed for the actual propagation

This commit is contained in:
Miriam Baglioni 2020-04-15 12:25:11 +02:00
parent 5a3487280d
commit 6a377a7582
1 changed files with 106 additions and 0 deletions
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106
dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java
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@ -1,4 +1,110 @@
package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Relation;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static eu.dnetlib.dhp.PropagationConstant.RELATION_RESULT_ORGANIZATION_REL_CLASS;
import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
public class PrepareResultInstRepoAssociation {
private static final Logger log = LoggerFactory.getLogger(PrepareResultInstRepoAssociation.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception{
String jsonConfiguration = IOUtils.toString(PrepareResultInstRepoAssociation.class
.getResourceAsStream("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_prepareresultorg_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String datasourceOrganizationPath = parser.get("datasourceOrganizationPath");
log.info("datasourceOrganizationPath {}: ", datasourceOrganizationPath);
final String alreadyLinkedPath = parser.get("alreadyLinkedPath");
log.info("alreadyLinkedPath {}: ", alreadyLinkedPath);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(conf, isSparkSessionManaged,
spark -> {
prepareAssociations(spark, inputPath, datasourceOrganizationPath, alreadyLinkedPath);
});
}
private static void prepareAssociations(SparkSession spark, String inputPath, String datasourceOrganizationPath,
String alreadyLinkedPath){
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
org.apache.spark.sql.Dataset<Datasource> datasource = spark.createDataset(sc.textFile(inputPath + "/datasource")
.map(item -> new ObjectMapper().readValue(item, Datasource.class)).rdd(), Encoders.bean(Datasource.class));
org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
org.apache.spark.sql.Dataset<Organization> organization = spark.createDataset(sc.textFile(inputPath + "/organization")
.map(item -> new ObjectMapper().readValue(item, Organization.class)).rdd(), Encoders.bean(Organization.class));
datasource.createOrReplaceTempView("datasource");
relation.createOrReplaceTempView("relation");
organization.createOrReplaceTempView("organization");
String query = "SELECT source datasourceId, target organizationId " +
"FROM ( SELECT id " +
"FROM datasource " +
"WHERE datasourcetype.classid = 'pubsrepository::institutional' " +
"AND datainfo.deletedbyinference = false ) d " +
"JOIN ( SELECT source, target " +
"FROM relation " +
"WHERE relclass = 'provides' " +
"AND datainfo.deletedbyinference = false ) rel " +
"ON d.id = rel.source ";
spark.sql(query)
.as(Encoders.bean(DatasourceOrganization.class))
.toJSON()
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.text(datasourceOrganizationPath);
query = "Select source, collect_set(target) organizationSet " +
"from relation " +
"where datainfo.deletedbyinference = false " +
"and relClass = '" + RELATION_RESULT_ORGANIZATION_REL_CLASS +"' " +
"group by source";
spark.sql(query)
.as(Encoders.bean(ResultOrganizationSet.class))
.toJSON()
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.text(alreadyLinkedPath);
}
}