From 418cf94642bc763e13b7e81aced14415072722d7 Mon Sep 17 00:00:00 2001 From: miconis Date: Fri, 17 Apr 2020 10:40:21 +0200 Subject: [PATCH 1/7] implementation of the deletedbyinference test in propagating relations --- .../dhp/oa/dedup/SparkPropagateRelation.java | 2 ++ .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 28 +++++++++++++++++++ 2 files changed, 30 insertions(+) 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 4e012293b9..32b01679f5 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 @@ -83,12 +83,14 @@ public class SparkPropagateRelation extends AbstractSparkAction { .textFile(relationPath) .map(patchRelFn(), Encoders.bean(Relation.class)); + //change raw ids with dedup ids Dataset newRels = processDataset( processDataset(rels, mergedIds, FieldType.SOURCE, getFixRelFn(FieldType.SOURCE)), mergedIds, FieldType.TARGET, getFixRelFn(FieldType.TARGET)) .filter(SparkPropagateRelation::containsDedup); + //update deletedbyinference Dataset updated = processDataset( processDataset(rels, mergedIds, FieldType.SOURCE, getDeletedFn()), mergedIds, FieldType.TARGET, getDeletedFn()); 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 880e917ce7..d0098e7e2c 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 @@ -4,17 +4,24 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.PairFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; +import scala.Tuple2; import java.io.File; import java.io.IOException; @@ -211,6 +218,27 @@ public class SparkDedupTest implements Serializable { assertEquals(826, relations); + //check deletedbyinference + final Dataset mergeRels = spark.read().load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*")).as(Encoders.bean(Relation.class)); + final JavaPairRDD mergedIds = mergeRels + .where("relClass == 'merges'") + .select(mergeRels.col("target")) + .distinct() + .toJavaRDD() + .mapToPair((PairFunction) r -> new Tuple2(r.getString(0), "d")); + + JavaRDD toCheck = jsc.textFile(testDedupGraphBasePath + "/relation") + .mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json)) + .join(mergedIds) + .map(t -> t._2()._1()) + .mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json)) + .join(mergedIds) + .map(t -> t._2()._1()); + + long deletedbyinference = toCheck.filter(this::isDeletedByInference).count(); + long updated = toCheck.count(); + + assertEquals(updated, deletedbyinference); } @AfterAll From 6450bb0daae9ce7a088a7a339bbc66f9012e74d4 Mon Sep 17 00:00:00 2001 From: miconis Date: Fri, 17 Apr 2020 17:31:59 +0200 Subject: [PATCH 2/7] test for softwares dedup added. definition of orp, dataset and sw dedup configurations --- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 17 +- .../dnetlib/dhp/dedup/conf/ds.curr.conf.json | 118 ++++++++++++++ .../dnetlib/dhp/dedup/conf/orp.curr.conf.json | 118 ++++++++++++++ .../dnetlib/dhp/dedup/conf/sw.curr.conf.json | 92 +++++++++++ .../eu/dnetlib/dhp/dedup/entities/datasource | 100 ++++++++++++ .../eu/dnetlib/dhp/dedup/entities/project | 100 ++++++++++++ .../eu/dnetlib/dhp/dedup/entities/software | 149 ++++++++++++++++++ .../dhp/dedup/profiles/mock_orchestrator.xml | 1 + 8 files changed, 694 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json 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 d0098e7e2c..bcc5ddeaa6 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 @@ -81,6 +81,10 @@ public class SparkDedupTest implements Serializable { lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); + + lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software"))) + .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"))); + } @Test @@ -101,9 +105,11 @@ public class SparkDedupTest implements Serializable { long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count(); long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count(); + long sw_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_simrel").count(); assertEquals(3288, orgs_simrel); assertEquals(7260, pubs_simrel); + assertEquals(344, sw_simrel); } @Test @@ -124,10 +130,11 @@ public class SparkDedupTest implements Serializable { long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count(); long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count(); + long sw_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel").count(); assertEquals(1244, orgs_mergerel); assertEquals(1460, pubs_mergerel); - + assertEquals(288, sw_mergerel); } @Test @@ -148,9 +155,11 @@ public class SparkDedupTest implements Serializable { long orgs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count(); long pubs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count(); + long sw_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord").count(); assertEquals(82, orgs_deduprecord); assertEquals(66, pubs_deduprecord); + assertEquals(51, sw_deduprecord); } @Test @@ -171,6 +180,9 @@ public class SparkDedupTest implements Serializable { long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count(); long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count(); + long projects = jsc.textFile(testDedupGraphBasePath + "/project").count(); + long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count(); + long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count(); long mergedOrgs = spark .read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").as(Encoders.bean(Relation.class)) @@ -188,6 +200,9 @@ public class SparkDedupTest implements Serializable { assertEquals(897, publications); assertEquals(835, organizations); + assertEquals(100, projects); + assertEquals(100, datasource); + assertEquals(200, softwares); long deletedOrgs = jsc.textFile(testDedupGraphBasePath + "/organization") .filter(this::isDeletedByInference).count(); 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 new file mode 100644 index 0000000000..5329005067 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json @@ -0,0 +1,118 @@ +{ + "wf" : { + "threshold" : "0.99", + "dedupRun" : "001", + "entityType" : "result", + "subEntityType" : "resulttype", + "subEntityValue" : "dataset", + "orderField" : "title", + "queueMaxSize" : "2000", + "groupMaxSize" : "100", + "maxChildren" : "100", + "slidingWindowSize" : "200", + "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" + }, + "pace" : { + "clustering" : [ + { "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" : { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.value", + "jpath_classid": "$.qualifier.classid" + } + } + ], + "threshold": 0.5, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "layer2", + "undefined": "layer2", + "ignoreUndefined": "true" + }, + "layer2" : { + "fields": [ + { + "field": "title", + "comparator": "titleVersionMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + }, + { + "field": "authors", + "comparator": "sizeMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 1.0, + "aggregation": "AND", + "positive": "layer3", + "negative": "NO_MATCH", + "undefined": "layer3", + "ignoreUndefined": "false" + }, + "layer3" : { + "fields": [ + { + "field": "title", + "comparator": "levensteinTitle", + "weight": 1.0, + "countIfUndefined": "true" + } + ], + "threshold": 0.99, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + } + }, + "model" : [ + { + "name" : "doi", + "type" : "String", + "path" : "$.pid[@.qualifier.classid = 'doi'].value" + }, + { + "name" : "pid", + "type" : "JSON", + "path" : "$.pid", + "overrideMatch" : "true" + }, + { + "name" : "title", + "type" : "String", + "path" : "$.title[@.qualifier.classid = 'main title'].value", + "length" : 250, + "size" : 5 + }, + { + "name" : "authors", + "type" : "String", + "path" : "$.author[*].fullname", + "size" : 200 + }, + { + "name" : "resulttype", + "type" : "String", + "path" : "$.resulttype.classid" + } + ], + "blacklists" : {}, + "synonyms" : {} + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json new file mode 100644 index 0000000000..76e656743f --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json @@ -0,0 +1,118 @@ +{ + "wf" : { + "threshold" : "0.99", + "dedupRun" : "001", + "entityType" : "result", + "subEntityType" : "resulttype", + "subEntityValue" : "otherresearchproduct", + "orderField" : "title", + "queueMaxSize" : "2000", + "groupMaxSize" : "100", + "maxChildren" : "100", + "slidingWindowSize" : "200", + "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ], + "includeChildren" : "true" + }, + "pace" : { + "clustering" : [ + { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} }, + { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } }, + { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } } + ], + "decisionTree" : { + "start" : { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.value", + "jpath_classid": "$.qualifier.classid" + } + } + ], + "threshold": 0.5, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "layer2", + "undefined": "layer2", + "ignoreUndefined": "true" + }, + "layer2" : { + "fields": [ + { + "field": "title", + "comparator": "titleVersionMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + }, + { + "field": "authors", + "comparator": "sizeMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 1.0, + "aggregation": "AND", + "positive": "layer3", + "negative": "NO_MATCH", + "undefined": "layer3", + "ignoreUndefined": "false" + }, + "layer3" : { + "fields": [ + { + "field": "title", + "comparator": "levensteinTitle", + "weight": 1.0, + "countIfUndefined": "true" + } + ], + "threshold": 0.99, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + } + }, + "model" : [ + { + "name" : "doi", + "type" : "String", + "path" : "$.pid[@.qualifier.classid = 'doi'}].value" + }, + { + "name" : "pid", + "type" : "JSON", + "path" : "$.pid", + "overrideMatch" : "true" + }, + { + "name" : "title", + "type" : "String", + "path" : "$.title[@.qualifier.classid = 'main title'].value", + "length" : 250, + "size" : 5 + }, + { + "name" : "authors", + "type" : "String", + "path" : "$.author[*].fullname", + "size" : 200 + }, + { + "name" : "resulttype", + "type" : "String", + "path" : "$.resulttype.classid" + } + ], + "blacklists" : {}, + "synonyms" : {} + } +} \ No newline at end of file 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 new file mode 100644 index 0000000000..815dd7a572 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json @@ -0,0 +1,92 @@ + { + "wf" : { + "threshold" : "0.99", + "dedupRun" : "001", + "entityType" : "result", + "subEntityType" : "resulttype", + "subEntityValue" : "software", + "orderField" : "title", + "queueMaxSize" : "2000", + "groupMaxSize" : "100", + "maxChildren" : "100", + "slidingWindowSize" : "200", + "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" + }, + "pace" : { + "clustering" : [ + { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} }, + { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } }, + { "name" : "lowercase", "fields" : [ "doi", "url" ], "params" : { } } + ], + "decisionTree": { + "start": { + "fields": [ + { + "field": "doi", + "comparator": "exactMatch", + "weight": 1, + "countIfUndefined": "false", + "params": {} + }, + { + "field": "url", + "comparator": "exactMatch", + "weight": 1, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 1, + "aggregation": "OR", + "positive": "MATCH", + "negative": "layer2", + "undefined": "layer2", + "ignoreUndefined": "false" + }, + "layer2": { + "fields": [ + { + "field": "title", + "comparator": "levensteinTitleIgnoreVersion", + "weight": 1, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 0.99, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "false" + } + }, + "model" : [ + { + "name" : "doi", + "type" : "String", + "path" : "$.pid[?(@.qualifier.classid == 'doi')].value" + }, + { + "name" : "title", + "type" : "String", + "path" : "$.title[?(@.qualifier.classid == 'main title')].value", + "length" : 250, + "size" : 5 + }, + { + "name" : "url", + "type" : "String", + "path" : "$.instance.url" + }, + { + "name" : "resulttype", + "type" : "String", + "path" : "$.resulttype.classid" + } + ], + "blacklists" : {}, + "synonyms": {} + } + } \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource index e69de29bb2..f54cbf0716 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource @@ -0,0 +1,100 @@ +{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:entityregistry', "classname": "sysimport:crosswalk:entityregistry', "schemename": "dnet:provenance_actions', "schemeid": "dnet:provenance_actions'}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9'}, "datauploadtype": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "accessinfopackage": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "https://dspace-cris.4science.cloud/oai/openairecris'}], "pid": [], "websiteurl": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "https://www.4science.it'}, "dateofvalidation": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "logourl": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "collectedfrom": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "", "key": ""}], "qualitymanagementkind": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "id": "10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556', "odnumberofitems": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "odnumberofitemsdate": {"dataInfo": 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Merged PR from Ibai

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    \\n
  • Now validates using Julia v0.6.3 against R package rdiversity v1.2
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  • More minor Julia v0.7 fixes
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This pre-release of the 2.2 version contains the state of master on 2017-04-19 08:33 (UTC)

\\n\\n

Features include:

\\n\\n
    \\n\\t
  • work on an installer for the planner edition (installs addin for ArcGIS Desktop 10.4)
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Simulation of long polymer chains under shear flow
\\n--------------------------------------------------
\\n************* by Airidas Korolkovas *************

\\n\\n


\\n--- Overview ---
\\nThis software numerically solves the equation of motion for a network of long (entangled) polymer chains.

\\n\\n

The physics and math were originally described in this publication: (attached here)
\\nAiridas Korolkovas, Philipp Gutfreund, and Jean-Louis Barrat. "Simulation of entangled polymer solutions." The Journal of Chemical Physics 145.12 (2016): 124113.

\\n\\n

The extension for shear flow is described in this article: (also attached)
\\nAiridas Korolkovas, Philipp Gutfreund, and Maximilian Wolff. "Dynamical structure of entangled polymers simulated under shear flow." (in preparation)

\\n\\n


\\n--- System requirements ---
\\nThe code runs in Matlab, and was tested for the Matlab 2016a version. There is both a CPU and a GPU option (about 10-50x faster).
\\nTo run the GPU code effectively, a CUDA-enabled Nvidia card is required. Quadro M5000 model was tested to give acceptable performance.

\\n\\n

 

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Bug fix:

\\n\\n
    \\n
  • When creating the StarModel.samples attribute, there used to be a hard-coded cut on lnprob that only made sense in a very limited circumstance. This has been replaced with a cut to cull the top 99.5% (as ranked by lnprob) samples.
    • \\n
\\n\\n

Feature added:

\\n\\n
    \\n
  • \\nTripleStarModel, along the lines of BinaryStarModel but with three stars.
    • \\n
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A wrapper and CLI to evaluate a TMVA Machine Learning classifier with as little boilerplate code as possible.

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    \\n
  • new global packet structure
    • \\n
  • moved releases to repo sotorrent/releases
    • \\n
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This is a beta release of StaG-mwc v0.3.0.

\\n

Several known issues exist, check or report issues in the issue tracker on Github. \\nKnown issues using the available rules for downloading reference databases.

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"Simulation of long polymer chains under shear flow
\\n--------------------------------------------------
\\n************* by Airidas Korolkovas *************\\n\\n
\\n--- Overview ---
\\nThis software numerically solves the equation of motion for a network of long (entangled) polymer chains.\\n\\nThe physics and math were originally described in this publication: (attached here)
\\nAiridas Korolkovas, Philipp Gutfreund, and Jean-Louis Barrat. \"Simulation of entangled polymer solutions.\" The Journal of Chemical Physics 145.12 (2016): 124113.\\n\\nThe extension for shear flow is described in this article: (also attached)
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\\n--- System requirements ---
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Simulation of long polymer chains under shear flow
\\n--------------------------------------------------
\\n************* by Airidas Korolkovas *************

\\n\\n


\\n--- Overview ---
\\nThis software numerically solves the equation of motion for a network of long (entangled) polymer chains.

\\n\\n

The physics and math were originally described in this publication: (attached here)
\\nAiridas Korolkovas, Philipp Gutfreund, and Jean-Louis Barrat. \"Simulation of entangled polymer solutions.\" The Journal of Chemical Physics 145.12 (2016): 124113.

\\n\\n

The extension for shear flow is described in this article: (also attached)
\\nAiridas Korolkovas, Philipp Gutfreund, and Maximilian Wolff. \"Dynamical structure of entangled polymers simulated under shear flow.\" (in preparation)

\\n\\n


\\n--- System requirements ---
\\nThe code runs in Matlab, and was tested for the Matlab 2016a version. There is both a CPU and a GPU option (about 10-50x faster).
\\nTo run the GPU code effectively, a CUDA-enabled Nvidia card is required. Quadro M5000 model was tested to give acceptable performance.

\\n\\n

\\xa0

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This is a python software that looks into the reduction of crime by the Los Angeles Police Department (L.A.P.D). The crimes are those that were reported to the various police divisions from the years 2010 to 2017. The software shows the most occurring crimes, the weapons used in perpetuating the crimes and the victims of the crimes. Also, a map showing the locations with most crimes and the nature of crimes that occurs most is included in the software. Bar charts were used to display various victims of crimes as well as the weapons used. Again, a pie chart was used to show the total number of crimes recorded in the various years. Further more, line graphs portraying the trend of crimes from the various years and a scatter plot displaying the various age ranges of the victims of crimes.

