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changed implementation using dataset and query on hive

This commit is contained in:
Miriam Baglioni 2020-03-23 17:11:00 +01:00
parent f09cd1e911
commit f1e9fe9752
1 changed files with 144 additions and 7 deletions
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151
dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java
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@ -3,14 +3,19 @@ package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
import eu.dnetlib.dhp.TypedRow;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FileSystem;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.apache.hadoop.io.Text;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.dhp.schema.oaf.*;
@ -23,10 +28,13 @@ public class SparkResultToOrganizationFromIstRepoJob {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToOrganizationFromIstRepoJob.class.getResourceAsStream("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_resulttoorganizationfrominstrepo_parameters.json")));
parser.parseArgument(args);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
final SparkSession spark = SparkSession
.builder()
.appName(SparkResultToOrganizationFromIstRepoJob.class.getSimpleName())
.master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
@ -34,12 +42,67 @@ public class SparkResultToOrganizationFromIstRepoJob {
final String inputPath = parser.get("sourcePath");
final String outputPath = "/tmp/provision/propagation/resulttoorganizationfrominstitutionalrepositories";
File directory = new File(outputPath);
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
if (!directory.exists()) {
directory.mkdirs();
}
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 + "/organziation")
.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 ds, target org " +
"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 ";
org.apache.spark.sql.Dataset<Row> rels = spark.sql(query);
rels.createOrReplaceTempView("rels");
org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(sc.textFile(inputPath + "/dataset")
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class)).rdd(),
Encoders.bean(eu.dnetlib.dhp.schema.oaf.Dataset.class));
org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(sc.textFile(inputPath + "/otherresearchproduct")
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class)).rdd(),
Encoders.bean(eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class));
org.apache.spark.sql.Dataset<Software> software = spark.createDataset(sc.textFile(inputPath + "/software")
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Software.class)).rdd(),
Encoders.bean(eu.dnetlib.dhp.schema.oaf.Software.class));
org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(sc.textFile(inputPath + "/publication")
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class)).rdd(),
Encoders.bean(eu.dnetlib.dhp.schema.oaf.Publication.class));
software.createOrReplaceTempView("software");
final JavaRDD<Row> toupdateresultsoftware = propagateOnResult(spark, "software");
dataset.createOrReplaceTempView("dataset");
final JavaRDD<Row> toupdateresultdataset = propagateOnResult(spark, "dataset");
other.createOrReplaceTempView("other");
final JavaRDD<Row> toupdateresultother = propagateOnResult(spark, "other");
publication.createOrReplaceTempView("publication");
final JavaRDD<Row> toupdateresultpublication = propagateOnResult(spark, "publication");
writeUpdates(toupdateresultsoftware, toupdateresultdataset, toupdateresultother, toupdateresultpublication, outputPath);
/*
//get the institutional repositories
JavaPairRDD<String, TypedRow> datasources = sc.sequenceFile(inputPath + "/datasource", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), Datasource.class))
@ -51,8 +114,11 @@ public class SparkResultToOrganizationFromIstRepoJob {
JavaPairRDD<String, TypedRow> rel_datasource_organization = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class))
.filter(r -> !r.getDataInfo().getDeletedbyinference())
.filter(r -> RELATION_DATASOURCEORGANIZATION_REL_TYPE.equals(r.getRelClass()) && RELATION_DATASOURCE_ORGANIZATION_REL_CLASS.equals(r.getRelType()))
.map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
.filter(r -> RELATION_DATASOURCEORGANIZATION_REL_TYPE.equals(r.getRelType()) && RELATION_DATASOURCE_ORGANIZATION_REL_CLASS.equals(r.getRelClass()))
.map(r -> {
TypedRow tp = new TypedRow(); tp.setSourceId(r.getSource()); tp.setTargetId(r.getTarget());
return tp;
})
.mapToPair(toPair());
JavaPairRDD<String, TypedRow> instdatasource_organization = datasources.join(rel_datasource_organization)
@ -70,6 +136,7 @@ public class SparkResultToOrganizationFromIstRepoJob {
JavaRDD<OtherResearchProduct> other = sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class));
JavaPairRDD<String, TypedRow> datasource_results = publications
.map(oaf -> getTypedRowsDatasourceResult(oaf))
.flatMapToPair(f -> {
@ -124,8 +191,78 @@ public class SparkResultToOrganizationFromIstRepoJob {
.saveAsTextFile(outputPath + "/relation_new");
newRels.union(relations).map(p -> new ObjectMapper().writeValueAsString(p))
.saveAsTextFile(outputPath + "/relation");
.saveAsTextFile(outputPath + "/relation");*/
}
private static void writeUpdates(JavaRDD<Row> toupdateresultsoftware, JavaRDD<Row> toupdateresultdataset, JavaRDD<Row> toupdateresultother, JavaRDD<Row> toupdateresultpublication, String outputPath) {
createUpdateForRelationWrite(toupdateresultsoftware, outputPath, "update_software");
createUpdateForRelationWrite(toupdateresultdataset, outputPath, "update_dataset");
createUpdateForRelationWrite(toupdateresultother, outputPath, "update_other");
createUpdateForRelationWrite(toupdateresultpublication, outputPath, "update_publication");
}
private static void createUpdateForRelationWrite(JavaRDD<Row> toupdaterelation, String outputPath, String update_type) {
toupdaterelation.map(s -> {
List<Relation> relationList = Arrays.asList();
List<String> orgs = s.getList(1);
String resId = s.getString(0);
for (String org : orgs) {
relationList.add(getRelation(org, resId, RELATION_ORGANIZATION_RESULT_REL_CLASS,
RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
relationList.add(getRelation(resId, org, RELATION_RESULT_ORGANIZATION_REL_CLASS,
RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
}
return relationList.iterator();
}).map(s -> new ObjectMapper().writeValueAsString(s)).saveAsTextFile(outputPath + "/" + update_type);
}
private static org.apache.spark.sql.Dataset<Row> instPropagationAssoc(SparkSession spark, String cfhbTable){
String query = "SELECT id, collect_set(org) org "+
"FROM ( SELECT id, org " +
"FROM rels " +
"JOIN " + cfhbTable +
" ON cf = ds " +
"UNION ALL " +
"SELECT id , org " +
"FROM rels " +
"JOIN " + cfhbTable +
" ON hb = ds ) tmp " +
"GROUP BY id";
return spark.sql(query);
}
private static JavaRDD<Row> propagateOnResult(SparkSession spark, String table) {
String query;
query = "SELECT id, inst.collectedfrom.key cf , inst.hostedby.key hb " +
"FROM ( SELECT id, instance " +
"FROM " + table +
" WHERE datainfo.deletedbyinference = false) ds " +
"LATERAL VIEW EXPLODE(instance) i AS inst";
org.apache.spark.sql.Dataset<Row> cfhb = spark.sql(query);
cfhb.createOrReplaceTempView("cfhb");
return organizationPropagationAssoc(spark, "cfhb").toJavaRDD();
}
private static org.apache.spark.sql.Dataset<Row> organizationPropagationAssoc(SparkSession spark, String cfhbTable){
String query = "SELECT id, collect_set(org) org "+
"FROM ( SELECT id, org " +
"FROM rels " +
"JOIN " + cfhbTable +
" ON cf = ds " +
"UNION ALL " +
"SELECT id , org " +
"FROM rels " +
"JOIN " + cfhbTable +
" ON hb = ds ) tmp " +
"GROUP BY id";
return spark.sql(query);
}
}