From 418cf94642bc763e13b7e81aced14415072722d7 Mon Sep 17 00:00:00 2001 From: miconis Date: Fri, 17 Apr 2020 10:40:21 +0200 Subject: [PATCH 01/19] 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 4e012293b..32b01679f 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 880e917ce..d0098e7e2 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 02/19] 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 d0098e7e2..bcc5ddeaa 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 000000000..532900506 --- /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" : "$.resulttype.classid" + } + ], + "blacklists" : {}, + "synonyms" : {} + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json new file mode 100644 index 000000000..76e656743 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json @@ -0,0 +1,118 @@ +{ + "wf" : { + "threshold" : "0.99", + "dedupRun" : "001", + "entityType" : "result", + "subEntityType" : "resulttype", + "subEntityValue" : "otherresearchproduct", + "orderField" : "title", + "queueMaxSize" : "2000", + "groupMaxSize" : "100", + "maxChildren" : "100", + "slidingWindowSize" : "200", + "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ], + "includeChildren" : "true" + }, + "pace" : { + "clustering" : [ + { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} }, + { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } }, + { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } } + ], + "decisionTree" : { + "start" : { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.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 000000000..815dd7a57 --- /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 e69de29bb..f54cbf071 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": {"deletedbyinference": false, 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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 9a4871223..42d3f0b69 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 03/19] 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 da16e6dff..1c957c9e0 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 c2b1fc9c2..8e90d2a1f 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 bcc5ddeaa..01cbf0489 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 478a958f094396d7081b84cab69696a845f64cf9 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 20 Apr 2020 09:15:27 +0200 Subject: [PATCH 04/19] tests --- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 160 +++++++++++------- .../dnetlib/dhp/oa/graph/raw/odf_dataset.xml | 1 + 2 files changed, 99 insertions(+), 62 deletions(-) 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 6af314d76..11228f426 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 @@ -1,14 +1,15 @@ 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 java.io.IOException; import java.util.List; import java.util.Map; + import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; @@ -17,86 +18,121 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; +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; + @ExtendWith(MockitoExtension.class) public class MappersTest { - @Mock private Map code2name; + @Mock + private Map code2name; - @BeforeEach - public void setUp() throws Exception { - when(code2name.get(anyString())).thenAnswer(invocation -> invocation.getArgument(0)); - } + @BeforeEach + public void setUp() throws Exception { + when(code2name.get(anyString())).thenAnswer(invocation -> invocation.getArgument(0)); + } - @Test - void testPublication() throws IOException { - final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml")); + @Test + void testPublication() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml")); - final List list = new OafToOafMapper(code2name).processMdRecord(xml); + final List list = new OafToOafMapper(code2name).processMdRecord(xml); - assertEquals(3, list.size()); - assertTrue(list.get(0) instanceof Publication); - assertTrue(list.get(1) instanceof Relation); - assertTrue(list.get(2) instanceof Relation); + assertEquals(3, list.size()); + assertTrue(list.get(0) instanceof Publication); + assertTrue(list.get(1) instanceof Relation); + assertTrue(list.get(2) instanceof Relation); - final Publication p = (Publication) list.get(0); - final Relation r1 = (Relation) list.get(1); - final Relation r2 = (Relation) list.get(2); + final Publication p = (Publication) list.get(0); + final Relation r1 = (Relation) list.get(1); + final Relation r2 = (Relation) list.get(2); - assertValidId(p.getId()); - assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); - assertTrue(p.getAuthor().size() > 0); - assertTrue(p.getSubject().size() > 0); - assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); - assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); + assertValidId(p.getId()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertTrue(p.getAuthor().size() > 0); + assertTrue(p.getSubject().size() > 0); + assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); + assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); - assertValidId(r1.getSource()); - assertValidId(r2.getSource()); - 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.getSource()); + assertValidId(r2.