\\n\\n

Last but not least, a heat map of the locations of all the crimes from the years 2010 to 2017, with places that recorded the most crimes having deeper colorization of the map.

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This is a python software that looks into the reduction of crime by the Los Angeles Police Department (L.A.P.D). The crimes are those that were reported to the various police divisions from the years 2010 to 2017. The\\xa0software shows the most occurring crimes, the weapons used in perpetuating the crimes and the victims of the crimes. Also, a map showing the locations\\xa0with most crimes and the nature of crimes that occurs most is included in the\\xa0software. Bar charts\\xa0were\\xa0used to display various victims of crimes as well as the weapons used. Again, a pie chart was used to show the total number of crimes recorded in the various years. Further more, line graphs portraying the trend of crimes from the various years and a scatter plot displaying the various age ranges of the victims of\\xa0crimes.

\\n\\n

Last but not least, a heat map of the locations of all the crimes from the years 2010 to 2017, with places that recorded\\xa0the most crimes having deeper colorization of the map.

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    \\n
  • introduced python3 compatibility
    • \\n
  • modernized cmake
    • \\n
  • improved CI
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Release 0.12.0-rc1 (April 20, 2016)

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    \\n\\t
  • ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
    • \\n\\t
  • ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
    • \\n\\t
  • FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
    • \\n\\t
  • FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
    • \\n\\t
  • FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
    • \\n\\t
  • ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography (https://github.com/nipy/nipype/pull/1090)
    • \\n\\t
  • ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360, https://github.com/nipy/nipype/pull/1361, https://github.com/nipy/nipype/pull/1382)
    • \\n\\t
  • ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)
    • \\n\\t
  • ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
    • \\n\\t
  • ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
    • \\n\\t
  • TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
    • \\n\\t
  • ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)
    • \\n\\t
  • ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)
    • \\n\\t
  • FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)
    • \\n\\t
  • FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
    • \\n\\t
  • ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
    • \\n\\t
  • FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
    • \\n\\t
  • ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
    • \\n\\t
  • ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
    • \\n\\t
  • API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
    • \\n\\t
  • ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
    • \\n\\t
  • ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
    • \\n\\t
  • FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
    • \\n\\t
  • FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
    • \\n\\t
  • ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
    • \\n\\t
  • FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
    • \\n\\t
  • ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
    • \\n
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This software is an implementation of the general error model described in the work entitled \"General error model for analysis of laser-induced incandescence
signals\" by T. A. Sipkens and coworkers, which simulates signals according to the described error model (sufficient for generating Figure 1 in the associated work) and demonstrates a fitting procedure to infer the error model parameters from the produced signals.

This software package was developed for use with MATLAB 2016a running on Windows. Users can execute the main script immediately, provided all attached files are located in the same directory and that directory is included in the MATLAB path. One must then enter \"main_simulate_C\" in the MATLAB command line.
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Updated Zenodo badge to point to v2.0 of the tutorial.

\\n\\n

Added updated citations and DOI (for PSA paper in PLOS Computational Biology):

\\n\\n

Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways. PLoS Comput Biol. doi: 10.1371/journal.pcbi.1004568 (also: arXiv:1505.04807 [q-bio.QM])

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A wrapper and CLI to evaluate a TMVA Machine Learning classifier with as little boilerplate code as possible.

