refactoring
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47561f3597
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a440152b46
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@ -18,6 +18,7 @@ import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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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.codehaus.janino.Java;
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import scala.Tuple2;
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import javax.sql.DataSource;
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@ -56,8 +57,6 @@ public class SparkCountryPropagationJob {
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datasource(spark, whitelist, outputPath, inputPath);
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//rdd(spark,whitelist,allowedtypes, outputPath, inputPath);
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}
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private static void datasource(SparkSession spark, List<String> whitelist, String outputPath, String inputPath){
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@ -83,33 +82,40 @@ public class SparkCountryPropagationJob {
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Dataset<Row> rels = spark.sql(query);
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rels.createOrReplaceTempView("rels");
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final JavaRDD<Row> toupdateresultsoftware = propagateOnResult(spark, "openaire.software");
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final JavaRDD<Row> toupdateresultdataset = propagateOnResult(spark, "openaire.dataset");
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final JavaRDD<Row> toupdateresultother = propagateOnResult(spark, "openaire.otherresearchproduct");
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final JavaRDD<Row> toupdateresultpublication = propagateOnResult(spark, "openaire.publication");
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writeUpdates(toupdateresultsoftware, toupdateresultdataset, toupdateresultother, toupdateresultpublication, outputPath);
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createUpdateForSoftwareDataset(toupdateresultsoftware, inputPath, spark)
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.map(s -> new ObjectMapper().writeValueAsString(s))
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.saveAsTextFile(outputPath + "/software");
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createUpdateForResultDatasetWrite(toupdateresultsoftware, outputPath, "update_software");
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JavaRDD<Row> toupdateresultdataset = propagateOnResult(spark, "openaire.dataset");
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createUpdateForDatasetDataset(toupdateresultdataset,inputPath,spark)
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.map(d -> new ObjectMapper().writeValueAsString(d))
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.saveAsTextFile(outputPath + "/dataset");
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createUpdateForResultDatasetWrite(toupdateresultdataset, outputPath, "update_dataset");
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JavaRDD<Row> toupdateresultother = propagateOnResult(spark, "openaire.otherresearchproduct");
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createUpdateForOtherDataset(toupdateresultother, inputPath, spark)
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.map(o -> new ObjectMapper().writeValueAsString(o))
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.saveAsTextFile(outputPath + "/otherresearchproduct");
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createUpdateForResultDatasetWrite(toupdateresultother, outputPath, "update_other");
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createUpdateForPublicationDataset(propagateOnResult(spark, "openaire.publication"), inputPath, spark)
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createUpdateForPublicationDataset(toupdateresultpublication, inputPath, spark)
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.map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath + "/publication");
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}
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private static void writeUpdates(JavaRDD<Row> software, JavaRDD<Row> dataset, JavaRDD<Row> other , JavaRDD<Row> publication, String outputPath){
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createUpdateForResultDatasetWrite(software, outputPath, "update_software");
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createUpdateForResultDatasetWrite(dataset, outputPath, "update_dataset");
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createUpdateForResultDatasetWrite(other, outputPath, "update_other");
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createUpdateForResultDatasetWrite(publication, outputPath, "update_publication");
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}
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private static JavaRDD<OtherResearchProduct> createUpdateForOtherDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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@ -273,290 +279,7 @@ public class SparkCountryPropagationJob {
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.saveAsTextFile(outputPath+"/"+type);
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}
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private static Dataset<Row> countryPropagation(SparkSession spark, String cfhbTable){
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String query = "SELECT id, collect_set(named_struct('classid', country, 'classname', country, " +
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"'datainfo', named_struct( 'deletedbyinference', false, " +
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"'inferenceprovenance','" + PROPAGATION_DATA_INFO_TYPE +"'," +
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"'inferred',true,'invisible',false, " +
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"'provenanceaction', named_struct('classid','" + PROPAGATION_COUNTRY_INSTREPO_CLASS_ID + "'," +
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"'classname','" + PROPAGATION_COUNTRY_INSTREPO_CLASS_NAME +"'," +
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"'schemeid','" + DNET_SCHEMA_ID +"'," +
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"'schemename','" + DNET_SCHEMA_NAME +"') , " +
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"'trust','0.9') ,'schemeid','" + DNET_COUNTRY_SCHEMA +"','schemename','" + DNET_COUNTRY_SCHEMA + "')) country " +
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"FROM ( SELECT id, country " +
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"FROM rels " +
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"JOIN " + cfhbTable +
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" ON cf = ds " +
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"UNION ALL " +
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"SELECT id , country " +
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"FROM rels " +
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"JOIN " + cfhbTable +
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" ON hb = ds ) tmp " +
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"GROUP BY id";
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return spark.sql(query);
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}
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private static void rdd(SparkSession spark, List<String> whitelist, List<String> allowedtypes, String outputPath, String inputPath) throws IOException {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaPairRDD<String, TypedRow> organizations = sc.textFile(inputPath + "/organization")
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.map(item -> new ObjectMapper().readValue(item, Organization.class))
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.filter(org -> !org.getDataInfo().getDeletedbyinference())
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.map(org -> {
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TypedRow tr = new TypedRow();
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tr.setSourceId(org.getId());
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tr.setValue(org.getCountry().getClassid());
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return tr;
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})
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.mapToPair(toPair());
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JavaPairRDD<String, TypedRow> organization_datasource =