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 - void testDataset() throws IOException { - final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml")); + // System.out.println(new ObjectMapper().writeValueAsString(r1)); + // System.out.println(new ObjectMapper().writeValueAsString(r2)); + } - final List list = new OdfToOafMapper(code2name).processMdRecord(xml); + @Test + void testDataset() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml")); - assertEquals(1, list.size()); - assertTrue(list.get(0) instanceof Dataset); + final List list = new OdfToOafMapper(code2name).processMdRecord(xml); - final Dataset d = (Dataset) list.get(0); + assertEquals(3, list.size()); + assertTrue(list.get(0) instanceof Dataset); + assertTrue(list.get(1) instanceof Relation); + assertTrue(list.get(2) instanceof Relation); - assertValidId(d.getId()); - assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); - assertTrue(d.getAuthor().size() > 0); - assertTrue(d.getSubject().size() > 0); - } + final Dataset d = (Dataset) list.get(0); + final Relation r1 = (Relation) list.get(1); + final Relation r2 = (Relation) list.get(2); - @Test - void testSoftware() throws IOException { - final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml")); + assertValidId(d.getId()); + assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); + assertTrue(d.getAuthor().size() > 0); + assertTrue(d.getSubject().size() > 0); - final List list = new OdfToOafMapper(code2name).processMdRecord(xml); + assertValidId(r1.getSource()); + assertValidId(r2.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())); + } - assertEquals(1, list.size()); - assertTrue(list.get(0) instanceof Software); + @Test + void testSoftware() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml")); - final Software s = (Software) list.get(0); + final List list = new OdfToOafMapper(code2name).processMdRecord(xml); - assertValidId(s.getId()); - assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); - assertTrue(s.getAuthor().size() > 0); - assertTrue(s.getSubject().size() > 0); - } + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Software); - private void assertValidId(final String id) { - assertEquals(49, id.length()); - assertEquals('|', id.charAt(2)); - assertEquals(':', id.charAt(15)); - assertEquals(':', id.charAt(16)); - } + final Software s = (Software) list.get(0); + + assertValidId(s.getId()); + assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); + assertTrue(s.getAuthor().size() > 0); + assertTrue(s.getSubject().size() > 0); + } + + private void assertValidId(final String id) { + assertEquals(49, id.length()); + assertEquals('|', id.charAt(2)); + assertEquals(':', id.charAt(15)); + assertEquals(':', id.charAt(16)); + } } 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 0c36e8686..94dc802fa 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 Date: Mon, 20 Apr 2020 09:31:14 +0200 Subject: [PATCH 05/19] tests --- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 4 +- .../raw/MigrateDbEntitiesApplicationTest.java | 511 +++++++++--------- 2 files changed, 268 insertions(+), 247 deletions(-) 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 11228f426..3fc1d72d6 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 @@ -58,7 +58,7 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); assertValidId(r1.getSource()); - assertValidId(r2.getTarget()); + assertValidId(r1.getTarget()); assertValidId(r2.getSource()); assertValidId(r2.getTarget()); assertNotNull(r1.getDataInfo()); @@ -97,7 +97,7 @@ public class MappersTest { assertTrue(d.getSubject().size() > 0); assertValidId(r1.getSource()); - assertValidId(r2.getTarget()); + assertValidId(r1.getTarget()); assertValidId(r2.getSource()); assertValidId(r2.getTarget()); assertNotNull(r1.getDataInfo()); 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 3c7bc684d..69a13fb81 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 +1,9 @@ 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 java.io.IOException; import java.sql.Array; import java.sql.Date; @@ -12,7 +11,9 @@ import java.sql.ResultSet; 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; @@ -20,294 +21,314 @@ import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; +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; + @ExtendWith(MockitoExtension.class) public class MigrateDbEntitiesApplicationTest { - private MigrateDbEntitiesApplication app; + private MigrateDbEntitiesApplication app; - @Mock private ResultSet rs; + @Mock + private ResultSet rs; - @BeforeEach - public void setUp() { - this.app = new MigrateDbEntitiesApplication(); - } + @BeforeEach + public void setUp() { + this.app = new MigrateDbEntitiesApplication(); + } - @Test - public void testProcessDatasource() throws