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b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml index 9a4871223c..42d3f0b698 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml @@ -14,6 +14,7 @@ + From a2938dd059797d09ccd3cc61fd9e73692bc26ebe Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Sat, 18 Apr 2020 12:24:22 +0200 Subject: [PATCH 3/7] cleanup --- .../java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java | 6 +++--- .../eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java | 5 +---- .../test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java | 5 ----- 3 files changed, 4 insertions(+), 12 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index da16e6dffe..1c957c9e09 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -27,15 +27,15 @@ public class DedupRecordFactory { .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); public static Dataset createDedupRecord( - final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, final Class clazz, final DedupConfig dedupConf) { + final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, final Class clazz) { long ts = System.currentTimeMillis(); // Dataset> entities = spark.read() .textFile(entitiesInputPath) - .map((MapFunction>) it -> { - T entity = OBJECT_MAPPER.readValue(it, clazz); + .map((MapFunction>) s -> { + T entity = OBJECT_MAPPER.readValue(s, clazz); return new Tuple2<>(entity.getId(), entity); }, Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java index c2b1fc9c24..8e90d2a1ff 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java @@ -10,10 +10,7 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; @@ -70,7 +67,7 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { Class clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); - DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf) + DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz) .map((MapFunction) value -> OBJECT_MAPPER.writeValueAsString(value), Encoders.STRING()) .write() .mode(SaveMode.Overwrite) 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 bcc5ddeaa6..01cbf04890 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 @@ -95,7 +95,6 @@ public class SparkDedupTest implements Serializable { IOUtils.toString( SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); parser.parseArgument(new String[]{ - "-mt", "local[*]", "-i", testGraphBasePath, "-asi", testActionSetId, "-la", "lookupurl", @@ -120,7 +119,6 @@ public class SparkDedupTest implements Serializable { IOUtils.toString( SparkCreateMergeRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); parser.parseArgument(new String[]{ - "-mt", "local[*]", "-i", testGraphBasePath, "-asi", testActionSetId, "-la", "lookupurl", @@ -145,7 +143,6 @@ public class SparkDedupTest implements Serializable { IOUtils.toString( SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); parser.parseArgument(new String[]{ - "-mt", "local[*]", "-i", testGraphBasePath, "-asi", testActionSetId, "-la", "lookupurl", @@ -170,7 +167,6 @@ public class SparkDedupTest implements Serializable { IOUtils.toString( SparkUpdateEntity.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); parser.parseArgument(new String[]{ - "-mt", "local[*]", "-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath @@ -221,7 +217,6 @@ public class SparkDedupTest implements Serializable { IOUtils.toString( SparkPropagateRelation.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); parser.parseArgument(new String[]{ - "-mt", "local[*]", "-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath From 4da13e457040ca406ca00cf2605c055ba3ab080e Mon Sep 17 00:00:00 2001 From: miconis Date: Mon, 20 Apr 2020 16:04:49 +0200 Subject: [PATCH 4/7] Revert "Merge branch 'master' into deduptesting" This reverts commit 772f75d167fda38dfb68ee7a353f0e04a11cab11, reversing changes made to 5f45f2c77f49eeae144628a414dae9149f3cec5b. --- .../java/eu/dnetlib/dhp/schema/oaf/Oaf.java | 11 - .../eu/dnetlib/dhp/schema/oaf/OafEntity.java | 10 + .../eu/dnetlib/dhp/schema/oaf/Relation.java | 18 +- .../relation_action_payload/result.json | 20 +- .../dhp/migration/actions/ProtoConverter.java | 2 +- .../dhp/oa/dedup/AbstractSparkAction.java | 30 +- .../dhp/oa/dedup/SparkCreateDedupRecord.java | 15 +- .../dhp/oa/dedup/SparkCreateMergeRels.java | 16 +- .../dhp/oa/dedup/SparkCreateSimRels.java | 3 +- .../dhp/oa/dedup/SparkPropagateRelation.java | 7 +- .../eu/dnetlib/dhp/dedup/entities/relation | 598 +++++++++--------- .../raw/AbstractMdRecordToOafMapper.java | 51 +- .../raw/MigrateDbEntitiesApplication.java | 59 +- .../dhp/oa/graph/raw/OafToOafMapper.java | 4 +- .../dhp/oa/graph/raw/OdfToOafMapper.java | 2 +- .../parser/AbstractScholexplorerParser.java | 4 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 42 +- .../raw/MigrateDbEntitiesApplicationTest.java | 53 +- .../dnetlib/dhp/oa/graph/raw/odf_dataset.xml | 1 - .../sample/relation/relation_100.json.gz | Bin 3637 -> 3639 bytes .../dhp/provision/scholix/Scholix.java | 4 +- .../eu/dnetlib/dhp/provision/relation.json | 2 +- .../dhp/oa/provision/PrepareRelationsJob.java | 13 +- .../oa/provision/utils/XmlRecordFactory.java | 303 ++++----- 24 files changed, 561 insertions(+), 707 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index 79138d641e..7a7a9a89cd 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -1,25 +1,14 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; -import java.util.List; import java.util.Objects; public abstract class Oaf implements Serializable { - protected List collectedfrom; - private DataInfo dataInfo; private Long lastupdatetimestamp; - public List getCollectedfrom() { - return collectedfrom; - } - - public void setCollectedfrom(List collectedfrom) { - this.collectedfrom = collectedfrom; - } - public DataInfo getDataInfo() { return dataInfo; } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java index 6db3b7f745..86f4ff616f 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java @@ -10,6 +10,8 @@ public abstract class OafEntity extends Oaf implements Serializable { private List originalId; + private List collectedfrom; + private List pid; private String dateofcollection; @@ -36,6 +38,14 @@ public abstract class OafEntity extends Oaf implements Serializable { this.originalId = originalId; } + public List getCollectedfrom() { + return collectedfrom; + } + + public void setCollectedfrom(List collectedfrom) { + this.collectedfrom = collectedfrom; + } + public List getPid() { return pid; } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index aaeecb8716..9d211d0586 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -18,6 +18,8 @@ public class Relation extends Oaf { private String target; + private List collectedFrom = new ArrayList<>(); + public String getRelType() { return relType; } @@ -58,6 +60,14 @@ public class Relation extends Oaf { this.target = target; } + public List getCollectedFrom() { + return collectedFrom; + } + + public void setCollectedFrom(final List collectedFrom) { + this.collectedFrom = collectedFrom; + } + public void mergeFrom(final Relation r) { checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal"); @@ -67,12 +77,12 @@ public class Relation extends Oaf { Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal"); checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal"); - setCollectedfrom( + setCollectedFrom( Stream.concat( - Optional.ofNullable(getCollectedfrom()) + Optional.ofNullable(getCollectedFrom()) .map(Collection::stream) .orElse(Stream.empty()), - Optional.ofNullable(r.getCollectedfrom()) + Optional.ofNullable(r.getCollectedFrom()) .map(Collection::stream) .orElse(Stream.empty())) .distinct() // relies on KeyValue.equals @@ -93,6 +103,6 @@ public class Relation extends Oaf { @Override public int hashCode() { - return Objects.hash(relType, subRelType, relClass, source, target, collectedfrom); + return Objects.hash(relType, subRelType, relClass, source, target, collectedFrom); } } diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json index 36d3fdd272..bc65230a84 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json +++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json @@ -1,10 +1,10 @@ -{"collectedfrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::d0bbea1f5bed5864d1904eb602e608a6"} -{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|OpenstarTs__::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::fc7459b8fed8c0d47947fe04275251c0"} -{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|NARCIS__cris::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::c978e29d3b2ddf4f0c2b6e60d6613426"} -{"collectedfrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::b58bdbe8ae5acead04fc76777d2f8017"} -{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::8de0f5a712997aafe0d794a53e51b75a"} -{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|UnityFVG____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::89bab7c5a227fc27b2b9cadf475a6b71"} -{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::007a4870b31056f89b768cf508e1538e"} -{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|VTTRsInSsCrs::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::735915884eb439d42953372eaf934782"} -{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::9ea9c0996c87e1dc7fc69f94b5ed0010"} -{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747","subRelType":"provision","target":"20|openaire____::c24a458004a31f9687089ea3d249de51"} +{"collectedFrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::d0bbea1f5bed5864d1904eb602e608a6"} +{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|OpenstarTs__::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::fc7459b8fed8c0d47947fe04275251c0"} +{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|NARCIS__cris::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::c978e29d3b2ddf4f0c2b6e60d6613426"} +{"collectedFrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::b58bdbe8ae5acead04fc76777d2f8017"} +{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::8de0f5a712997aafe0d794a53e51b75a"} +{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|UnityFVG____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::89bab7c5a227fc27b2b9cadf475a6b71"} +{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::007a4870b31056f89b768cf508e1538e"} +{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|VTTRsInSsCrs::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::735915884eb439d42953372eaf934782"} +{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::9ea9c0996c87e1dc7fc69f94b5ed0010"} +{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747","subRelType":"provision","target":"20|openaire____::c24a458004a31f9687089ea3d249de51"} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java index 5188cf55a2..b5d027c03a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java @@ -41,7 +41,7 @@ public class ProtoConverter implements Serializable { rel.setRelType(r.getRelType().toString()); rel.setSubRelType(r.getSubRelType().toString()); rel.setRelClass(r.getRelClass()); - rel.setCollectedfrom( + rel.setCollectedFrom( r.getCollectedfromCount() > 0 ? r.getCollectedfromList().stream() .map(kv -> mapKV(kv)) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java index 3c3a63ca49..bb310050ce 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java @@ -14,9 +14,7 @@ import java.io.StringReader; import java.util.ArrayList; import java.util.List; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.Document; @@ -26,9 +24,6 @@ import org.dom4j.io.SAXReader; abstract class AbstractSparkAction implements Serializable { - protected static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup"; - protected static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions"; - protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); @@ -89,29 +84,8 @@ abstract class AbstractSparkAction implements Serializable { return SparkSession.builder().config(conf).getOrCreate(); } - protected static void save(Dataset dataset, String outPath, SaveMode mode) { - dataset.map( - (MapFunction) value -> OBJECT_MAPPER.writeValueAsString(value), - Encoders.STRING()) - .write() - .option("compression", "gzip") - .mode(mode) - .text(outPath); - } - - protected static DataInfo getDataInfo() { - DataInfo info = new DataInfo(); - info.setDeletedbyinference(false); - info.setInferred(true); - info.setInvisible(false); - - Qualifier provenanceAction = new Qualifier(); - provenanceAction.setClassid(PROVENANCE_ACTION_CLASS); - provenanceAction.setClassname(PROVENANCE_ACTION_CLASS); - provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS); - provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS); - info.setProvenanceaction(provenanceAction); - return info; + protected static void save(Dataset dataset, String outPath, SaveMode mode) { + dataset.write().option("compression", "gzip").mode(mode).json(outPath); } protected static void removeOutputDir(SparkSession spark, String path) { diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java index a4e69e6db1..127a19139e 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java @@ -11,6 +11,8 @@ import eu.dnetlib.pace.config.DedupConfig; import java.io.IOException; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; @@ -69,11 +71,14 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { Class clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); - save( - DedupRecordFactory.createDedupRecord( - spark, mergeRelPath, entityPath, clazz, dedupConf), - outputPath, - SaveMode.Overwrite); + DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf) + .map( + (MapFunction) + value -> OBJECT_MAPPER.writeValueAsString(value), + Encoders.STRING()) + .write() + .mode(SaveMode.Overwrite) + .json(outputPath); } } } 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 cfd541f297..ca6d04d496 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 @@ -6,6 +6,7 @@ import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent; import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; @@ -34,7 +35,9 @@ import scala.Tuple2; public class SparkCreateMergeRels extends AbstractSparkAction { + public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup"; private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class); + public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions"; public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); @@ -145,13 +148,22 @@ public class SparkCreateMergeRels extends AbstractSparkAction { r.setRelClass(relClass); r.setSubRelType("dedup"); - DataInfo info = getDataInfo(); + DataInfo info = new DataInfo(); + info.setDeletedbyinference(false); + info.setInferred(true); + info.setInvisible(false); info.setInferenceprovenance(dedupConf.getWf().getConfigurationId()); + Qualifier provenanceAction = new Qualifier(); + provenanceAction.setClassid(PROVENANCE_ACTION_CLASS); + provenanceAction.setClassname(PROVENANCE_ACTION_CLASS); + provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS); + provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS); + info.setProvenanceaction(provenanceAction); // TODO calculate the trust value based on the similarity score of the elements in the CC // info.setTrust(); - r.setDataInfo(getDataInfo()); + r.setDataInfo(info); return r; } 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 186b21ef2c..2fd807ccb2 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 @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.dedup; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.dedup.model.Block; +import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; @@ -114,7 +115,7 @@ public class SparkCreateSimRels extends AbstractSparkAction { r.setTarget(target); r.setSubRelType("dedupSimilarity"); r.setRelClass("isSimilarTo"); - r.setDataInfo(getDataInfo()); + r.setDataInfo(new DataInfo()); switch (entity) { case "result": 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 b983f5a297..17c99c0023 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 @@ -4,6 +4,7 @@ import static org.apache.spark.sql.functions.col; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -124,7 +125,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { return value -> { final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class); if (rel.getDataInfo() == null) { - rel.setDataInfo(getDataInfo()); + rel.setDataInfo(new DataInfo()); } return rel; }; @@ -148,7 +149,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { Relation r = value._1()._2(); String id = value._2()._2(); if (r.getDataInfo() == null) { - r.setDataInfo(getDataInfo()); + r.setDataInfo(new DataInfo()); } r.getDataInfo().setDeletedbyinference(false); switch (type) { @@ -172,7 +173,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { if (value._2() != null) { Relation r = value._1()._2(); if (r.getDataInfo() == null) { - r.setDataInfo(getDataInfo()); + r.setDataInfo(new DataInfo()); } r.getDataInfo().setDeletedbyinference(true); return r; diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/relation b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/relation index b9b9c22ba3..50e71c3662 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/relation +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/relation @@ -98,305 +98,305 @@ {"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::21abe5a91c2949aba6ef77033a5f98f3", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eac934a34bf16c5f0de8ce743bd0b4"} {"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|dedup_wf_001::5614cb4fbc9f3be07aedd6d627470e58", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eb4e57e351343377f693ee714500b4"} {"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": 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"resultProject", "source": "40|corda_______::ae9a0c1b9384e04476ad3571d04be237"} {"subRelType": "outcome", "relClass": "produces", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|od______1106::aabdb9c07beef7bdf7a93b6455f75e06", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::ae9a0c1b9384e04476ad3571d04be237"} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index a7aa600cff..f1058db385 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -1,38 +1,9 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.dataInfo; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.journal; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.keyValue; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.GeoLocation; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.OAIProvenance; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Date; -import java.util.HashMap; -import java.util.List; -import java.util.Map; +import eu.dnetlib.dhp.schema.oaf.*; +import java.util.*; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.DocumentFactory; @@ -58,12 +29,6 @@ public abstract class AbstractMdRecordToOafMapper { qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies"); protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies"); - protected static final Qualifier REPOSITORY_QUALIFIER = - qualifier( - "sysimport:crosswalk:repository", - "sysimport:crosswalk:repository", - "dnet:provenanceActions", - "dnet:provenanceActions"); protected AbstractMdRecordToOafMapper(final Map code2name) { this.code2name = code2name; @@ -90,13 +55,13 @@ public abstract class AbstractMdRecordToOafMapper { final String type = doc.valueOf("//dr:CobjCategory/@type"); final KeyValue collectedFrom = keyValue( - createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true), + doc.valueOf("//oaf:collectedFrom/@id"), doc.valueOf("//oaf:collectedFrom/@name")); final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom : keyValue( - createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), + doc.valueOf("//oaf:hostedBy/@id"), doc.valueOf("//oaf:hostedBy/@name")); final DataInfo info = prepareDataInfo(doc); @@ -189,7 +154,7 @@ public abstract class AbstractMdRecordToOafMapper { r1.setRelClass("isProducedBy"); r1.setSource(docId); r1.setTarget(projectId); - r1.setCollectedfrom(Arrays.asList(collectedFrom)); + r1.setCollectedFrom(Arrays.asList(collectedFrom)); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r1); @@ -200,7 +165,7 @@ public abstract class AbstractMdRecordToOafMapper { r2.setRelClass("produces"); r2.setSource(projectId); r2.setTarget(docId); - r2.setCollectedfrom(Arrays.asList(collectedFrom)); + r2.setCollectedFrom(Arrays.asList(collectedFrom)); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r2); @@ -433,7 +398,7 @@ public abstract class AbstractMdRecordToOafMapper { final Node n = doc.selectSingleNode("//oaf:datainfo"); if (n == null) { - return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9"); + return null; } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 476e617d78..6de7303c35 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -1,35 +1,11 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.asString; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.dataInfo; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.journal; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listKeyValues; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; import java.io.Closeable; import java.io.IOException; import java.sql.Array; @@ -143,8 +119,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); ds.setCollectedfrom( listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname"))); + rs.getString("collectedfromid"), rs.getString("collectedfromname"))); ds.setPid(new ArrayList<>()); ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); ds.setDateoftransformation(null); // Value not returned by the SQL query @@ -210,8 +185,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication p.setOriginalId(Arrays.asList(rs.getString("projectid"))); p.setCollectedfrom( listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname"))); + rs.getString("collectedfromid"), rs.getString("collectedfromname"))); p.setPid(new ArrayList<>()); p.setDateofcollection(asString(rs.getDate("dateofcollection"))); p.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); @@ -266,8 +240,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); o.setCollectedfrom( listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname"))); + rs.getString("collectedfromid"), rs.getString("collectedfromname"))); o.setPid(new ArrayList<>()); o.setDateofcollection(asString(rs.getDate("dateofcollection"))); o.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); @@ -312,8 +285,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final String dsId = createOpenaireId(10, rs.getString("datasource"), true); final List collectedFrom = listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname")); + rs.getString("collectedfromid"), rs.getString("collectedfromname")); final Relation r1 = new Relation(); r1.setRelType("datasourceOrganization"); @@ -321,7 +293,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r1.setRelClass("isProvidedBy"); r1.setSource(dsId); r1.setTarget(orgId); - r1.setCollectedfrom(collectedFrom); + r1.setCollectedFrom(collectedFrom); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); @@ -331,7 +303,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r2.setRelClass("provides"); r2.setSource(orgId); r2.setTarget(dsId); - r2.setCollectedfrom(collectedFrom); + r2.setCollectedFrom(collectedFrom); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); @@ -348,8 +320,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final String projectId = createOpenaireId(40, rs.getString("project"), true); final List collectedFrom = listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname")); + rs.getString("collectedfromid"), rs.getString("collectedfromname")); final Relation r1 = new Relation(); r1.setRelType("projectOrganization"); @@ -357,7 +328,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r1.setRelClass("isParticipant"); r1.setSource(projectId); r1.setTarget(orgId); - r1.setCollectedfrom(collectedFrom); + r1.setCollectedFrom(collectedFrom); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); @@ -367,7 +338,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r2.setRelClass("hasParticipant"); r2.setSource(orgId); r2.setTarget(projectId); - r2.setCollectedfrom(collectedFrom); + r2.setCollectedFrom(collectedFrom); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); @@ -392,9 +363,6 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication "dnet:provenanceActions"), "0.9"); - final List collectedFrom = - listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE"); - try { if (rs.getString("source_type").equals("context")) { @@ -413,7 +381,6 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r.setLastupdatetimestamp(lastUpdateTimestamp); r.setContext(prepareContext(rs.getString("source_id"), info)); r.setDataInfo(info); - r.setCollectedfrom(collectedFrom); return Arrays.asList(r); } else { @@ -428,22 +395,18 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final Relation r2 = new Relation(); if (rs.getString("source_type").equals("project")) { - r1.setCollectedfrom(collectedFrom); r1.setRelType("resultProject"); r1.setSubRelType("outcome"); r1.setRelClass("produces"); - r2.setCollectedfrom(collectedFrom); r2.setRelType("resultProject"); r2.setSubRelType("outcome"); r2.setRelClass("isProducedBy"); } else { - r1.setCollectedfrom(collectedFrom); r1.setRelType("resultResult"); r1.setSubRelType("relationship"); r1.setRelClass("isRelatedTo"); - r2.setCollectedfrom(collectedFrom); r2.setRelType("resultResult"); r2.setSubRelType("relationship"); r2.setRelClass("isRelatedTo"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 6b304c9b0b..e77b1f87fe 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -232,7 +232,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { r1.setRelClass("isRelatedTo"); r1.setSource(docId); r1.setTarget(otherId); - r1.setCollectedfrom(Arrays.asList(collectedFrom)); + r1.setCollectedFrom(Arrays.asList(collectedFrom)); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r1); @@ -243,7 +243,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { r2.setRelClass("isRelatedTo"); r2.setSource(otherId); r2.setTarget(docId); - r2.setCollectedfrom(Arrays.asList(collectedFrom)); + r2.setCollectedFrom(Arrays.asList(collectedFrom)); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r2); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index f6fab499bf..5e64624170 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -334,7 +334,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { r.setRelClass(relClass); r.setSource(source); r.setTarget(target); - r.setCollectedfrom(Arrays.asList(collectedFrom)); + r.setCollectedFrom(Arrays.asList(collectedFrom)); r.setDataInfo(info); r.setLastupdatetimestamp(lastUpdateTimestamp); return r; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java index 4d3cb02d68..bfd5d5c7f4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java @@ -186,7 +186,7 @@ public abstract class AbstractScholexplorerParser { r.setTarget(targetId); r.setRelType(relationSemantic); r.setRelClass("datacite"); - r.setCollectedfrom(parsedObject.getCollectedfrom()); + r.setCollectedFrom(parsedObject.getCollectedfrom()); r.setDataInfo(di); rels.add(r); r = new DLIRelation(); @@ -195,7 +195,7 @@ public abstract class AbstractScholexplorerParser { r.setTarget(parsedObject.getId()); r.setRelType(inverseRelation); r.setRelClass("datacite"); - r.setCollectedfrom(parsedObject.getCollectedfrom()); + r.setCollectedFrom(parsedObject.getCollectedfrom()); r.setDateOfCollection(dateOfCollection); rels.add(r); if ("unknown".equalsIgnoreCase(relatedType)) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index b09c5d6385..6af314d76e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -1,16 +1,11 @@ package eu.dnetlib.dhp.oa.graph.raw; import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertTrue; import static org.mockito.ArgumentMatchers.anyString; import static org.mockito.Mockito.when; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.*; import java.io.IOException; import java.util.List; import java.util.Map; @@ -48,7 +43,6 @@ public class MappersTest { final Relation r2 = (Relation) list.get(2); assertValidId(p.getId()); - assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); assertTrue(p.getAuthor().size() > 0); assertTrue(p.getSubject().size() > 0); @@ -56,24 +50,13 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); assertValidId(r1.getSource()); - assertValidId(r1.getTarget()); assertValidId(r2.getSource()); - assertValidId(r2.getTarget()); - assertValidId(r1.getCollectedfrom().get(0).getKey()); - assertValidId(r2.getCollectedfrom().get(0).getKey()); - assertNotNull(r1.getDataInfo()); - assertNotNull(r2.getDataInfo()); - assertNotNull(r1.getDataInfo().getTrust()); - assertNotNull(r2.getDataInfo().getTrust()); assertEquals(r1.getSource(), r2.getTarget()); assertEquals(r2.getSource(), r1.getTarget()); assertTrue(StringUtils.isNotBlank(r1.getRelClass())); assertTrue(StringUtils.isNotBlank(r2.getRelClass())); assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r2.getRelType())); - - // System.out.println(new ObjectMapper().writeValueAsString(r1)); - // System.out.println(new ObjectMapper().writeValueAsString(r2)); } @Test @@ -82,35 +65,15 @@ public class MappersTest { final List list = new OdfToOafMapper(code2name).processMdRecord(xml); - assertEquals(3, list.size()); + assertEquals(1, list.size()); assertTrue(list.get(0) instanceof Dataset); - assertTrue(list.get(1) instanceof Relation); - assertTrue(list.get(2) instanceof Relation); final Dataset d = (Dataset) list.get(0); - final Relation r1 = (Relation) list.get(1); - final Relation r2 = (Relation) list.get(2); assertValidId(d.getId()); - assertValidId(d.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); assertTrue(d.getAuthor().size() > 0); assertTrue(d.getSubject().size() > 0); - - assertValidId(r1.getSource()); - assertValidId(r1.getTarget()); - assertValidId(r2.getSource()); - assertValidId(r2.getTarget()); - assertNotNull(r1.getDataInfo()); - assertNotNull(r2.getDataInfo()); - assertNotNull(r1.getDataInfo().getTrust()); - assertNotNull(r2.getDataInfo().getTrust()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - assertTrue(StringUtils.isNotBlank(r1.getRelClass())); - assertTrue(StringUtils.isNotBlank(r2.getRelClass())); - assertTrue(StringUtils.isNotBlank(r1.getRelType())); - assertTrue(StringUtils.isNotBlank(r2.getRelType())); } @Test @@ -125,7 +88,6 @@ public class MappersTest { final Software s = (Software) list.get(0); assertValidId(s.getId()); - assertValidId(s.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); assertTrue(s.getAuthor().size() > 0); assertTrue(s.getSubject().size() > 0); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index b88731ba24..3c7bc684d3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -1,17 +1,10 @@ package eu.dnetlib.dhp.oa.graph.raw; import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertNotNull; -import static org.junit.jupiter.api.Assertions.assertTrue; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.*; import java.io.IOException; import java.sql.Array; import java.sql.Date; @@ -20,7 +13,6 @@ import java.sql.SQLException; import java.util.List; import java.util.Objects; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; @@ -50,13 +42,14 @@ public class MigrateDbEntitiesApplicationTest { final Datasource ds = (Datasource) list.get(0); assertValidId(ds.getId()); - assertValidId(ds.getCollectedfrom().get(0).getKey()); assertEquals(ds.getOfficialname().getValue(), getValueAsString("officialname", fields)); assertEquals(ds.getEnglishname().getValue(), getValueAsString("englishname", fields)); assertEquals(ds.getContactemail().getValue(), getValueAsString("contactemail", fields)); assertEquals(ds.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); assertEquals( ds.getNamespaceprefix().getValue(), getValueAsString("namespaceprefix", fields)); + assertEquals( + ds.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); assertEquals( ds.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); @@ -72,9 +65,10 @@ public class MigrateDbEntitiesApplicationTest { final Project p = (Project) list.get(0); assertValidId(p.getId()); - assertValidId(p.getCollectedfrom().get(0).getKey()); assertEquals(p.getAcronym().getValue(), getValueAsString("acronym", fields)); assertEquals(p.getTitle().getValue(), getValueAsString("title", fields)); + assertEquals( + p.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); assertEquals( p.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); @@ -92,7 +86,6 @@ public class MigrateDbEntitiesApplicationTest { final Organization o = (Organization) list.get(0); assertValidId(o.getId()); - assertValidId(o.getCollectedfrom().get(0).getKey()); assertEquals(o.getLegalshortname().getValue(), getValueAsString("legalshortname", fields)); assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields)); assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); @@ -105,6 +98,8 @@ public class MigrateDbEntitiesApplicationTest { assertEquals( o.getCountry().getSchemename(), getValueAsString("country", fields).split("@@@")[3]); + assertEquals( + o.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); assertEquals( o.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); @@ -142,8 +137,6 @@ public class MigrateDbEntitiesApplicationTest { assertValidId(r2.getSource()); assertEquals(r1.getSource(), r2.getTarget()); assertEquals(r2.getSource(), r1.getTarget()); - assertValidId(r1.getCollectedfrom().get(0).getKey()); - assertValidId(r2.getCollectedfrom().get(0).getKey()); } @Test @@ -153,12 +146,7 @@ public class MigrateDbEntitiesApplicationTest { final List list = app.processClaims(rs); assertEquals(1, list.size()); - assertTrue(list.get(0) instanceof Result); - final Result r = (Result) list.get(0); - verifyMocks(fields); - - assertValidId(r.getCollectedfrom().get(0).getKey()); } @Test @@ -169,33 +157,6 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(2, list.size()); verifyMocks(fields); - - assertTrue(list.get(0) instanceof Relation); - assertTrue(list.get(1) instanceof Relation); - - final Relation r1 = (Relation) list.get(0); - final Relation r2 = (Relation) list.get(1); - - assertValidId(r1.getSource()); - assertValidId(r1.getTarget()); - assertValidId(r2.getSource()); - assertValidId(r2.getTarget()); - assertNotNull(r1.getDataInfo()); - assertNotNull(r2.getDataInfo()); - assertNotNull(r1.getDataInfo().getTrust()); - assertNotNull(r2.getDataInfo().getTrust()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - assertTrue(StringUtils.isNotBlank(r1.getRelClass())); - assertTrue(StringUtils.isNotBlank(r2.getRelClass())); - assertTrue(StringUtils.isNotBlank(r1.getRelType())); - assertTrue(StringUtils.isNotBlank(r2.getRelType())); - - assertValidId(r1.getCollectedfrom().get(0).getKey()); - assertValidId(r2.getCollectedfrom().get(0).getKey()); - - // System.out.println(new ObjectMapper().writeValueAsString(r1)); - // System.out.println(new ObjectMapper().writeValueAsString(r2)); } private List prepareMocks(final String jsonFile) throws IOException, SQLException { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml index 94dc802fac..0c36e8686f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml @@ -87,7 +87,6 @@ und - corda_______::226852 &2J-DpY^S#Y3pZoM_ZWd z(=|BXypplZ9V^4h>SD{i{SEDu`{Un_h=s$iT2VFA@fb%?r8m5F%3-I$!H(bF=U@#U zzv5D~@mV0tVa-UOt??vr?pw^srgGJ1R6K@>QgyIkk0Da3ls{{(G0)EKkq!JX$7~+1RXIBD>k?YvID*=&eaqO!D~Hym zFZ+o3cG_)`u_{^R;4?=bhgre$HuUr~USN1jMRTMdcRn&(v6)24$~zCJA{HE@!YJ`` zhtou^!?#tR&Kpk)-A_KF@VCVKJSfg4PJwt)C}|hP7KM;ZpJz0WcMBOoIUiNKOe=5&~Wt) zL3G5*(iS~Vv0RY48PViXpahtPiMQGuA14=WR3MHXqv2GA5<6E$O=$o$l!5viV=noEfk>*=oRGz zK-86x3bW?R?$^Iw$fO%VQ(rnzzE__jO!4OGO6#t?QT`&lMNwKt(Z8W7z9Hq2Bm&W)9E0JBJf7i?d5{KmC7OdY4PHBX};ymK^#K}Yp726SdK;*MI_YU(@`D& zaYP4xyvll}aaQ{9^K`}R#w@+!6L^p^Yg8Nk=<)4Sb>0I%ReKGuef(%bKPtMJO@fM6 zZj*tU{<=QMqeOVbobIS=c}shdEmZ0cukK7n-OFj_i7mxCPehofL&GLoqMLJL?&SR% zqSRss{n4ZlkA~i6S77ds?joT^GcW{m?pvO~ti<+ipc*W9_JFxRraPJ`pMeyS9G5Bj z70z2dQp;$BATvFcIA;D~9SiRv8ikT$eZ-ERpLBkfoeQ&fFq^*_Ckg)WD%uce#W`Zd zk^aEa^=B~42+Gk9WV&yuz#U^DdFYK&wzpM9j@~kkm>j|q5UEMdGm+1YoQ#nZ5Yg$M z_k0pt3`O5@>y9^T`$;N*U#inf^oNgeAL0>|KGPI)Ml@GaDo%+(3%a8i$kP(?uoc|wF5)Cht0ULnO*qowF~HmpLu#M~0)E~BzhJwk>$$yN~Wt#8d#O$HKjehsXK~HXluw!3b zn?$6BR0yyhsK%;4cIx!+Z%K;MXx&n~H9b5P{!2`j4%LX3ZJB2kTv68(-Qg0zI5NJ?0wq(eMbYr+dmO&W%L ztaIq2yk-Md0|#aJiqroH&iZOL$@%Of2|iGt-8fVb)P4aOnTq~D8>G5k#L!-r_YJsjfVB`2ans%0+L8{-1P9enx z($c@t=TTdlLDM|Lf952KxZ7*i{gH9&q1U=PmCGTi`hGflS~IEk(^il4X4n)UWgc`pm6*lObo@q7xD@`HHlU{Cr!|@)!120%8FDUQ<8xW^VSV)* zeO?34y0BcZF~2$sz_z?Y)hJ{&TTOE@j@3irkwq|>kQ$3nN=*BRtm5vpIn7pByAaC_ z?TQ$;+d+af4Z3r%g*s0`k6=z6N_wKwe-vxV&$V48oORnE__?E!lW{8LrUrLkB&erk zm5%1gw-+RYv=4qy2+{gY;tSn`p-}XLmV&`y3l2M zzzWHc8O5(fz6u*9IqN3S)Uzb<(wi7(j1n(iCbb}ZQGRZ$7TE1_&6gp_%Z8=H@-rU| 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zYb;*zK{=S4AFf<4ib_8SVdlbCoZ7Xsa{>RCnT__Ht}BK)jH_(lBb7w)C+8xf--g^{c!3F346w{l{ z%v4*9%0JhN7oFSZf7xz={Bs1WM9Lp!D&9Pj9=yW`Go&Wz+VD#aboM^(vYK`E*nyj~ zR65^BS#u-uPuXexdjcVw+QuK;tfGPT_cw6b((eBgKNjEp_plX#4R;m9v}4cb)mE;g z$KfrFx6SP;G z!okzPFjf*ZHh8VjMoFzIgl4siHz9As`6{8tnVCV8c*@FX5#jbrFdH2E0vwm04J_*V zV$Hv&)r{j2hA)?eY~T!mT_N%Ctpm_DdN!NAU6gDVk3)Qm;;p#m7a!6+3qtYxt0`k{ zzScWRKO26|zXAM+8j}TCW>37Xut}({wCx6|5<*(YJ3D^fOmmllY~Dk~7V?krSW!W> z1+$G=#u!u1DO-nmZ_SAONz7Q(y4ofkH3VmWFXkDqSnxR$rFkN`Q(AZ~-PKXSQ{$S` zg&gH!