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sc.textFile(inputPath + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class))
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.filter(r -> !r.getDataInfo().getDeletedbyinference())
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.filter(r -> RELATION_DATASOURCEORGANIZATION_REL_TYPE.equals(r.getRelType()) &&
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RELATION_ORGANIZATION_DATASOURCE_REL_CLASS.equals(r.getRelClass()))
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.map(r -> {
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TypedRow tp = new TypedRow(); tp.setSourceId(r.getSource()); tp.setTargetId(r.getTarget());
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return tp;
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})
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.mapToPair(toPair()); //id is the organization identifier
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JavaPairRDD<String, TypedRow> datasources = sc.textFile(inputPath + "/datasource")
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.map(item -> new ObjectMapper().readValue(item, Datasource.class))
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.filter(ds -> whitelist.contains(ds.getId()) || allowedtypes.contains(ds.getDatasourcetype().getClassid()))
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.map(ds -> new TypedRow().setSourceId(ds.getId()))
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.mapToPair(toPair());
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JavaPairRDD<String, TypedRow> datasource_country = organizations.join(organization_datasource)
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.map(x -> x._2()._1().setSourceId(x._2()._2().getTargetId())) // (OrganizationId,(TypedRow for Organization, TypedRow for Relation)
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.mapToPair(toPair()); //(DatasourceId, TypedRowforOrganziation)
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JavaPairRDD<String, TypedRow> alloweddatasources_country = datasources.join(datasource_country)
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.mapToPair(ds -> new Tuple2<>(ds._1(), ds._2()._2())).cache();
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// System.out.println("OUTPUT *** ORGANIZATION COUNT *** " + organizations.count());
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// System.out.println("OUTPUT *** ORGANIZATION DATASOURCE RELATIONS COUNT *** " + organization_datasource.count());
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// System.out.println("OUTPUT *** DATASOURCE COUNT *** " + datasources.count());
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// System.out.println("OUTPUT *** ALLOWED_DATASOURCE-COUNTRY COUNT *** " + alloweddatasources_country.count());
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// alloweddatasources_country.map(p -> new ObjectMapper().writeValueAsString(p))
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// .saveAsTextFile(outputPath+"/datasource_country");
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JavaRDD<Software> software = sc.textFile(inputPath + "/software")
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.map(item -> new ObjectMapper().readValue(item, Software.class));
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JavaPairRDD<String, TypedRow> datasource_software = software
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.map(oaf -> getTypedRowsDatasourceResult(oaf))
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.flatMapToPair(f -> {
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ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
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for (TypedRow t : f) {
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ret.add(new Tuple2<>(t.getSourceId(), t));
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}
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return ret.iterator();
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});
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datasource_software.map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath+"/datasource_software");
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JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
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JavaPairRDD<String,TypedRow> toupdateresult = alloweddatasources_country.join(datasource_software)
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.map(u -> {
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TypedRow tp = u._2()._2();
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tp.setValue(u._2()._1().getValue());
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return tp;
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})
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.mapToPair(toPair())
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.reduceByKey((a, p) -> {
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if (a == null) {
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return p;
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}
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if (p == null) {
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return a;
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}
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a.addAll(p.getAccumulator());
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return a;
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});
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toupdateresult.map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath+"/toupdateresult");
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//updateResult(sfw, toupdateresult, outputPath, "software");
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// createUpdateForResult(toupdateresult, outputPath, "software");
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/* JavaRDD<Publication> publications = sc.textFile(inputPath + "/publication")
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.map(item -> new ObjectMapper().readValue(item, Publication.class));
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JavaPairRDD<String, TypedRow> datasource_publication = publications
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.map(oaf -> getTypedRowsDatasourceResult(oaf))
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.flatMapToPair(f -> {
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ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
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for (TypedRow t : f) {
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ret.add(new Tuple2<>(t.getSourceId(), t));
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}
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return ret.iterator();
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});
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JavaPairRDD<String,TypedRow> toupdateresult = alloweddatasources_country.join(datasource_publication)
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.map(u -> u._2()._2().setValue(u._2()._1().getValue()))
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.mapToPair(toPair())
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.reduceByKey((a, p) -> {
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if (a == null) {
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return p;
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}
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if (p == null) {
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return a;
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}
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a.addAll(p.getAccumulator());
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return a;
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});
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JavaRDD<Publication> publications = sc.textFile(inputPath + "/publication")
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.map(item -> new ObjectMapper().readValue(item, Publication.class));
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JavaRDD<Dataset> datasets = sc.textFile(inputPath + "/dataset")
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.map(item -> new ObjectMapper().readValue(item, Dataset.class));
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JavaRDD<Software> software = sc.textFile(inputPath + "/software")
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.map(item -> new ObjectMapper().readValue(item, Software.class));
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JavaRDD<OtherResearchProduct> other = sc.textFile(inputPath + "/otherresearchproduct")
