bug fixing for implementation with dataset
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@ -26,7 +26,7 @@ import static eu.dnetlib.dhp.PropagationConstant.*;
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public class SparkResultToOrganizationFromIstRepoJob {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToOrganizationFromIstRepoJob.class.getResourceAsStream("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_resulttoorganizationfrominstrepo_parameters.json")));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToOrganizationFromIstRepoJob.class.getResourceAsStream("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_propagationresulaffiliationfrominstrepo_parameters.json")));
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parser.parseArgument(args);
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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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@ -102,96 +102,6 @@ public class SparkResultToOrganizationFromIstRepoJob {
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writeUpdates(toupdateresultsoftware, toupdateresultdataset, toupdateresultother, toupdateresultpublication, outputPath);
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/*
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//get the institutional repositories
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JavaPairRDD<String, TypedRow> datasources = sc.sequenceFile(inputPath + "/datasource", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Datasource.class))
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.filter(ds -> INSTITUTIONAL_REPO_TYPE.equals(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> rel_datasource_organization = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class))
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.filter(r -> !r.getDataInfo().getDeletedbyinference())
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.filter(r -> RELATION_DATASOURCEORGANIZATION_REL_TYPE.equals(r.getRelType()) && RELATION_DATASOURCE_ORGANIZATION_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());
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JavaPairRDD<String, TypedRow> instdatasource_organization = datasources.join(rel_datasource_organization)
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.map(x -> x._2()._2())
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.mapToPair(toPair());
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JavaRDD<Relation> relations = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class));
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JavaRDD<Publication> publications = sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class));
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JavaRDD<Dataset> datasets = sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class));
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JavaRDD<Software> software = sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class));
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JavaRDD<OtherResearchProduct> other = sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), 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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JavaRDD<Relation> newRels = instdatasource_organization.join(datasource_results)
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.flatMap(c -> {
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List<Relation> rels = new ArrayList();
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String orgId = c._2()._1().getTargetId();
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String resId = c._2()._2().getTargetId();
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rels.add(getRelation(orgId, resId, RELATION_ORGANIZATION_RESULT_REL_CLASS,
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RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
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rels.add(getRelation(resId, orgId, RELATION_RESULT_ORGANIZATION_REL_CLASS,
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RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
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return rels.iterator();
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});
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newRels.map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath + "/relation_new");
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newRels.union(relations).map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath + "/relation");*/
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}
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private static void writeUpdates(JavaRDD<Row> toupdateresultsoftware, JavaRDD<Row> toupdateresultdataset, JavaRDD<Row> toupdateresultother, JavaRDD<Row> toupdateresultpublication, String outputPath) {
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@ -203,8 +113,8 @@ public class SparkResultToOrganizationFromIstRepoJob {
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}
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private static void createUpdateForRelationWrite(JavaRDD<Row> toupdaterelation, String outputPath, String update_type) {
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toupdaterelation.map(s -> {
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List<Relation> relationList = Arrays.asList();
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toupdaterelation.flatMap(s -> {
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List<Relation> relationList = new ArrayList<>();
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List<String> orgs = s.getList(1);
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String resId = s.getString(0);
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for (String org : orgs) {
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@ -220,22 +130,6 @@ public class SparkResultToOrganizationFromIstRepoJob {
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}).map(s -> new ObjectMapper().writeValueAsString(s)).saveAsTextFile(outputPath + "/" + update_type);
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}
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private static org.apache.spark.sql.Dataset<Row> instPropagationAssoc(SparkSession spark, String cfhbTable){
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String query = "SELECT id, collect_set(org) org "+
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"FROM ( SELECT id, org " +
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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 , org " +
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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 JavaRDD<Row> propagateOnResult(SparkSession spark, String table) {
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String query;
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query = "SELECT id, inst.collectedfrom.key cf , inst.hostedby.key hb " +
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