_}i{t)a945W#OH`D$`UB(P)dj 0) s.setPublicationDate(scholixSummary.getDate().get(0)); s.setLinkprovider( - rel.getCollectedfrom().stream() + rel.getCollectedFrom().stream() .map( cf -> new ScholixEntityId( @@ -73,7 +73,7 @@ public class Scholix implements Serializable { if (scholixSummary.getDate() != null && scholixSummary.getDate().size() > 0) s.setPublicationDate(scholixSummary.getDate().get(0)); s.setLinkprovider( - rel.getCollectedfrom().stream() + rel.getCollectedFrom().stream() .map( cf -> new ScholixEntityId( diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json index 3cca6e370f..e029ddf625 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json @@ -1 +1 @@ -{"dataInfo":{"invisible":false,"inferred":null,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":null},"lastupdatetimestamp":null,"relType":"IsReferencedBy","subRelType":null,"relClass":"datacite","source":"50|dedup_______::4f00e4f0e82bb4cbb35261478e55568e","target":"60|97519e00ee2cddfa1f5bcb5220429b8f","collectedfrom":[{"key":"dli_________::europe_pmc__","value":"Europe PMC","dataInfo":null}]} \ No newline at end of file +{"dataInfo":{"invisible":false,"inferred":null,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":null},"lastupdatetimestamp":null,"relType":"IsReferencedBy","subRelType":null,"relClass":"datacite","source":"50|dedup_______::4f00e4f0e82bb4cbb35261478e55568e","target":"60|97519e00ee2cddfa1f5bcb5220429b8f","collectedFrom":[{"key":"dli_________::europe_pmc__","value":"Europe PMC","dataInfo":null}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java index b663a8082e..a6c261ec72 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java @@ -95,18 +95,7 @@ public class PrepareRelationsJob { readPathRelation(spark, inputRelationsPath) .filter( (FilterFunction) - r -> { - try { - return r != null - && r.getDataInfo() != null - && !r.getDataInfo().getDeletedbyinference(); - } catch (NullPointerException e) { - log.info( - "invalid NPE '{}'", - OBJECT_MAPPER.writeValueAsString(r)); - throw e; - } - }) + value -> value.getDataInfo().getDeletedbyinference() == false) .groupByKey( (MapFunction) value -> value.getSource(), Encoders.STRING()) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 874c34c090..3455cb5f3b 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -22,7 +22,6 @@ import java.io.IOException; import java.io.Serializable; import java.io.StringReader; import java.io.StringWriter; -import java.util.ArrayList; import java.util.List; import java.util.Map; import java.util.Set; @@ -42,7 +41,6 @@ import org.dom4j.io.XMLWriter; public class XmlRecordFactory implements Serializable { - public static final String REL_SUBTYPE_DEDUP = "dedup"; private Map accumulators; private Set specialDatasourceTypes; @@ -93,14 +91,7 @@ public class XmlRecordFactory implements Serializable { // rels has to be processed before the contexts because they enrich the contextMap with // the // funding info. - final List relations = - je.getLinks().stream() - .filter( - t -> - !REL_SUBTYPE_DEDUP.equalsIgnoreCase( - t.getRelation().getSubRelType())) - .map(link -> mapRelation(link, templateFactory, contexts)) - .collect(Collectors.toCollection(ArrayList::new)); + final List relations = listRelations(je, templateFactory, contexts); final String mainType = ModelSupport.getMainType(type); metadata.addAll(buildContexts(mainType, contexts)); @@ -111,7 +102,7 @@ public class XmlRecordFactory implements Serializable { mainType, metadata, relations, - listChildren(entity, je, templateFactory), + listChildren(entity, je.getEntity().getType(), templateFactory), listExtraInfo(entity)); return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent); @@ -928,149 +919,171 @@ public class XmlRecordFactory implements Serializable { metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", dsType)); } - private String mapRelation(Tuple2 link, TemplateFactory templateFactory, Set contexts) { - final Relation rel = link.getRelation(); - final RelatedEntity re = link.getRelatedEntity(); - final String targetType = link.getRelatedEntity().getType(); + private Qualifier getBestAccessright(final Result r) { + Qualifier bestAccessRight = new Qualifier(); + bestAccessRight.setClassid("UNKNOWN"); + bestAccessRight.setClassname("not available"); + bestAccessRight.setSchemeid("dnet:access_modes"); + bestAccessRight.setSchemename("dnet:access_modes"); - final List metadata = Lists.newArrayList(); - switch (EntityType.valueOf(targetType)) { - case publication: - case dataset: - case otherresearchproduct: - case software: - if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) { - metadata.add( - XmlSerializationUtils.mapStructuredProperty("title", re.getTitle())); - } - if (isNotBlank(re.getDateofacceptance())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "dateofacceptance", re.getDateofacceptance())); - } - if (isNotBlank(re.getPublisher())) { - metadata.add( - XmlSerializationUtils.asXmlElement("publisher", re.getPublisher())); - } - if (isNotBlank(re.getCodeRepositoryUrl())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "coderepositoryurl", re.getCodeRepositoryUrl())); - } - if (re.getResulttype() != null & re.getResulttype().isBlank()) { - metadata.add( - XmlSerializationUtils.mapQualifier("resulttype", re.getResulttype())); - } - if (re.getCollectedfrom() != null) { - metadata.addAll( - re.getCollectedfrom().stream() - .map( - kv -> - XmlSerializationUtils.mapKeyValue( - "collectedfrom", kv)) - .collect(Collectors.toList())); - } - if (re.getPid() != null) { - metadata.addAll( - re.getPid().stream() - .map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p)) - .collect(Collectors.toList())); - } - break; - case datasource: - if (isNotBlank(re.getOfficialname())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "officialname", re.getOfficialname())); - } - if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) { - mapDatasourceType(metadata, re.getDatasourcetype()); - } - if (re.getOpenairecompatibility() != null - & !re.getOpenairecompatibility().isBlank()) { - metadata.add( - XmlSerializationUtils.mapQualifier( - "openairecompatibility", re.getOpenairecompatibility())); - } - break; - case organization: - if (isNotBlank(re.getLegalname())) { - metadata.add( - XmlSerializationUtils.asXmlElement("legalname", re.getLegalname())); - } - if (isNotBlank(re.getLegalshortname())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "legalshortname", re.getLegalshortname())); - } - if (re.getCountry() != null & !re.getCountry().isBlank()) { - metadata.add(XmlSerializationUtils.mapQualifier("country", re.getCountry())); - } - break; - case project: - if (isNotBlank(re.getProjectTitle())) { - metadata.add(XmlSerializationUtils.asXmlElement("title", re.getProjectTitle())); - } - if (isNotBlank(re.getCode())) { - metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode())); - } - if (isNotBlank(re.getAcronym())) { - metadata.add(XmlSerializationUtils.asXmlElement("acronym", re.getAcronym())); - } - if (re.getContracttype() != null & !re.getContracttype().isBlank()) { - metadata.add( - XmlSerializationUtils.mapQualifier( - "contracttype", re.getContracttype())); - } - if (re.getFundingtree() != null & contexts != null) { - metadata.addAll( - re.getFundingtree().stream() - .peek(ft -> fillContextMap(ft, contexts)) - .map(ft -> getRelFundingTree(ft)) - .collect(Collectors.toList())); - } - break; - default: - throw new IllegalArgumentException("invalid target type: " + targetType); + final LicenseComparator lc = new LicenseComparator(); + for (final Instance instance : r.getInstance()) { + if (lc.compare(bestAccessRight, instance.getAccessright()) > 0) { + bestAccessRight = instance.getAccessright(); + } } - final DataInfo info = rel.getDataInfo(); - final String scheme = ModelSupport.getScheme(re.getType(), targetType); + return bestAccessRight; + } - if (StringUtils.isBlank(scheme)) { - throw new IllegalArgumentException( - String.format("missing scheme for: <%s - %s>", re.getType(), targetType)); + private List listRelations( + final JoinedEntity je, TemplateFactory templateFactory, final Set contexts) { + final List rels = Lists.newArrayList(); + + for (final Tuple2 link : je.getLinks()) { + + final Relation rel = link.getRelation(); + final RelatedEntity re = link.getRelatedEntity(); + final String targetType = link.getRelatedEntity().getType(); + + final List metadata = Lists.newArrayList(); + switch (EntityType.valueOf(targetType)) { + case publication: + case dataset: + case otherresearchproduct: + case software: + if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) { + metadata.add( + XmlSerializationUtils.mapStructuredProperty( + "title", re.getTitle())); + } + if (isNotBlank(re.getDateofacceptance())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "dateofacceptance", re.getDateofacceptance())); + } + if (isNotBlank(re.getPublisher())) { + metadata.add( + XmlSerializationUtils.asXmlElement("publisher", re.getPublisher())); + } + if (isNotBlank(re.getCodeRepositoryUrl())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "coderepositoryurl", re.getCodeRepositoryUrl())); + } + if (re.getResulttype() != null & re.getResulttype().isBlank()) { + metadata.add( + XmlSerializationUtils.mapQualifier( + "resulttype", re.getResulttype())); + } + if (re.getCollectedfrom() != null) { + metadata.addAll( + re.getCollectedfrom().stream() + .map( + kv -> + XmlSerializationUtils.mapKeyValue( + "collectedfrom", kv)) + .collect(Collectors.toList())); + } + if (re.getPid() != null) { + metadata.addAll( + re.getPid().stream() + .map( + p -> + XmlSerializationUtils.mapStructuredProperty( + "pid", p)) + .collect(Collectors.toList())); + } + break; + case datasource: + if (isNotBlank(re.getOfficialname())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "officialname", re.getOfficialname())); + } + if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) { + mapDatasourceType(metadata, re.getDatasourcetype()); + } + if (re.getOpenairecompatibility() != null + & !re.getOpenairecompatibility().isBlank()) { + metadata.add( + XmlSerializationUtils.mapQualifier( + "openairecompatibility", re.getOpenairecompatibility())); + } + break; + case organization: + if (isNotBlank(re.getLegalname())) { + metadata.add( + XmlSerializationUtils.asXmlElement("legalname", re.getLegalname())); + } + if (isNotBlank(re.getLegalshortname())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "legalshortname", re.getLegalshortname())); + } + if (re.getCountry() != null & !re.getCountry().isBlank()) { + metadata.add( + XmlSerializationUtils.mapQualifier("country", re.getCountry())); + } + break; + case project: + if (isNotBlank(re.getProjectTitle())) { + metadata.add( + XmlSerializationUtils.asXmlElement("title", re.getProjectTitle())); + } + if (isNotBlank(re.getCode())) { + metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode())); + } + if (isNotBlank(re.getAcronym())) { + metadata.add( + XmlSerializationUtils.asXmlElement("acronym", re.getAcronym())); + } + if (re.getContracttype() != null & !re.getContracttype().isBlank()) { + metadata.add( + XmlSerializationUtils.mapQualifier( + "contracttype", re.getContracttype())); + } + if (re.getFundingtree() != null) { + metadata.addAll( + re.getFundingtree().stream() + .peek(ft -> fillContextMap(ft, contexts)) + .map(ft -> getRelFundingTree(ft)) + .collect(Collectors.toList())); + } + break; + default: + throw new IllegalArgumentException("invalid target type: " + targetType); + } + final DataInfo info = rel.getDataInfo(); + final String scheme = ModelSupport.getScheme(re.getType(), targetType); + + if (StringUtils.isBlank(scheme)) { + throw new IllegalArgumentException( + String.format("missing scheme for: <%s - %s>", re.getType(), targetType)); + } + + final String accumulatorName = + getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass()); + if (accumulators.containsKey(accumulatorName)) { + accumulators.get(accumulatorName).add(1); + } + + rels.add( + templateFactory.getRel( + targetType, + rel.getTarget(), + Sets.newHashSet(metadata), + rel.getRelClass(), + scheme, + info)); } - - final String accumulatorName = - getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass()); - if (accumulators.containsKey(accumulatorName)) { - accumulators.get(accumulatorName).add(1); - } - - return templateFactory.getRel( - targetType, - rel.getTarget(), - Sets.newHashSet(metadata), - rel.getRelClass(), - scheme, - info); + return rels; } private List listChildren( - final OafEntity entity, JoinedEntity je, TemplateFactory templateFactory) { + final OafEntity entity, String type, TemplateFactory templateFactory) { final List children = Lists.newArrayList(); - EntityType entityType = EntityType.valueOf(je.getEntity().getType()); - - children.addAll( - je.getLinks().stream() - .filter( - link -> - REL_SUBTYPE_DEDUP.equalsIgnoreCase( - link.getRelation().getSubRelType())) - .map(link -> mapRelation(link, templateFactory, null)) - .collect(Collectors.toCollection(ArrayList::new))); - + EntityType entityType = EntityType.valueOf(type); if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) { final List instances = ((Result) entity).getInstance(); if (instances != null) { From 1102e3246263c4687715490907206e01b897ff99 Mon Sep 17 00:00:00 2001 From: miconis Date: Mon, 20 Apr 2020 16:49:01 +0200 Subject: [PATCH 5/7] SparkDedupTest updated and organization dump fixed --- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 312 ++++++++---------- .../dnetlib/dhp/dedup/entities/organization | 28 +- 2 files changed, 153 insertions(+), 187 deletions(-) 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 7ad2f6d17a..ce0be4f915 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 @@ -1,29 +1,37 @@ package eu.dnetlib.dhp.oa.dedup; -import static java.nio.file.Files.createTempDirectory; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.mockito.Mockito.lenient; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import java.io.File; -import java.io.IOException; -import java.io.Serializable; -import java.net.URISyntaxException; -import java.nio.file.Paths; +import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.PairFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; +import scala.Tuple2; + +import java.io.File; +import java.io.IOException; +import java.io.Serializable; +import java.net.URISyntaxException; +import java.nio.file.Paths; + +import static java.nio.file.Files.createTempDirectory; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.mockito.Mockito.lenient; @ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) @@ -38,224 +46,164 @@ public class SparkDedupTest implements Serializable { private static String testGraphBasePath; private static String testOutputBasePath; private static String testDedupGraphBasePath; - private static final String testActionSetId = "test-orchestrator"; + private final static String testActionSetId = "test-orchestrator"; @BeforeAll private static void cleanUp() throws IOException, URISyntaxException { - testGraphBasePath = - Paths.get( - SparkDedupTest.class - .getResource("/eu/dnetlib/dhp/dedup/entities") - .toURI()) - .toFile() - .getAbsolutePath(); + testGraphBasePath = Paths.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath(); - testOutputBasePath = - createTempDirectory(SparkDedupTest.class.getSimpleName() + "-") - .toAbsolutePath() - .toString(); - testDedupGraphBasePath = - createTempDirectory(SparkDedupTest.class.getSimpleName() + "-") - .toAbsolutePath() - .toString(); + testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString(); + testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString(); FileUtils.deleteDirectory(new File(testOutputBasePath)); FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); - spark = - SparkSession.builder() - .appName(SparkCreateSimRels.class.getSimpleName()) - .master("local[*]") - .config(new SparkConf()) - .getOrCreate(); + spark = SparkSession + .builder() + .appName(SparkCreateSimRels.class.getSimpleName()) + .master("local[*]") + .config(new SparkConf()) + .getOrCreate(); jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + } @BeforeEach private void setUp() throws IOException, ISLookUpException { - lenient() - .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) - .thenReturn( - IOUtils.toString( - SparkDedupTest.class.getResourceAsStream( - "/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); + lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) + .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); - lenient() - .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) - .thenReturn( - IOUtils.toString( - SparkDedupTest.class.getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); + lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) + .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); + + lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) + .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); + + lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software"))) + .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"))); - lenient() - .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) - .thenReturn( - IOUtils.toString( - SparkDedupTest.class.getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); } @Test @Order(1) public void createSimRelsTest() throws Exception { - ArgumentApplicationParser parser = - new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateSimRels.class.getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); - parser.parseArgument( - new String[] { - "-mt", "local[*]", - "-i", testGraphBasePath, - "-asi", testActionSetId, - "-la", "lookupurl", - "-w", testOutputBasePath - }); + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); + parser.parseArgument(new String[]{ + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath}); new SparkCreateSimRels(parser, spark).run(isLookUpService); - long orgs_simrel = - spark.read() - .load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel") - .count(); - long pubs_simrel = - spark.read() - .load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel") - .count(); + long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count(); + long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count(); + long sw_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_simrel").count(); - assertEquals(3288, orgs_simrel); + assertEquals(3432, orgs_simrel); assertEquals(7260, pubs_simrel); + assertEquals(344, sw_simrel); } @Test @Order(2) public void createMergeRelsTest() throws Exception { - ArgumentApplicationParser parser = - new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateMergeRels.class.getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); - parser.parseArgument( - new String[] { - "-mt", "local[*]", - "-i", testGraphBasePath, - "-asi", testActionSetId, - "-la", "lookupurl", - "-w", testOutputBasePath - }); + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateMergeRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + parser.parseArgument(new String[]{ + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath}); new SparkCreateMergeRels(parser, spark).run(isLookUpService); - long orgs_mergerel = - spark.read() - .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") - .count(); - long pubs_mergerel = - spark.read() - .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") - .count(); + long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count(); + long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count(); + long sw_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel").count(); - assertEquals(1244, orgs_mergerel); + assertEquals(1276, orgs_mergerel); assertEquals(1460, pubs_mergerel); + assertEquals(288, sw_mergerel); } @Test @Order(3) public void createDedupRecordTest() throws Exception { - ArgumentApplicationParser parser = - new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateDedupRecord.class.getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); - parser.parseArgument( - new String[] { - "-mt", "local[*]", - "-i", testGraphBasePath, - "-asi", testActionSetId, - "-la", "lookupurl", - "-w", testOutputBasePath - }); + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); + parser.parseArgument(new String[]{ + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath}); new SparkCreateDedupRecord(parser, spark).run(isLookUpService); - long orgs_deduprecord = - jsc.textFile( - testOutputBasePath - + "/" - + testActionSetId - + "/organization_deduprecord") - .count(); - long pubs_deduprecord = - jsc.textFile( - testOutputBasePath - + "/" - + testActionSetId - + "/publication_deduprecord") - .count(); + long orgs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count(); + long pubs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count(); + long sw_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord").count(); assertEquals(82, orgs_deduprecord); assertEquals(66, pubs_deduprecord); + assertEquals(51, sw_deduprecord); } @Test @Order(4) public void updateEntityTest() throws Exception { - ArgumentApplicationParser parser = - new ArgumentApplicationParser( - IOUtils.toString( - SparkUpdateEntity.class.getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); - parser.parseArgument( - new String[] { - "-mt", "local[*]", - "-i", testGraphBasePath, - "-w", testOutputBasePath, - "-o", testDedupGraphBasePath - }); + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkUpdateEntity.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); + parser.parseArgument(new String[]{ + "-i", testGraphBasePath, + "-w", testOutputBasePath, + "-o", testDedupGraphBasePath + }); new SparkUpdateEntity(parser, spark).run(isLookUpService); long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count(); long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count(); + long projects = jsc.textFile(testDedupGraphBasePath + "/project").count(); + long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count(); + long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count(); - long mergedOrgs = - spark.read() - .