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.map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class));
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JavaPairRDD<String, TypedRow> datasource_results = publications
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.map(oaf -> getTypedRowsDatasourceResult(oaf))
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.flatMapToPair(f -> {
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ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
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for (TypedRow t : f) {
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ret.add(new Tuple2<>(t.getSourceId(), t));
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}
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return ret.iterator();
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})
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.union(datasets
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.map(oaf -> getTypedRowsDatasourceResult(oaf))
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.flatMapToPair(f -> {
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ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
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for (TypedRow t : f) {
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ret.add(new Tuple2<>(t.getSourceId(), t));
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}
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return ret.iterator();
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}))
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.union(software
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.map(oaf -> getTypedRowsDatasourceResult(oaf))
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.flatMapToPair(f -> {
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ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
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for (TypedRow t : f) {
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ret.add(new Tuple2<>(t.getSourceId(), t));
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}
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return ret.iterator();
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}))
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.union(other
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.map(oaf -> getTypedRowsDatasourceResult(oaf))
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.flatMapToPair(f -> {
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ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
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for (TypedRow t : f) {
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ret.add(new Tuple2<>(t.getSourceId(), t));
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}
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return ret.iterator();
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}));
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JavaPairRDD<String,TypedRow> toupdateresult = alloweddatasources_country.join(datasource_results)
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.map(u -> u._2()._2().setValue(u._2()._1().getValue()))
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.mapToPair(toPair())
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.reduceByKey((a, p) -> {
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if (a == null) {
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return p;
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}
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if (p == null) {
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return a;
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}
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a.addAll(p.getAccumulator());
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return a;
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});
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JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
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JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
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JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
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JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
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updateResult(pubs, toupdateresult, outputPath, "publication");
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updateResult(dss, toupdateresult, outputPath, "dataset");
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updateResult(sfw, toupdateresult, outputPath, "software");
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updateResult(orp, toupdateresult, outputPath, "otherresearchproduct");
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//we use leftOuterJoin because we want to rebuild the entire structure
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*/
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}
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private static void createUpdateForResult(JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type){
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toupdateresult.map(c -> {
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List<Country> countryList = new ArrayList<>();
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for (String country : c._2.getAccumulator()) {
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countryList.add(getCountry(country));
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}
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switch(type ){
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case "software":
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Software s = new Software();
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s.setId(c._1());
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s.setCountry(countryList);
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return s;
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case "publication":
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break;
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case "dataset":
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break;
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case "otherresearchproduct":
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break;
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}
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return null;
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}).map(r ->new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath+"/"+type);
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}
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private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type) {
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results.leftOuterJoin(toupdateresult)
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.map(c -> {
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Result oaf = c._2()._1();
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List<Country> countryList = oaf.getCountry();
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if (c._2()._2().isPresent()) {
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HashSet<String> countries = new HashSet<>();
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for (Qualifier country : countryList) {
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countries.add(country.getClassid());
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}
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TypedRow t = c._2()._2().get();
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for (String country : t.getAccumulator()) {
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if (!countries.contains(country)) {
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countryList.add(getCountry(country));
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}
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}
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oaf.setCountry(countryList);
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}
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return oaf;
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})
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.map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath+"/"+type);
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}
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}
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