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WIP SparkCreateMergeRels distinct relations

This commit is contained in:
Claudio Atzori 2020-07-13 15:30:57 +02:00
parent d561b2dd21
commit 8a612d861a
9 changed files with 61 additions and 52 deletions
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9
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java
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@ -80,16 +80,10 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
try {
cut = Integer.parseInt(parser.get("cutConnectedComponent"));
} catch (Throwable e) {
log.error("unable to parse " + parser.get(" cut-off threshold"));
}
log.info("graphBasePath: '{}'", graphBasePath);
log.info("isLookUpUrl: '{}'", isLookUpUrl);
log.info("actionSetId: '{}'", actionSetId);
@ -134,9 +128,6 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
mergeRels.write().mode(SaveMode.Append).parquet(mergeRelPath);
}
}

21
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java
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@ -34,6 +34,8 @@ public class SparkCreateSimRels extends AbstractSparkAction {
private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
public static final int NUM_PARTITIONS = 10000;
public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
}
@ -48,13 +50,6 @@ public class SparkCreateSimRels extends AbstractSparkAction {
parser.parseArgument(args);
SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf
.registerKryoClasses(
new Class[] {
MapDocument.class, FieldListImpl.class, FieldValueImpl.class, Block.class
});
new SparkCreateSimRels(parser, getSparkSession(conf))
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
}
@ -88,7 +83,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
JavaPairRDD<String, MapDocument> mapDocuments = sc
.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
.repartition(10000)
.repartition(NUM_PARTITIONS)
.mapToPair(
(PairFunction<String, String, MapDocument>) s -> {
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
@ -98,21 +93,15 @@ public class SparkCreateSimRels extends AbstractSparkAction {
// create blocks for deduplication
JavaPairRDD<String, Block> blocks = Deduper
.createSortedBlocks(mapDocuments, dedupConf)
.repartition(10000);
.repartition(NUM_PARTITIONS);
// create relations by comparing only elements in the same group
Deduper
.computeRelations(sc, blocks, dedupConf)
.map(t -> createSimRel(t._1(), t._2(), entity))
.repartition(10000)
.repartition(NUM_PARTITIONS)
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
.saveAsTextFile(outputPath);
// save the simrel in the workingdir
/*
* spark .createDataset(relations.rdd(), Encoders.bean(Relation.class)) .write() .mode(SaveMode.Append)
* .save(outputPath);
*/
}
}

18
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
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@ -4,7 +4,9 @@ package eu.dnetlib.dhp.oa.dedup;
import static org.apache.spark.sql.functions.col;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
@ -95,11 +97,17 @@ public class SparkPropagateRelation extends AbstractSparkAction {
FieldType.TARGET,
getDeletedFn());
save(distinctRelations(newRels.union(updated).union(mergeRels)), outputRelationPath, SaveMode.Overwrite);
save(
newRels
.union(updated)
.union(mergeRels)
.map((MapFunction<Relation, Relation>) r -> r, Encoders.kryo(Relation.class)),
outputRelationPath, SaveMode.Overwrite);
}
private Dataset<Relation> distinctRelations(Dataset<Relation> rels) {
return rels
.filter(getRelationFilterFunction())
.groupByKey((MapFunction<Relation, String>) r -> ModelSupport.idFn().apply(r), Encoders.STRING())
.agg(new RelationAggregator().toColumn())
.map((MapFunction<Tuple2<String, Relation>, Relation>) t -> t._2(), Encoders.bean(Relation.class));
@ -119,6 +127,14 @@ public class SparkPropagateRelation extends AbstractSparkAction {
.map(mapFn, Encoders.bean(Relation.class));
}
private FilterFunction<Relation> getRelationFilterFunction() {
return (FilterFunction<Relation>) r -> StringUtils.isNotBlank(r.getSource()) ||
StringUtils.isNotBlank(r.getTarget()) ||
StringUtils.isNotBlank(r.getRelClass()) ||
StringUtils.isNotBlank(r.getSubRelType()) ||
StringUtils.isNotBlank(r.getRelClass());
}
private static MapFunction<String, Relation> patchRelFn() {
return value -> {
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);

1
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java
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@ -22,7 +22,6 @@ public class ConnectedComponent implements Serializable {
public ConnectedComponent() {
}
public ConnectedComponent(Set<String> docIds, final int cut) {
this.docIds = docIds;
createID();

28
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
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@ -166,23 +166,31 @@ public class SparkDedupTest implements Serializable {
long orgs_simrel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
.count();
long pubs_simrel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
.count();
long sw_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_simrel").count();
long ds_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/dataset_simrel").count();
long sw_simrel = spark
.read()
.textFile(testOutputBasePath + "/" + testActionSetId + "/software_simrel")
.count();
long ds_simrel = spark
.read()
.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_simrel")
.count();
long orp_simrel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_simrel")
.textFile(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_simrel")
.count();
assertEquals(3432, orgs_simrel);
assertEquals(7054, pubs_simrel);
assertEquals(7152, pubs_simrel);
assertEquals(344, sw_simrel);
assertEquals(458, ds_simrel);
assertEquals(6750, orp_simrel);
@ -225,8 +233,10 @@ public class SparkDedupTest implements Serializable {
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
.count();
long ds_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel").count();
long ds_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
.count();
long orp_mergerel = spark
.read()
@ -234,7 +244,7 @@ public class SparkDedupTest implements Serializable {
.count();
assertEquals(1276, orgs_mergerel);
assertEquals(1440, pubs_mergerel);
assertEquals(1442, pubs_mergerel);
assertEquals(288, sw_mergerel);
assertEquals(472, ds_mergerel);
assertEquals(718, orp_mergerel);

7
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json
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@ -6,10 +6,10 @@
"subEntityType" : "resulttype",
"subEntityValue" : "dataset",
"orderField" : "title",
"queueMaxSize" : "800",
"queueMaxSize" : "100",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "80",
"slidingWindowSize" : "100",
"rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true",
"idPath" : "$.id",
@ -17,7 +17,8 @@
},
"pace" : {
"clustering" : [
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree" : {

7
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json
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@ -6,10 +6,10 @@
"subEntityType" : "resulttype",
"subEntityValue" : "otherresearchproduct",
"orderField" : "title",
"queueMaxSize" : "800",
"queueMaxSize" : "100",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "80",
"slidingWindowSize" : "100",
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true",
"idPath" : "$.id",
@ -17,7 +17,8 @@
},
"pace" : {
"clustering" : [
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree" : {

7
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json
View File

@ -6,10 +6,10 @@
"subEntityType": "resulttype",
"subEntityValue": "publication",
"orderField": "title",
"queueMaxSize": "800",
"queueMaxSize": "100",
"groupMaxSize": "100",
"maxChildren": "100",
"slidingWindowSize": "80",
"slidingWindowSize": "100",
"rootBuilder": [
"result",
"resultProject_outcome_isProducedBy",
@ -29,7 +29,8 @@
},
"pace": {
"clustering" : [
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree": {

9
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json
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@ -6,10 +6,10 @@
"subEntityType" : "resulttype",
"subEntityValue" : "software",
"orderField" : "title",
"queueMaxSize" : "800",
"queueMaxSize" : "100",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "80",
"slidingWindowSize" : "100",
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true",
"idPath" : "$.id",
@ -17,8 +17,9 @@
},
"pace" : {
"clustering" : [
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi", "url" ], "params" : { } }
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree": {
"start": {