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bug fixing for implementation with dataset

This commit is contained in:
Miriam Baglioni 2020-03-24 16:19:36 +01:00
parent ad712f2d79
commit 46094a3eec
1 changed files with 4 additions and 110 deletions
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112
dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java
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@ -26,7 +26,7 @@ import static eu.dnetlib.dhp.PropagationConstant.*;
public class SparkResultToOrganizationFromIstRepoJob { public class SparkResultToOrganizationFromIstRepoJob {
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToOrganizationFromIstRepoJob.class.getResourceAsStream("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_resulttoorganizationfrominstrepo_parameters.json"))); final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToOrganizationFromIstRepoJob.class.getResourceAsStream("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_propagationresulaffiliationfrominstrepo_parameters.json")));
parser.parseArgument(args); parser.parseArgument(args);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
@ -102,96 +102,6 @@ public class SparkResultToOrganizationFromIstRepoJob {
writeUpdates(toupdateresultsoftware, toupdateresultdataset, toupdateresultother, toupdateresultpublication, outputPath); 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))
.filter(ds -> INSTITUTIONAL_REPO_TYPE.equals(ds.getDatasourcetype().getClassid()))
.map(ds -> new TypedRow().setSourceId(ds.getId()))
.mapToPair(toPair());
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.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)
.map(x -> x._2()._2())
.mapToPair(toPair());
JavaRDD<Relation> relations = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class));
JavaRDD<Publication> publications = sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class));
JavaRDD<Dataset> datasets = sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class));
JavaRDD<Software> software = sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class));
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 -> {
ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
for (TypedRow t : f) {
ret.add(new Tuple2<>(t.getSourceId(), t));
}
return ret.iterator();
})
.union(datasets
.map(oaf -> getTypedRowsDatasourceResult(oaf))
.flatMapToPair(f -> {
ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
for (TypedRow t : f) {
ret.add(new Tuple2<>(t.getSourceId(), t));
}
return ret.iterator();
}))
.union(software
.map(oaf -> getTypedRowsDatasourceResult(oaf))
.flatMapToPair(f -> {
ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
for (TypedRow t : f) {
ret.add(new Tuple2<>(t.getSourceId(), t));
}
return ret.iterator();
}))
.union(other
.map(oaf -> getTypedRowsDatasourceResult(oaf))
.flatMapToPair(f -> {
ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
for (TypedRow t : f) {
ret.add(new Tuple2<>(t.getSourceId(), t));
}
return ret.iterator();
}));
JavaRDD<Relation> newRels = instdatasource_organization.join(datasource_results)
.flatMap(c -> {
List<Relation> rels = new ArrayList();
String orgId = c._2()._1().getTargetId();
String resId = c._2()._2().getTargetId();
rels.add(getRelation(orgId, 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));
rels.add(getRelation(resId, orgId, 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 rels.iterator();
});
newRels.map(p -> new ObjectMapper().writeValueAsString(p))
.saveAsTextFile(outputPath + "/relation_new");
newRels.union(relations).map(p -> new ObjectMapper().writeValueAsString(p))
.saveAsTextFile(outputPath + "/relation");*/
} }
private static void writeUpdates(JavaRDD<Row> toupdateresultsoftware, JavaRDD<Row> toupdateresultdataset, JavaRDD<Row> toupdateresultother, JavaRDD<Row> toupdateresultpublication, String outputPath) { private static void writeUpdates(JavaRDD<Row> toupdateresultsoftware, JavaRDD<Row> toupdateresultdataset, JavaRDD<Row> toupdateresultother, JavaRDD<Row> toupdateresultpublication, String outputPath) {
@ -203,8 +113,8 @@ public class SparkResultToOrganizationFromIstRepoJob {
} }
private static void createUpdateForRelationWrite(JavaRDD<Row> toupdaterelation, String outputPath, String update_type) { private static void createUpdateForRelationWrite(JavaRDD<Row> toupdaterelation, String outputPath, String update_type) {
toupdaterelation.map(s -> { toupdaterelation.flatMap(s -> {
List<Relation> relationList = Arrays.asList(); List<Relation> relationList = new ArrayList<>();
List<String> orgs = s.getList(1); List<String> orgs = s.getList(1);
String resId = s.getString(0); String resId = s.getString(0);
for (String org : orgs) { for (String org : orgs) {
@ -220,22 +130,6 @@ public class SparkResultToOrganizationFromIstRepoJob {
}).map(s -> new ObjectMapper().writeValueAsString(s)).saveAsTextFile(outputPath + "/" + update_type); }).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) { private static JavaRDD<Row> propagateOnResult(SparkSession spark, String table) {
String query; String query;
query = "SELECT id, inst.collectedfrom.key cf , inst.hostedby.key hb " + query = "SELECT id, inst.collectedfrom.key cf , inst.hostedby.key hb " +