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") - .as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) - .distinct() - .count(); + long mergedOrgs = spark + .read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct().count(); - long mergedPubs = - spark.read() - .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") - .as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) - .distinct() - .count(); + long mergedPubs = spark + .read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct().count(); - assertEquals(897, publications); + assertEquals(831, publications); assertEquals(835, organizations); + assertEquals(100, projects); + assertEquals(100, datasource); + assertEquals(200, softwares); - long deletedOrgs = - jsc.textFile(testDedupGraphBasePath + "/organization") - .filter(this::isDeletedByInference) - .count(); - long deletedPubs = - jsc.textFile(testDedupGraphBasePath + "/publication") - .filter(this::isDeletedByInference) - .count(); + long deletedOrgs = jsc.textFile(testDedupGraphBasePath + "/organization") + .filter(this::isDeletedByInference).count(); + long deletedPubs = jsc.textFile(testDedupGraphBasePath + "/publication") + .filter(this::isDeletedByInference).count(); assertEquals(mergedOrgs, deletedOrgs); assertEquals(mergedPubs, deletedPubs); @@ -265,24 +213,42 @@ public class SparkDedupTest implements Serializable { @Order(5) public void propagateRelationTest() throws Exception { - ArgumentApplicationParser parser = - new ArgumentApplicationParser( - IOUtils.toString( - SparkPropagateRelation.class.getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); - parser.parseArgument( - new String[] { - "-mt", "local[*]", - "-i", testGraphBasePath, - "-w", testOutputBasePath, - "-o", testDedupGraphBasePath - }); + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString( + SparkPropagateRelation.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); + parser.parseArgument(new String[]{ + "-i", testGraphBasePath, + "-w", testOutputBasePath, + "-o", testDedupGraphBasePath + }); new SparkPropagateRelation(parser, spark).run(isLookUpService); long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); assertEquals(826, relations); + + //check deletedbyinference + final Dataset mergeRels = spark.read().load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*")).as(Encoders.bean(Relation.class)); + final JavaPairRDD mergedIds = mergeRels + .where("relClass == 'merges'") + .select(mergeRels.col("target")) + .distinct() + .toJavaRDD() + .mapToPair((PairFunction) r -> new Tuple2(r.getString(0), "d")); + + JavaRDD toCheck = jsc.textFile(testDedupGraphBasePath + "/relation") + .mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json)) + .join(mergedIds) + .map(t -> t._2()._1()) + .mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json)) + .join(mergedIds) + .map(t -> t._2()._1()); + + long deletedbyinference = toCheck.filter(this::isDeletedByInference).count(); + long updated = toCheck.count(); + + assertEquals(updated, deletedbyinference); } @AfterAll @@ -292,6 +258,6 @@ public class SparkDedupTest implements Serializable { } public boolean isDeletedByInference(String s) { - return s.contains("\"deletedbyinference\":true"); + return s.contains("\"deletedbyinference\":true"); } -} +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/organization b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/organization index 7e34ad1335..1a0ef251af 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/organization +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/organization @@ -198,7 +198,7 @@ {"eclegalbody": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}, "ecresearchorganization": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, 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"provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}, "id": "20|re3data_____::bd7f4f7c6cb526dcf763cb5698ba5249", "eclegalperson": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}, "lastupdatetimestamp": 0, "ecinternationalorganizationeurinterests": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}, "dateofcollection": "2018-04-03", "dateoftransformation": "2018-06-04", "ecnonprofit": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "true"}, "ecenterprise": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}, "ecinternationalorganization": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}, "legalshortname": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "EPFL"}, "country": {"classid": "CH", "classname": "Switzerland", "schemename": "dnet:countries", "schemeid": "dnet:countries"}, "extraInfo": [], "originalId": ["re3data_____::89da7b473c2c8c7781291b80eb286d64"], "ecsmevalidated": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}} From eb8a02085952da25970cbfcdc57bac8904c64b53 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 20 Apr 2020 18:44:06 +0200 Subject: [PATCH 6/7] fixed behaviour of DedupRecordFactory --- .../dhp/oa/dedup/DedupRecordFactory.java | 47 ++- .../dhp/oa/dedup/SparkCreateDedupRecord.java | 2 +- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 329 ++++++++++++------ 3 files changed, 239 insertions(+), 139 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index 1cb04d02f7..e5c8a4606e 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -5,29 +5,29 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.pace.config.DedupConfig; import java.util.Collection; import java.util.Iterator; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import scala.Tuple2; public class DedupRecordFactory { + private static final Logger log = LoggerFactory.getLogger(DedupRecordFactory.class); + protected static final ObjectMapper OBJECT_MAPPER = - new com.fasterxml.jackson.databind.ObjectMapper() - .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); public static Dataset createDedupRecord( final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, - final Class clazz, - final DedupConfig dedupConf) { + final Class clazz) { long ts = System.currentTimeMillis(); @@ -54,40 +54,39 @@ public class DedupRecordFactory { r -> new Tuple2<>(r.getSource(), r.getTarget()), Encoders.tuple(Encoders.STRING(), Encoders.STRING())); - // return mergeRels - .joinWith(entities, mergeRels.col("_1").equalTo(entities.col("_1")), "left_outer") - .filter( - (FilterFunction, Tuple2>>) - value -> value._2() != null) + .joinWith(entities, mergeRels.col("_2").equalTo(entities.col("_1")), "inner") .map( - (MapFunction, Tuple2>, T>) - value -> value._2()._2(), - Encoders.kryo(clazz)) - .groupByKey((MapFunction) value -> value.getId(), Encoders.STRING()) + (MapFunction< + Tuple2, Tuple2>, + Tuple2>) + value -> new Tuple2<>(value._1()._1(), value._2()._2()), + Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))) + .groupByKey( + (MapFunction, String>) entity -> entity._1(), + Encoders.STRING()) .mapGroups( - (MapGroupsFunction) + (MapGroupsFunction, T>) (key, values) -> entityMerger(key, values, ts, clazz), Encoders.bean(clazz)); } private static T entityMerger( - String id, Iterator entities, final long ts, Class clazz) { + String id, Iterator> entities, long ts, Class clazz) { try { T entity = clazz.newInstance(); entity.setId(id); - if (entity.getDataInfo() == null) { - entity.setDataInfo(new DataInfo()); - } + entity.setDataInfo(new DataInfo()); entity.getDataInfo().setTrust("0.9"); entity.setLastupdatetimestamp(ts); final Collection dates = Lists.newArrayList(); entities.forEachRemaining( - e -> { - entity.mergeFrom(e); - if (ModelSupport.isSubClass(e, Result.class)) { - Result r1 = (Result) e; + t -> { + T duplicate = t._2(); + entity.mergeFrom(duplicate); + if (ModelSupport.isSubClass(duplicate, Result.class)) { + Result r1 = (Result) duplicate; Result er = (Result) entity; er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor())); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java index 127a19139e..d442d73a89 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java @@ -71,7 +71,7 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { Class clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); - DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf) + DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz) .map( (MapFunction) value -> OBJECT_MAPPER.writeValueAsString(value), 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 ce0be4f915..8fd7a0ec9c 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 @@ -1,10 +1,19 @@ package eu.dnetlib.dhp.oa.dedup; +import static java.nio.file.Files.createTempDirectory; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.mockito.Mockito.lenient; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.util.MapDocumentUtil; +import java.io.File; +import java.io.IOException; +import java.io.Serializable; +import java.net.URISyntaxException; +import java.nio.file.Paths; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -23,16 +32,6 @@ import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; import scala.Tuple2; -import java.io.File; -import java.io.IOException; -import java.io.Serializable; -import java.net.URISyntaxException; -import java.nio.file.Paths; - -import static java.nio.file.Files.createTempDirectory; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.mockito.Mockito.lenient; - @ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class SparkDedupTest implements Serializable { @@ -46,65 +45,104 @@ public class SparkDedupTest implements Serializable { private static String testGraphBasePath; private static String testOutputBasePath; private static String testDedupGraphBasePath; - private final static String testActionSetId = "test-orchestrator"; + private static final String testActionSetId = "test-orchestrator"; @BeforeAll - private static void cleanUp() throws IOException, URISyntaxException { + public static void cleanUp() throws IOException, URISyntaxException { - testGraphBasePath = Paths.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath(); + testGraphBasePath = + Paths.get( + SparkDedupTest.class + .getResource("/eu/dnetlib/dhp/dedup/entities") + .toURI()) + .toFile() + .getAbsolutePath(); - testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString(); - testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString(); + testOutputBasePath = + createTempDirectory(SparkDedupTest.class.getSimpleName() + "-") + .toAbsolutePath() + .toString(); + testDedupGraphBasePath = + createTempDirectory(SparkDedupTest.class.getSimpleName() + "-") + .toAbsolutePath() + .toString(); FileUtils.deleteDirectory(new File(testOutputBasePath)); FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); - spark = SparkSession - .builder() - .appName(SparkCreateSimRels.class.getSimpleName()) - .master("local[*]") - .config(new SparkConf()) - .getOrCreate(); + spark = + SparkSession.builder() + .appName(SparkCreateSimRels.class.getSimpleName()) + .master("local[*]") + .config(new SparkConf()) + .getOrCreate(); jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - } @BeforeEach - private void setUp() throws IOException, ISLookUpException { + public void setUp() throws IOException, ISLookUpException { - lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) - .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) + .thenReturn( + IOUtils.toString( + SparkDedupTest.class.getResourceAsStream( + "/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); - lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) - .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) + .thenReturn( + IOUtils.toString( + SparkDedupTest.class.getResourceAsStream( + "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); - lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) - .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); - - lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software"))) - .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"))); + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) + .thenReturn( + IOUtils.toString( + SparkDedupTest.class.getResourceAsStream( + "/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software"))) + .thenReturn( + IOUtils.toString( + SparkDedupTest.class.getResourceAsStream( + "/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"))); } @Test @Order(1) public void createSimRelsTest() throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); - parser.parseArgument(new String[]{ - "-i", testGraphBasePath, - "-asi", testActionSetId, - "-la", "lookupurl", - "-w", testOutputBasePath}); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateSimRels.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); + parser.parseArgument( + new String[] { + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath + }); new SparkCreateSimRels(parser, spark).run(isLookUpService); - long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count(); - long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count(); - long sw_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_simrel").count(); + long orgs_simrel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel") + .count(); + long pubs_simrel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel") + .count(); + long sw_simrel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/software_simrel") + .count(); assertEquals(3432, orgs_simrel); assertEquals(7260, pubs_simrel); @@ -115,20 +153,33 @@ public class SparkDedupTest implements Serializable { @Order(2) public void createMergeRelsTest() throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateMergeRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); - parser.parseArgument(new String[]{ - "-i", testGraphBasePath, - "-asi", testActionSetId, - "-la", "lookupurl", - "-w", testOutputBasePath}); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateMergeRels.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + parser.parseArgument( + new String[] { + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath + }); new SparkCreateMergeRels(parser, spark).run(isLookUpService); - long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count(); - long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count(); - long sw_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel").count(); + long orgs_mergerel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") + .count(); + long pubs_mergerel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .count(); + long sw_mergerel = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") + .count(); assertEquals(1276, orgs_mergerel); assertEquals(1460, pubs_mergerel); @@ -139,20 +190,38 @@ public class SparkDedupTest implements Serializable { @Order(3) public void createDedupRecordTest() throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); - parser.parseArgument(new String[]{ - "-i", testGraphBasePath, - "-asi", testActionSetId, - "-la", "lookupurl", - "-w", testOutputBasePath}); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkCreateDedupRecord.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); + parser.parseArgument( + new String[] { + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath + }); new SparkCreateDedupRecord(parser, spark).run(isLookUpService); - long orgs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count(); - long pubs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count(); - long sw_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord").count(); + long orgs_deduprecord = + jsc.textFile( + testOutputBasePath + + "/" + + testActionSetId + + "/organization_deduprecord") + .count(); + long pubs_deduprecord = + jsc.textFile( + testOutputBasePath + + "/" + + testActionSetId + + "/publication_deduprecord") + .count(); + long sw_deduprecord = + jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord") + .count(); assertEquals(82, orgs_deduprecord); assertEquals(66, pubs_deduprecord); @@ -163,14 +232,17 @@ public class SparkDedupTest implements Serializable { @Order(4) public void updateEntityTest() throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkUpdateEntity.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); - parser.parseArgument(new String[]{ - "-i", testGraphBasePath, - "-w", testOutputBasePath, - "-o", testDedupGraphBasePath - }); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkUpdateEntity.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); + parser.parseArgument( + new String[] { + "-i", testGraphBasePath, + "-w", testOutputBasePath, + "-o", testDedupGraphBasePath + }); new SparkUpdateEntity(parser, spark).run(isLookUpService); @@ -180,19 +252,25 @@ public class SparkDedupTest implements Serializable { long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count(); long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count(); - long mergedOrgs = spark - .read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) - .distinct().count(); + long mergedOrgs = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); - long mergedPubs = spark - .read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) - .distinct().count(); + long mergedPubs = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); assertEquals(831, publications); assertEquals(835, organizations); @@ -200,10 +278,15 @@ public class SparkDedupTest implements Serializable { assertEquals(100, datasource); assertEquals(200, softwares); - long deletedOrgs = jsc.textFile(testDedupGraphBasePath + "/organization") - .filter(this::isDeletedByInference).count(); - long deletedPubs = jsc.textFile(testDedupGraphBasePath + "/publication") - .filter(this::isDeletedByInference).count(); + long deletedOrgs = + jsc.textFile(testDedupGraphBasePath + "/organization") + .filter(this::isDeletedByInference) + .count(); + + long deletedPubs = + jsc.textFile(testDedupGraphBasePath + "/publication") + .filter(this::isDeletedByInference) + .count(); assertEquals(mergedOrgs, deletedOrgs); assertEquals(mergedPubs, deletedPubs); @@ -213,14 +296,17 @@ public class SparkDedupTest implements Serializable { @Order(5) public void propagateRelationTest() throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkPropagateRelation.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); - parser.parseArgument(new String[]{ - "-i", testGraphBasePath, - "-w", testOutputBasePath, - "-o", testDedupGraphBasePath - }); + ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + SparkPropagateRelation.