From 8a612d861a89bb7dbe1da3992b9cc6730a4d5125 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 13 Jul 2020 15:30:57 +0200 Subject: [PATCH] WIP SparkCreateMergeRels distinct relations --- .../dhp/oa/dedup/SparkCreateMergeRels.java | 11 +------- .../dhp/oa/dedup/SparkCreateSimRels.java | 21 ++++---------- .../dhp/oa/dedup/SparkPropagateRelation.java | 18 +++++++++++- .../oa/dedup/graph/ConnectedComponent.java | 5 ++-- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 28 +++++++++++++------ .../dnetlib/dhp/dedup/conf/ds.curr.conf.json | 7 +++-- .../dnetlib/dhp/dedup/conf/orp.curr.conf.json | 7 +++-- .../dnetlib/dhp/dedup/conf/pub.curr.conf.json | 7 +++-- .../dnetlib/dhp/dedup/conf/sw.curr.conf.json | 9 +++--- 9 files changed, 61 insertions(+), 52 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java index 0c31f5fa2..0b44935d0 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java @@ -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.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); - - - } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java index 1be2b9e31..2e96b3563 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java @@ -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 mapDocuments = sc .textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) - .repartition(10000) + .repartition(NUM_PARTITIONS) .mapToPair( (PairFunction) s -> { MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); @@ -98,21 +93,15 @@ public class SparkCreateSimRels extends AbstractSparkAction { // create blocks for deduplication JavaPairRDD 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); - */ } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index c19769749..88fe5b26d 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -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) r -> r, Encoders.kryo(Relation.class)), + outputRelationPath, SaveMode.Overwrite); } private Dataset distinctRelations(Dataset rels) { return rels + .filter(getRelationFilterFunction()) .groupByKey((MapFunction) r -> ModelSupport.idFn().apply(r), Encoders.STRING()) .agg(new RelationAggregator().toColumn()) .map((MapFunction, 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 getRelationFilterFunction() { + return (FilterFunction) r -> StringUtils.isNotBlank(r.getSource()) || + StringUtils.isNotBlank(r.getTarget()) || + StringUtils.isNotBlank(r.getRelClass()) || + StringUtils.isNotBlank(r.getSubRelType()) || + StringUtils.isNotBlank(r.getRelClass()); + } + private static MapFunction patchRelFn() { return value -> { final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java index fd6e70916..c5f893668 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java @@ -22,12 +22,11 @@ public class ConnectedComponent implements Serializable { public ConnectedComponent() { } - public ConnectedComponent(Set docIds, final int cut) { this.docIds = docIds; createID(); - if (cut > 0 && docIds.size() > cut){ - docIds = docIds.stream().filter(s -> !ccId.equalsIgnoreCase(s)).limit(cut -1).collect(Collectors.toSet()); + if (cut > 0 && docIds.size() > cut) { + docIds = docIds.stream().filter(s -> !ccId.equalsIgnoreCase(s)).limit(cut - 1).collect(Collectors.toSet()); docIds.add(ccId); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 88d5f24f9..8e1ef8f9c 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -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); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json index 2469b2cc0..fa889d63b 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json @@ -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" : "$.id", @@ -17,7 +17,8 @@ }, "pace" : { "clustering" : [ - { "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } }, + { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} }, + { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } }, { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } } ], "decisionTree" : { diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json index 4adcc0439..b45b6ae83 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json @@ -6,10 +6,10 @@ "subEntityType" : "resulttype", "subEntityValue" : "otherresearchproduct", "orderField" : "title", - "queueMaxSize" : "800", + "queueMaxSize" : "100", "groupMaxSize" : "100", "maxChildren" : "100", - "slidingWindowSize" : "80", + "slidingWindowSize" : "100", "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ], "includeChildren" : "true", "idPath" : "$.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" : { diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json index ef0b26af4..15ebc7a6a 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json @@ -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": { diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json index 623abbf9f..f53ff385f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json @@ -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": {