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); + parser.parseArgument( + new String[] { + "-i", testGraphBasePath, + "-w", testOutputBasePath, + "-o", testDedupGraphBasePath + }); new SparkPropagateRelation(parser, spark).run(isLookUpService); @@ -228,22 +314,37 @@ public class SparkDedupTest implements Serializable { assertEquals(826, relations); - //check deletedbyinference - final Dataset mergeRels = spark.read().load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*")).as(Encoders.bean(Relation.class)); - final JavaPairRDD mergedIds = mergeRels - .where("relClass == 'merges'") - .select(mergeRels.col("target")) - .distinct() - .toJavaRDD() - .mapToPair((PairFunction) r -> new Tuple2(r.getString(0), "d")); + // check deletedbyinference + final Dataset mergeRels = + spark.read() + .load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*")) + .as(Encoders.bean(Relation.class)); + final JavaPairRDD mergedIds = + mergeRels + .where("relClass == 'merges'") + .select(mergeRels.col("target")) + .distinct() + .toJavaRDD() + .mapToPair( + (PairFunction) + r -> new Tuple2(r.getString(0), "d")); - JavaRDD toCheck = jsc.textFile(testDedupGraphBasePath + "/relation") - .mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json)) - .join(mergedIds) - .map(t -> t._2()._1()) - .mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json)) - .join(mergedIds) - .map(t -> t._2()._1()); + JavaRDD toCheck = + jsc.textFile(testDedupGraphBasePath + "/relation") + .mapToPair( + json -> + new Tuple2<>( + MapDocumentUtil.getJPathString("$.source", json), + json)) + .join(mergedIds) + .map(t -> t._2()._1()) + .mapToPair( + json -> + new Tuple2<>( + MapDocumentUtil.getJPathString("$.target", json), + json)) + .join(mergedIds) + .map(t -> t._2()._1()); long deletedbyinference = toCheck.filter(this::isDeletedByInference).count(); long updated = toCheck.count(); @@ -258,6 +359,6 @@ public class SparkDedupTest implements Serializable { } public boolean isDeletedByInference(String s) { - return s.contains("\"deletedbyinference\":true"); + return s.contains("\"deletedbyinference\":true"); } -} \ No newline at end of file +} From d772d967aa837a7614ca2a5de51fbe42a33040b9 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 20 Apr 2020 18:53:06 +0200 Subject: [PATCH 7/7] restored changes from master branch --- .../java/eu/dnetlib/dhp/schema/oaf/Oaf.java | 11 + .../eu/dnetlib/dhp/schema/oaf/OafEntity.java | 10 - .../eu/dnetlib/dhp/schema/oaf/Relation.java | 18 +- .../migration/ProtoConverter.java | 2 +- .../relation_action_payload/result.json | 20 +- .../raw/AbstractMdRecordToOafMapper.java | 51 ++- .../raw/MigrateDbEntitiesApplication.java | 59 +++- .../dhp/oa/graph/raw/OafToOafMapper.java | 4 +- .../dhp/oa/graph/raw/OdfToOafMapper.java | 2 +- .../parser/AbstractScholexplorerParser.java | 4 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 42 ++- .../raw/MigrateDbEntitiesApplicationTest.java | 53 ++- .../dnetlib/dhp/oa/graph/raw/odf_dataset.xml | 1 + .../sample/relation/relation_100.json.gz | Bin 3639 -> 3637 bytes .../dhp/provision/scholix/Scholix.java | 4 +- .../eu/dnetlib/dhp/provision/relation.json | 2 +- .../dhp/oa/provision/PrepareRelationsJob.java | 13 +- .../oa/provision/utils/XmlRecordFactory.java | 303 +++++++++--------- 18 files changed, 369 insertions(+), 230 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index 7a7a9a89cd..79138d641e 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -1,14 +1,25 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.List; import java.util.Objects; public abstract class Oaf implements Serializable { + protected List collectedfrom; + private DataInfo dataInfo; private Long lastupdatetimestamp; + public List getCollectedfrom() { + return collectedfrom; + } + + public void setCollectedfrom(List collectedfrom) { + this.collectedfrom = collectedfrom; + } + public DataInfo getDataInfo() { return dataInfo; } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java index 86f4ff616f..6db3b7f745 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java @@ -10,8 +10,6 @@ public abstract class OafEntity extends Oaf implements Serializable { private List originalId; - private List collectedfrom; - private List pid; private String dateofcollection; @@ -38,14 +36,6 @@ public abstract class OafEntity extends Oaf implements Serializable { this.originalId = originalId; } - public List getCollectedfrom() { - return collectedfrom; - } - - public void setCollectedfrom(List collectedfrom) { - this.collectedfrom = collectedfrom; - } - public List getPid() { return pid; } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index 9d211d0586..aaeecb8716 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -18,8 +18,6 @@ public class Relation extends Oaf { private String target; - private List collectedFrom = new ArrayList<>(); - public String getRelType() { return relType; } @@ -60,14 +58,6 @@ public class Relation extends Oaf { this.target = target; } - public List getCollectedFrom() { - return collectedFrom; - } - - public void setCollectedFrom(final List collectedFrom) { - this.collectedFrom = collectedFrom; - } - public void mergeFrom(final Relation r) { checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal"); @@ -77,12 +67,12 @@ public class Relation extends Oaf { Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal"); checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal"); - setCollectedFrom( + setCollectedfrom( Stream.concat( - Optional.ofNullable(getCollectedFrom()) + Optional.ofNullable(getCollectedfrom()) .map(Collection::stream) .orElse(Stream.empty()), - Optional.ofNullable(r.getCollectedFrom()) + Optional.ofNullable(r.getCollectedfrom()) .map(Collection::stream) .orElse(Stream.empty())) .distinct() // relies on KeyValue.equals @@ -103,6 +93,6 @@ public class Relation extends Oaf { @Override public int hashCode() { - return Objects.hash(relType, subRelType, relClass, source, target, collectedFrom); + return Objects.hash(relType, subRelType, relClass, source, target, collectedfrom); } } diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java index c56ded1458..adeffa9fcd 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java @@ -46,7 +46,7 @@ public class ProtoConverter implements Serializable { rel.setRelType(r.getRelType().toString()); rel.setSubRelType(r.getSubRelType().toString()); rel.setRelClass(r.getRelClass()); - rel.setCollectedFrom( + rel.setCollectedfrom( r.getCollectedfromCount() > 0 ? r.getCollectedfromList().stream() .map(kv -> mapKV(kv)) diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json index bc65230a84..36d3fdd272 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json +++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/output/graph/merge_from_and_get/relation/relation_action_payload/result.json @@ -1,10 +1,10 @@ -{"collectedFrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::d0bbea1f5bed5864d1904eb602e608a6"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|OpenstarTs__::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::fc7459b8fed8c0d47947fe04275251c0"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|NARCIS__cris::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::c978e29d3b2ddf4f0c2b6e60d6613426"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::b58bdbe8ae5acead04fc76777d2f8017"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::8de0f5a712997aafe0d794a53e51b75a"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|UnityFVG____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::89bab7c5a227fc27b2b9cadf475a6b71"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::007a4870b31056f89b768cf508e1538e"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|VTTRsInSsCrs::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::735915884eb439d42953372eaf934782"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::9ea9c0996c87e1dc7fc69f94b5ed0010"} -{"collectedFrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747","subRelType":"provision","target":"20|openaire____::c24a458004a31f9687089ea3d249de51"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::d0bbea1f5bed5864d1904eb602e608a6"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|OpenstarTs__::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::fc7459b8fed8c0d47947fe04275251c0"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|NARCIS__cris::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::c978e29d3b2ddf4f0c2b6e60d6613426"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::b58bdbe8ae5acead04fc76777d2f8017"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|MetisRadboud::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::8de0f5a712997aafe0d794a53e51b75a"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|UnityFVG____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::89bab7c5a227fc27b2b9cadf475a6b71"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::007a4870b31056f89b768cf508e1538e"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|VTTRsInSsCrs::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|openaire____::735915884eb439d42953372eaf934782"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":true,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","subRelType":"provision","target":"20|dedup_wf_001::9ea9c0996c87e1dc7fc69f94b5ed0010"} +{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":0,"relClass":"provides","relType":"datasourceOrganization","source":"10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747","subRelType":"provision","target":"20|openaire____::c24a458004a31f9687089ea3d249de51"} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index f1058db385..a7aa600cff 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -1,9 +1,38 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.dataInfo; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.journal; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.keyValue; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; -import eu.dnetlib.dhp.schema.oaf.*; -import java.util.*; +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.GeoLocation; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.OAIProvenance; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Date; +import java.util.HashMap; +import java.util.List; +import java.util.Map; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.DocumentFactory; @@ -29,6 +58,12 @@ public abstract class AbstractMdRecordToOafMapper { qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies"); protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies"); + protected static final Qualifier REPOSITORY_QUALIFIER = + qualifier( + "sysimport:crosswalk:repository", + "sysimport:crosswalk:repository", + "dnet:provenanceActions", + "dnet:provenanceActions"); protected AbstractMdRecordToOafMapper(final Map code2name) { this.code2name = code2name; @@ -55,13 +90,13 @@ public abstract class AbstractMdRecordToOafMapper { final String type = doc.valueOf("//dr:CobjCategory/@type"); final KeyValue collectedFrom = keyValue( - doc.valueOf("//oaf:collectedFrom/@id"), + createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true), doc.valueOf("//oaf:collectedFrom/@name")); final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom : keyValue( - doc.valueOf("//oaf:hostedBy/@id"), + createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), doc.valueOf("//oaf:hostedBy/@name")); final DataInfo info = prepareDataInfo(doc); @@ -154,7 +189,7 @@ public abstract class AbstractMdRecordToOafMapper { r1.setRelClass("isProducedBy"); r1.setSource(docId); r1.setTarget(projectId); - r1.setCollectedFrom(Arrays.asList(collectedFrom)); + r1.setCollectedfrom(Arrays.asList(collectedFrom)); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r1); @@ -165,7 +200,7 @@ public abstract class AbstractMdRecordToOafMapper { r2.setRelClass("produces"); r2.setSource(projectId); r2.setTarget(docId); - r2.setCollectedFrom(Arrays.asList(collectedFrom)); + r2.setCollectedfrom(Arrays.asList(collectedFrom)); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r2); @@ -398,7 +433,7 @@ public abstract class AbstractMdRecordToOafMapper { final Node n = doc.selectSingleNode("//oaf:datainfo"); if (n == null) { - return null; + return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9"); } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 6de7303c35..476e617d78 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -1,11 +1,35 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.asString; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.dataInfo; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.journal; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listKeyValues; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; -import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import java.io.Closeable; import java.io.IOException; import java.sql.Array; @@ -119,7 +143,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); ds.setCollectedfrom( listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname"))); ds.setPid(new ArrayList<>()); ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); ds.setDateoftransformation(null); // Value not returned by the SQL query @@ -185,7 +210,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication p.setOriginalId(Arrays.asList(rs.getString("projectid"))); p.setCollectedfrom( listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname"))); p.setPid(new ArrayList<>()); p.setDateofcollection(asString(rs.getDate("dateofcollection"))); p.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); @@ -240,7 +266,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); o.setCollectedfrom( listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname"))); o.setPid(new ArrayList<>()); o.setDateofcollection(asString(rs.getDate("dateofcollection"))); o.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); @@ -285,7 +312,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final String dsId = createOpenaireId(10, rs.getString("datasource"), true); final List collectedFrom = listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname")); + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname")); final Relation r1 = new Relation(); r1.setRelType("datasourceOrganization"); @@ -293,7 +321,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r1.setRelClass("isProvidedBy"); r1.setSource(dsId); r1.setTarget(orgId); - r1.setCollectedFrom(collectedFrom); + r1.setCollectedfrom(collectedFrom); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); @@ -303,7 +331,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r2.setRelClass("provides"); r2.setSource(orgId); r2.setTarget(dsId); - r2.setCollectedFrom(collectedFrom); + r2.setCollectedfrom(collectedFrom); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); @@ -320,7 +348,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final String projectId = createOpenaireId(40, rs.getString("project"), true); final List collectedFrom = listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname")); + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname")); final Relation r1 = new Relation(); r1.setRelType("projectOrganization"); @@ -328,7 +357,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r1.setRelClass("isParticipant"); r1.setSource(projectId); r1.setTarget(orgId); - r1.setCollectedFrom(collectedFrom); + r1.setCollectedfrom(collectedFrom); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); @@ -338,7 +367,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r2.setRelClass("hasParticipant"); r2.setSource(orgId); r2.setTarget(projectId); - r2.setCollectedFrom(collectedFrom); + r2.setCollectedfrom(collectedFrom); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); @@ -363,6 +392,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication "dnet:provenanceActions"), "0.9"); + final List collectedFrom = + listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE"); + try { if (rs.getString("source_type").equals("context")) { @@ -381,6 +413,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication r.setLastupdatetimestamp(lastUpdateTimestamp); r.setContext(prepareContext(rs.getString("source_id"), info)); r.setDataInfo(info); + r.setCollectedfrom(collectedFrom); return Arrays.asList(r); } else { @@ -395,18 +428,22 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final Relation r2 = new Relation(); if (rs.getString("source_type").equals("project")) { + r1.setCollectedfrom(collectedFrom); r1.setRelType("resultProject"); r1.setSubRelType("outcome"); r1.setRelClass("produces"); + r2.setCollectedfrom(collectedFrom); r2.setRelType("resultProject"); r2.setSubRelType("outcome"); r2.setRelClass("isProducedBy"); } else { + r1.setCollectedfrom(collectedFrom); r1.setRelType("resultResult"); r1.setSubRelType("relationship"); r1.setRelClass("isRelatedTo"); + r2.setCollectedfrom(collectedFrom); r2.setRelType("resultResult"); r2.setSubRelType("relationship"); r2.setRelClass("isRelatedTo"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index e77b1f87fe..6b304c9b0b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -232,7 +232,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { r1.setRelClass("isRelatedTo"); r1.setSource(docId); r1.setTarget(otherId); - r1.setCollectedFrom(Arrays.asList(collectedFrom)); + r1.setCollectedfrom(Arrays.asList(collectedFrom)); r1.setDataInfo(info); r1.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r1); @@ -243,7 +243,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { r2.setRelClass("isRelatedTo"); r2.setSource(otherId); r2.setTarget(docId); - r2.setCollectedFrom(Arrays.asList(collectedFrom)); + r2.setCollectedfrom(Arrays.asList(collectedFrom)); r2.setDataInfo(info); r2.setLastupdatetimestamp(lastUpdateTimestamp); res.add(r2); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 5e64624170..f6fab499bf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -334,7 +334,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { r.setRelClass(relClass); r.setSource(source); r.setTarget(target); - r.setCollectedFrom(Arrays.asList(collectedFrom)); + r.setCollectedfrom(Arrays.asList(collectedFrom)); r.setDataInfo(info); r.setLastupdatetimestamp(lastUpdateTimestamp); return r; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java index bfd5d5c7f4..4d3cb02d68 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java @@ -186,7 +186,7 @@ public abstract class AbstractScholexplorerParser { r.setTarget(targetId); r.setRelType(relationSemantic); r.setRelClass("datacite"); - r.setCollectedFrom(parsedObject.getCollectedfrom()); + r.setCollectedfrom(parsedObject.getCollectedfrom()); r.setDataInfo(di); rels.add(r); r = new DLIRelation(); @@ -195,7 +195,7 @@ public abstract class AbstractScholexplorerParser { r.setTarget(parsedObject.getId()); r.setRelType(inverseRelation); r.setRelClass("datacite"); - r.setCollectedFrom(parsedObject.getCollectedfrom()); + r.setCollectedfrom(parsedObject.getCollectedfrom()); r.setDateOfCollection(dateOfCollection); rels.add(r); if ("unknown".equalsIgnoreCase(relatedType)) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 6af314d76e..b09c5d6385 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -1,11 +1,16 @@ package eu.dnetlib.dhp.oa.graph.raw; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertTrue; import static org.mockito.ArgumentMatchers.anyString; import static org.mockito.Mockito.when; -import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Software; import java.io.IOException; import java.util.List; import java.util.Map; @@ -43,6 +48,7 @@ public class MappersTest { final Relation r2 = (Relation) list.get(2); assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); assertTrue(p.getAuthor().size() > 0); assertTrue(p.getSubject().size() > 0); @@ -50,13 +56,24 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); assertValidId(r1.getSource()); + assertValidId(r1.getTarget()); assertValidId(r2.getSource()); + assertValidId(r2.getTarget()); + assertValidId(r1.getCollectedfrom().get(0).getKey()); + assertValidId(r2.getCollectedfrom().get(0).getKey()); + assertNotNull(r1.getDataInfo()); + assertNotNull(r2.getDataInfo()); + assertNotNull(r1.getDataInfo().getTrust()); + assertNotNull(r2.getDataInfo().getTrust()); assertEquals(r1.getSource(), r2.getTarget()); assertEquals(r2.getSource(), r1.getTarget()); assertTrue(StringUtils.isNotBlank(r1.getRelClass())); assertTrue(StringUtils.isNotBlank(r2.getRelClass())); assertTrue(StringUtils.isNotBlank(r1.getRelType())); assertTrue(StringUtils.isNotBlank(r2.getRelType())); + + // System.out.println(new ObjectMapper().writeValueAsString(r1)); + // System.out.println(new ObjectMapper().writeValueAsString(r2)); } @Test @@ -65,15 +82,35 @@ public class MappersTest { final List list = new OdfToOafMapper(code2name).processMdRecord(xml); - assertEquals(1, list.size()); + assertEquals(3, list.size()); assertTrue(list.get(0) instanceof Dataset); + assertTrue(list.get(1) instanceof Relation); + assertTrue(list.get(2) instanceof Relation); final Dataset d = (Dataset) list.get(0); + final Relation r1 = (Relation) list.get(1); + final Relation r2 = (Relation) list.get(2); assertValidId(d.getId()); + assertValidId(d.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); assertTrue(d.getAuthor().size() > 0); assertTrue(d.getSubject().size() > 0); + + assertValidId(r1.getSource()); + assertValidId(r1.getTarget()); + assertValidId(r2.getSource()); + assertValidId(r2.getTarget()); + assertNotNull(r1.getDataInfo()); + assertNotNull(r2.getDataInfo()); + assertNotNull(r1.getDataInfo().getTrust()); + assertNotNull(r2.getDataInfo().getTrust()); + assertEquals(r1.getSource(), r2.getTarget()); + assertEquals(r2.getSource(), r1.getTarget()); + assertTrue(StringUtils.isNotBlank(r1.getRelClass())); + assertTrue(StringUtils.isNotBlank(r2.getRelClass())); + assertTrue(StringUtils.isNotBlank(r1.getRelType())); + assertTrue(StringUtils.isNotBlank(r2.getRelType())); } @Test @@ -88,6 +125,7 @@ public class MappersTest { final Software s = (Software) list.get(0); assertValidId(s.getId()); + assertValidId(s.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); assertTrue(s.getAuthor().size() > 0); assertTrue(s.getSubject().size() > 0); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 3c7bc684d3..b88731ba24 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -1,10 +1,17 @@ package eu.dnetlib.dhp.oa.graph.raw; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Result; import java.io.IOException; import java.sql.Array; import java.sql.Date; @@ -13,6 +20,7 @@ import java.sql.SQLException; import java.util.List; import java.util.Objects; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; @@ -42,14 +50,13 @@ public class MigrateDbEntitiesApplicationTest { final Datasource ds = (Datasource) list.get(0); assertValidId(ds.getId()); + assertValidId(ds.getCollectedfrom().get(0).getKey()); assertEquals(ds.getOfficialname().getValue(), getValueAsString("officialname", fields)); assertEquals(ds.getEnglishname().getValue(), getValueAsString("englishname", fields)); assertEquals(ds.getContactemail().getValue(), getValueAsString("contactemail", fields)); assertEquals(ds.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); assertEquals( ds.getNamespaceprefix().getValue(), getValueAsString("namespaceprefix", fields)); - assertEquals( - ds.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); assertEquals( ds.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); @@ -65,10 +72,9 @@ public class MigrateDbEntitiesApplicationTest { final Project p = (Project) list.get(0); assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); assertEquals(p.getAcronym().getValue(), getValueAsString("acronym", fields)); assertEquals(p.getTitle().getValue(), getValueAsString("title", fields)); - assertEquals( - p.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); assertEquals( p.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); @@ -86,6 +92,7 @@ public class MigrateDbEntitiesApplicationTest { final Organization o = (Organization) list.get(0); assertValidId(o.getId()); + assertValidId(o.getCollectedfrom().get(0).getKey()); assertEquals(o.getLegalshortname().getValue(), getValueAsString("legalshortname", fields)); assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields)); assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); @@ -98,8 +105,6 @@ public class MigrateDbEntitiesApplicationTest { assertEquals( o.getCountry().getSchemename(), getValueAsString("country", fields).split("@@@")[3]); - assertEquals( - o.getCollectedfrom().get(0).getKey(), getValueAsString("collectedfromid", fields)); assertEquals( o.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); @@ -137,6 +142,8 @@ public class MigrateDbEntitiesApplicationTest { assertValidId(r2.getSource()); assertEquals(r1.getSource(), r2.getTarget()); assertEquals(r2.getSource(), r1.getTarget()); + assertValidId(r1.getCollectedfrom().get(0).getKey()); + assertValidId(r2.getCollectedfrom().get(0).getKey()); } @Test @@ -146,7 +153,12 @@ public class MigrateDbEntitiesApplicationTest { final List list = app.processClaims(rs); assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Result); + final Result r = (Result) list.get(0); + verifyMocks(fields); + + assertValidId(r.getCollectedfrom().get(0).getKey()); } @Test @@ -157,6 +169,33 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(2, list.size()); verifyMocks(fields); + + assertTrue(list.get(0) instanceof Relation); + assertTrue(list.get(1) instanceof Relation); + + final Relation r1 = (Relation) list.get(0); + final Relation r2 = (Relation) list.get(1); + + assertValidId(r1.getSource()); + assertValidId(r1.getTarget()); + assertValidId(r2.getSource()); + assertValidId(r2.getTarget()); + assertNotNull(r1.getDataInfo()); + assertNotNull(r2.getDataInfo()); + assertNotNull(r1.getDataInfo().getTrust()); + assertNotNull(r2.getDataInfo().getTrust()); + assertEquals(r1.getSource(), r2.getTarget()); + assertEquals(r2.getSource(), r1.getTarget()); + assertTrue(StringUtils.isNotBlank(r1.getRelClass())); + assertTrue(StringUtils.isNotBlank(r2.getRelClass())); + assertTrue(StringUtils.isNotBlank(r1.getRelType())); + assertTrue(StringUtils.isNotBlank(r2.getRelType())); + + assertValidId(r1.getCollectedfrom().get(0).getKey()); + assertValidId(r2.getCollectedfrom().get(0).getKey()); + + // System.out.println(new ObjectMapper().writeValueAsString(r1)); + // System.out.println(new ObjectMapper().writeValueAsString(r2)); } private List prepareMocks(final String jsonFile) throws IOException, SQLException { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml index 0c36e8686f..94dc802fac 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml @@ -87,6 +87,7 @@ und + corda_______::226852 S79;np!`GDvxyhN($ZdpVq!`P& z+~+ViYpymw)$jLs{Qmqr9-qhi@qRqtuR|n;oxKQ|<;cY1^T6YtuRGGq2_!EMM4*sf zOsnGr6s+zQ)5ZaV515VRZ5D!Wko|l%E)3aktx4AuQoMXe#~=j=*SVyb-7qIL!%BPw znX|K4mzyogP&DG%b*C0Y&J%P%3ruO`yZ`ma!QOja?Sq6~n^D>3p%|n5Wh{Ce2^#mP zra!*f|8U%W_PT$|cj3K9ljG!{kNv#^rx}o|6E!gOAp&(!H9;I#M>;w=g@tZT^CyfC zt`fG0KE|V~R$-Yjs~M||qmBh-ECoWkh)d7ArcKT8=yOKX%uFMsORV0$6k zaW)|4bS^ry;`{O;dYiJQPnVmRXr72fx9q+0Dr4O8FK^JCc!*|fF!t!(u=wZwGdMRMIQ+CH=}j8=;a4fNhyZ~`*&kjXZ6 zxP80pSJ#?>S3`??4oZ5VT8CG>bKM3q)Y>vLknFEuOKb;eWlmSiXW}NqwnciI19z16 zS4EV7mT3B<)8T50G}Q^VSX!r1C$b!J>cgb3#=o=yuwOR6<{;RqyNab&Pyv#A3VYx3 zDHL4R(F@B}>M}kCCOi>U`ha0p^~17TEb<1K{{k>QRzY(Svu_mjM0E6y+R%#~JgL~& zm1=Q;DCWX#Uy%NKb}ZojBfz%fuaA=|J~NP$$BbTncXmdZz4xbK2P{8F6B*jb{n3g* zxkhx(P6SvUwYST`fq7li#JxQN0LIS>s%j 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zAEkZG$KbKf){yoXA1Yenk(JRGcMxQR&$ec2UibD$KZ9EJQkM5PHtGb5;UG@ zK(QCtJ;nwBe`_m@0Yy*jrgBDP0QslkYgd`+IfO1cQTRtfQYhiBm?qx%H zaiyBg{IC za>DVe3UMWu6(-e)2@*EEs6#yfJ*zj9PE>(sbW6YD(3Vi0j`kx#_sDD!E>iZ1eDyt} zNnyO=UaI?E&CxF4W226OJv>*z*UnewUI6lW$6suw+3aF&{bX>(_3q`!J?~y?M&-dq taWxjm&MH`kc`@W6*68G-PkwopAJ(cI 0) s.setPublicationDate(scholixSummary.getDate().get(0)); s.setLinkprovider( - rel.getCollectedFrom().stream() + rel.getCollectedfrom().stream() .map( cf -> new ScholixEntityId( @@ -73,7 +73,7 @@ public class Scholix implements Serializable { if (scholixSummary.getDate() != null && scholixSummary.getDate().size() > 0) s.setPublicationDate(scholixSummary.getDate().get(0)); s.setLinkprovider( - rel.getCollectedFrom().stream() + rel.getCollectedfrom().stream() .map( cf -> new ScholixEntityId( diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json index e029ddf625..3cca6e370f 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/relation.json @@ -1 +1 @@ -{"dataInfo":{"invisible":false,"inferred":null,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":null},"lastupdatetimestamp":null,"relType":"IsReferencedBy","subRelType":null,"relClass":"datacite","source":"50|dedup_______::4f00e4f0e82bb4cbb35261478e55568e","target":"60|97519e00ee2cddfa1f5bcb5220429b8f","collectedFrom":[{"key":"dli_________::europe_pmc__","value":"Europe PMC","dataInfo":null}]} \ No newline at end of file +{"dataInfo":{"invisible":false,"inferred":null,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":null},"lastupdatetimestamp":null,"relType":"IsReferencedBy","subRelType":null,"relClass":"datacite","source":"50|dedup_______::4f00e4f0e82bb4cbb35261478e55568e","target":"60|97519e00ee2cddfa1f5bcb5220429b8f","collectedfrom":[{"key":"dli_________::europe_pmc__","value":"Europe PMC","dataInfo":null}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java index a6c261ec72..b663a8082e 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java @@ -95,7 +95,18 @@ public class PrepareRelationsJob { readPathRelation(spark, inputRelationsPath) .filter( (FilterFunction) - value -> value.getDataInfo().getDeletedbyinference() == false) + r -> { + try { + return r != null + && r.getDataInfo() != null + && !r.getDataInfo().getDeletedbyinference(); + } catch (NullPointerException e) { + log.info( + "invalid NPE '{}'", + OBJECT_MAPPER.writeValueAsString(r)); + throw e; + } + }) .groupByKey( (MapFunction) value -> value.getSource(), Encoders.STRING()) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 3455cb5f3b..874c34c090 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -22,6 +22,7 @@ import java.io.IOException; import java.io.Serializable; import java.io.StringReader; import java.io.StringWriter; +import java.util.ArrayList; import java.util.List; import java.util.Map; import java.util.Set; @@ -41,6 +42,7 @@ import org.dom4j.io.XMLWriter; public class XmlRecordFactory implements Serializable { + public static final String REL_SUBTYPE_DEDUP = "dedup"; private Map accumulators; private Set specialDatasourceTypes; @@ -91,7 +93,14 @@ public class XmlRecordFactory implements Serializable { // rels has to be processed before the contexts because they enrich the contextMap with // the // funding info. - final List relations = listRelations(je, templateFactory, contexts); + final List relations = + je.getLinks().stream() + .filter( + t -> + !REL_SUBTYPE_DEDUP.equalsIgnoreCase( + t.getRelation().getSubRelType())) + .map(link -> mapRelation(link, templateFactory, contexts)) + .collect(Collectors.toCollection(ArrayList::new)); final String mainType = ModelSupport.getMainType(type); metadata.addAll(buildContexts(mainType, contexts)); @@ -102,7 +111,7 @@ public class XmlRecordFactory implements Serializable { mainType, metadata, relations, - listChildren(entity, je.getEntity().getType(), templateFactory), + listChildren(entity, je, templateFactory), listExtraInfo(entity)); return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent); @@ -919,171 +928,149 @@ public class XmlRecordFactory implements Serializable { metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", dsType)); } - private Qualifier getBestAccessright(final Result r) { - Qualifier bestAccessRight = new Qualifier(); - bestAccessRight.setClassid("UNKNOWN"); - bestAccessRight.setClassname("not available"); - bestAccessRight.setSchemeid("dnet:access_modes"); - bestAccessRight.setSchemename("dnet:access_modes"); + private String mapRelation(Tuple2 link, TemplateFactory templateFactory, Set contexts) { + final Relation rel = link.getRelation(); + final RelatedEntity re = link.getRelatedEntity(); + final String targetType = link.getRelatedEntity().getType(); - final LicenseComparator lc = new LicenseComparator(); - for (final Instance instance : r.getInstance()) { - if (lc.compare(bestAccessRight, instance.getAccessright()) > 0) { - bestAccessRight = instance.getAccessright(); - } + final List metadata = Lists.newArrayList(); + switch (EntityType.valueOf(targetType)) { + case publication: + case dataset: + case otherresearchproduct: + case software: + if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) { + metadata.add( + XmlSerializationUtils.mapStructuredProperty("title", re.getTitle())); + } + if (isNotBlank(re.getDateofacceptance())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "dateofacceptance", re.getDateofacceptance())); + } + if (isNotBlank(re.getPublisher())) { + metadata.add( + XmlSerializationUtils.asXmlElement("publisher", re.getPublisher())); + } + if (isNotBlank(re.getCodeRepositoryUrl())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "coderepositoryurl", re.getCodeRepositoryUrl())); + } + if (re.getResulttype() != null & re.getResulttype().isBlank()) { + metadata.add( + XmlSerializationUtils.mapQualifier("resulttype", re.getResulttype())); + } + if (re.getCollectedfrom() != null) { + metadata.addAll( + re.getCollectedfrom().stream() + .map( + kv -> + XmlSerializationUtils.mapKeyValue( + "collectedfrom", kv)) + .collect(Collectors.toList())); + } + if (re.getPid() != null) { + metadata.addAll( + re.getPid().stream() + .map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p)) + .collect(Collectors.toList())); + } + break; + case datasource: + if (isNotBlank(re.getOfficialname())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "officialname", re.getOfficialname())); + } + if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) { + mapDatasourceType(metadata, re.getDatasourcetype()); + } + if (re.getOpenairecompatibility() != null + & !re.getOpenairecompatibility().isBlank()) { + metadata.add( + XmlSerializationUtils.mapQualifier( + "openairecompatibility", re.getOpenairecompatibility())); + } + break; + case organization: + if (isNotBlank(re.getLegalname())) { + metadata.add( + XmlSerializationUtils.asXmlElement("legalname", re.getLegalname())); + } + if (isNotBlank(re.getLegalshortname())) { + metadata.add( + XmlSerializationUtils.asXmlElement( + "legalshortname", re.getLegalshortname())); + } + if (re.getCountry() != null & !re.getCountry().isBlank()) { + metadata.add(XmlSerializationUtils.mapQualifier("country", re.getCountry())); + } + break; + case project: + if (isNotBlank(re.getProjectTitle())) { + metadata.add(XmlSerializationUtils.asXmlElement("title", re.getProjectTitle())); + } + if (isNotBlank(re.getCode())) { + metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode())); + } + if (isNotBlank(re.getAcronym())) { + metadata.add(XmlSerializationUtils.asXmlElement("acronym", re.getAcronym())); + } + if (re.getContracttype() != null & !re.getContracttype().isBlank()) { + metadata.add( + XmlSerializationUtils.mapQualifier( + "contracttype", re.getContracttype())); + } + if (re.getFundingtree() != null & contexts != null) { + metadata.addAll( + re.getFundingtree().stream() + .peek(ft -> fillContextMap(ft, contexts)) + .map(ft -> getRelFundingTree(ft)) + .collect(Collectors.toList())); + } + break; + default: + throw new IllegalArgumentException("invalid target type: " + targetType); } - return bestAccessRight; - } + final DataInfo info = rel.getDataInfo(); + final String scheme = ModelSupport.getScheme(re.getType(), targetType); - private List listRelations( - final JoinedEntity je, TemplateFactory templateFactory, final Set contexts) { - final List rels = Lists.newArrayList(); - - for (final Tuple2 link : je.getLinks()) { - - final Relation rel = link.getRelation(); - final RelatedEntity re = link.getRelatedEntity(); - final String targetType = link.getRelatedEntity().getType(); - - final List metadata = Lists.newArrayList(); - switch (EntityType.valueOf(targetType)) { - case publication: - case dataset: - case otherresearchproduct: - case software: - if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) { - metadata.add( - XmlSerializationUtils.mapStructuredProperty( - "title", re.getTitle())); - } - if (isNotBlank(re.getDateofacceptance())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "dateofacceptance", re.getDateofacceptance())); - } - if (isNotBlank(re.getPublisher())) { - metadata.add( - XmlSerializationUtils.asXmlElement("publisher", re.getPublisher())); - } - if (isNotBlank(re.getCodeRepositoryUrl())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "coderepositoryurl", re.getCodeRepositoryUrl())); - } - if (re.getResulttype() != null & re.getResulttype().isBlank()) { - metadata.add( - XmlSerializationUtils.mapQualifier( - "resulttype", re.getResulttype())); - } - if (re.getCollectedfrom() != null) { - metadata.addAll( - re.getCollectedfrom().stream() - .map( - kv -> - XmlSerializationUtils.mapKeyValue( - "collectedfrom", kv)) - .collect(Collectors.toList())); - } - if (re.getPid() != null) { - metadata.addAll( - re.getPid().stream() - .map( - p -> - XmlSerializationUtils.mapStructuredProperty( - "pid", p)) - .collect(Collectors.toList())); - } - break; - case datasource: - if (isNotBlank(re.getOfficialname())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "officialname", re.getOfficialname())); - } - if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) { - mapDatasourceType(metadata, re.getDatasourcetype()); - } - if (re.getOpenairecompatibility() != null - & !re.getOpenairecompatibility().isBlank()) { - metadata.add( - XmlSerializationUtils.mapQualifier( - "openairecompatibility", re.getOpenairecompatibility())); - } - break; - case organization: - if (isNotBlank(re.getLegalname())) { - metadata.add( - XmlSerializationUtils.asXmlElement("legalname", re.getLegalname())); - } - if (isNotBlank(re.getLegalshortname())) { - metadata.add( - XmlSerializationUtils.asXmlElement( - "legalshortname", re.getLegalshortname())); - } - if (re.getCountry() != null & !re.getCountry().isBlank()) { - metadata.add( - XmlSerializationUtils.mapQualifier("country", re.getCountry())); - } - break; - case project: - if (isNotBlank(re.getProjectTitle())) { - metadata.add( - XmlSerializationUtils.asXmlElement("title", re.getProjectTitle())); - } - if (isNotBlank(re.getCode())) { - metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode())); - } - if (isNotBlank(re.getAcronym())) { - metadata.add( - XmlSerializationUtils.asXmlElement("acronym", re.getAcronym())); - } - if (re.getContracttype() != null & !re.getContracttype().isBlank()) { - metadata.add( - XmlSerializationUtils.mapQualifier( - "contracttype", re.getContracttype())); - } - if (re.getFundingtree() != null) { - metadata.addAll( - re.getFundingtree().stream() - .peek(ft -> fillContextMap(ft, contexts)) - .map(ft -> getRelFundingTree(ft)) - .collect(Collectors.toList())); - } - break; - default: - throw new IllegalArgumentException("invalid target type: " + targetType); - } - final DataInfo info = rel.getDataInfo(); - final String scheme = ModelSupport.getScheme(re.getType(), targetType); - - if (StringUtils.isBlank(scheme)) { - throw new IllegalArgumentException( - String.format("missing scheme for: <%s - %s>", re.getType(), targetType)); - } - - final String accumulatorName = - getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass()); - if (accumulators.containsKey(accumulatorName)) { - accumulators.get(accumulatorName).add(1); - } - - rels.add( - templateFactory.getRel( - targetType, - rel.getTarget(), - Sets.newHashSet(metadata), - rel.getRelClass(), - scheme, - info)); + if (StringUtils.isBlank(scheme)) { + throw new IllegalArgumentException( + String.format("missing scheme for: <%s - %s>", re.getType(), targetType)); } - return rels; + + final String accumulatorName = + getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass()); + if (accumulators.containsKey(accumulatorName)) { + accumulators.get(accumulatorName).add(1); + } + + return templateFactory.getRel( + targetType, + rel.getTarget(), + Sets.newHashSet(metadata), + rel.getRelClass(), + scheme, + info); } private List listChildren( - final OafEntity entity, String type, TemplateFactory templateFactory) { + final OafEntity entity, JoinedEntity je, TemplateFactory templateFactory) { final List children = Lists.newArrayList(); - EntityType entityType = EntityType.valueOf(type); + EntityType entityType = EntityType.valueOf(je.getEntity().getType()); + + children.addAll( + je.getLinks().stream() + .filter( + link -> + REL_SUBTYPE_DEDUP.equalsIgnoreCase( + link.getRelation().getSubRelType())) + .map(link -> mapRelation(link, templateFactory, null)) + .collect(Collectors.toCollection(ArrayList::new))); + if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) { final List instances = ((Result) entity).getInstance(); if (instances != null) {