Exception { - final List fields = prepareMocks("datasources_resultset_entry.json"); + @Test + public void testProcessDatasource() throws Exception { + final List fields = prepareMocks("datasources_resultset_entry.json"); - final List list = app.processDatasource(rs); - assertEquals(1, list.size()); - verifyMocks(fields); + final List list = app.processDatasource(rs); + assertEquals(1, list.size()); + verifyMocks(fields); - final Datasource ds = (Datasource) list.get(0); - assertValidId(ds.getId()); - 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)); - } + final Datasource ds = (Datasource) list.get(0); + assertValidId(ds.getId()); + 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)); + } - @Test - public void testProcessProject() throws Exception { - final List fields = prepareMocks("projects_resultset_entry.json"); + @Test + public void testProcessProject() throws Exception { + final List fields = prepareMocks("projects_resultset_entry.json"); - final List list = app.processProject(rs); - assertEquals(1, list.size()); - verifyMocks(fields); + final List list = app.processProject(rs); + assertEquals(1, list.size()); + verifyMocks(fields); - final Project p = (Project) list.get(0); - assertValidId(p.getId()); - 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)); - } + final Project p = (Project) list.get(0); + assertValidId(p.getId()); + 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)); + } - @Test - public void testProcessOrganization() throws Exception { - final List fields = prepareMocks("organizations_resultset_entry.json"); + @Test + public void testProcessOrganization() throws Exception { + final List fields = prepareMocks("organizations_resultset_entry.json"); - final List list = app.processOrganization(rs); + final List list = app.processOrganization(rs); - assertEquals(1, list.size()); + assertEquals(1, list.size()); - verifyMocks(fields); + verifyMocks(fields); - final Organization o = (Organization) list.get(0); - assertValidId(o.getId()); - assertEquals(o.getLegalshortname().getValue(), getValueAsString("legalshortname", fields)); - assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields)); - assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); - assertEquals( - o.getCountry().getClassid(), getValueAsString("country", fields).split("@@@")[0]); - assertEquals( - o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]); - assertEquals( - o.getCountry().getSchemeid(), getValueAsString("country", fields).split("@@@")[2]); - 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)); - } + final Organization o = (Organization) list.get(0); + assertValidId(o.getId()); + assertEquals(o.getLegalshortname().getValue(), getValueAsString("legalshortname", fields)); + assertEquals(o.getLegalname().getValue(), getValueAsString("legalname", fields)); + assertEquals(o.getWebsiteurl().getValue(), getValueAsString("websiteurl", fields)); + assertEquals(o.getCountry().getClassid(), getValueAsString("country", fields).split("@@@")[0]); + assertEquals(o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]); + assertEquals(o.getCountry().getSchemeid(), getValueAsString("country", fields).split("@@@")[2]); + 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)); + } - @Test - public void testProcessDatasourceOrganization() throws Exception { - final List fields = prepareMocks("datasourceorganization_resultset_entry.json"); + @Test + public void testProcessDatasourceOrganization() throws Exception { + final List fields = prepareMocks("datasourceorganization_resultset_entry.json"); - final List list = app.processDatasourceOrganization(rs); + final List list = app.processDatasourceOrganization(rs); - assertEquals(2, list.size()); - verifyMocks(fields); + assertEquals(2, list.size()); + verifyMocks(fields); - final Relation r1 = (Relation) list.get(0); - final Relation r2 = (Relation) list.get(1); - assertValidId(r1.getSource()); - assertValidId(r2.getSource()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - } + final Relation r1 = (Relation) list.get(0); + final Relation r2 = (Relation) list.get(1); + assertValidId(r1.getSource()); + assertValidId(r2.getSource()); + assertEquals(r1.getSource(), r2.getTarget()); + assertEquals(r2.getSource(), r1.getTarget()); + } - @Test - public void testProcessProjectOrganization() throws Exception { - final List fields = prepareMocks("projectorganization_resultset_entry.json"); + @Test + public void testProcessProjectOrganization() throws Exception { + final List fields = prepareMocks("projectorganization_resultset_entry.json"); - final List list = app.processProjectOrganization(rs); + final List list = app.processProjectOrganization(rs); - assertEquals(2, list.size()); - verifyMocks(fields); + assertEquals(2, list.size()); + verifyMocks(fields); - final Relation r1 = (Relation) list.get(0); - final Relation r2 = (Relation) list.get(1); - assertValidId(r1.getSource()); - assertValidId(r2.getSource()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - } + final Relation r1 = (Relation) list.get(0); + final Relation r2 = (Relation) list.get(1); + assertValidId(r1.getSource()); + assertValidId(r2.getSource()); + assertEquals(r1.getSource(), r2.getTarget()); + assertEquals(r2.getSource(), r1.getTarget()); + } - @Test - public void testProcessClaims_context() throws Exception { - final List fields = prepareMocks("claimscontext_resultset_entry.json"); + @Test + public void testProcessClaims_context() throws Exception { + final List fields = prepareMocks("claimscontext_resultset_entry.json"); - final List list = app.processClaims(rs); + final List list = app.processClaims(rs); - assertEquals(1, list.size()); - verifyMocks(fields); - } + assertEquals(1, list.size()); - @Test - public void testProcessClaims_rels() throws Exception { - final List fields = prepareMocks("claimsrel_resultset_entry.json"); + verifyMocks(fields); + } - final List list = app.processClaims(rs); + @Test + public void testProcessClaims_rels() throws Exception { + final List fields = prepareMocks("claimsrel_resultset_entry.json"); - assertEquals(2, list.size()); - verifyMocks(fields); - } + final List list = app.processClaims(rs); - private List prepareMocks(final String jsonFile) throws IOException, SQLException { - final String json = IOUtils.toString(getClass().getResourceAsStream(jsonFile)); - final ObjectMapper mapper = new ObjectMapper(); - final List list = - mapper.readValue(json, new TypeReference>() {}); + assertEquals(2, list.size()); + verifyMocks(fields); - for (final TypedField tf : list) { - if (tf.getValue() == null) { - switch (tf.getType()) { - case "not_used": - break; - case "boolean": - Mockito.when(rs.getBoolean(tf.getField())).thenReturn(false); - break; - case "date": - Mockito.when(rs.getDate(tf.getField())).thenReturn(null); - break; - case "int": - Mockito.when(rs.getInt(tf.getField())).thenReturn(0); - break; - case "double": - Mockito.when(rs.getDouble(tf.getField())).thenReturn(0.0); - break; - case "array": - Mockito.when(rs.getArray(tf.getField())).thenReturn(null); - break; - case "string": - default: - Mockito.when(rs.getString(tf.getField())).thenReturn(null); - break; - } - } else { - switch (tf.getType()) { - case "not_used": - break; - case "boolean": - Mockito.when(rs.getBoolean(tf.getField())) - .thenReturn(Boolean.parseBoolean(tf.getValue().toString())); - break; - case "date": - Mockito.when(rs.getDate(tf.getField())) - .thenReturn(Date.valueOf(tf.getValue().toString())); - break; - case "int": - Mockito.when(rs.getInt(tf.getField())) - .thenReturn(new Integer(tf.getValue().toString())); - break; - case "double": - Mockito.when(rs.getDouble(tf.getField())) - .thenReturn(new Double(tf.getValue().toString())); - break; - case "array": - final Array arr = Mockito.mock(Array.class); - final String[] values = - ((List) tf.getValue()) - .stream() - .filter(Objects::nonNull) - .map(o -> o.toString()) - .toArray(String[]::new); + assertTrue(list.get(0) instanceof Relation); + assertTrue(list.get(1) instanceof Relation); - Mockito.when(arr.getArray()).thenReturn(values); - Mockito.when(rs.getArray(tf.getField())).thenReturn(arr); - break; - case "string": - default: - Mockito.when(rs.getString(tf.getField())) - .thenReturn(tf.getValue().toString()); - break; - } - } - } + final Relation r1 = (Relation) list.get(0); + final Relation r2 = (Relation) list.get(1); - return list; - } + 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())); - private void verifyMocks(final List list) throws SQLException { - for (final TypedField tf : list) { + // System.out.println(new ObjectMapper().writeValueAsString(r1)); + // System.out.println(new ObjectMapper().writeValueAsString(r2)); + } - switch (tf.getType()) { - case "not_used": - break; - case "boolean": - Mockito.verify(rs, Mockito.atLeastOnce()).getBoolean(tf.getField()); - break; - case "date": - Mockito.verify(rs, Mockito.atLeastOnce()).getDate(tf.getField()); - break; - case "int": - Mockito.verify(rs, Mockito.atLeastOnce()).getInt(tf.getField()); - break; - case "double": - Mockito.verify(rs, Mockito.atLeastOnce()).getDouble(tf.getField()); - break; - case "array": - Mockito.verify(rs, Mockito.atLeastOnce()).getArray(tf.getField()); - break; - case "string": - default: - Mockito.verify(rs, Mockito.atLeastOnce()).getString(tf.getField()); - break; - } - } - } + private List prepareMocks(final String jsonFile) throws IOException, SQLException { + final String json = IOUtils.toString(getClass().getResourceAsStream(jsonFile)); + final ObjectMapper mapper = new ObjectMapper(); + final List list = + mapper.readValue(json, new TypeReference>() {}); - private void assertValidId(final String id) { - assertEquals(49, id.length()); - assertEquals('|', id.charAt(2)); - assertEquals(':', id.charAt(15)); - assertEquals(':', id.charAt(16)); - } + for (final TypedField tf : list) { + if (tf.getValue() == null) { + switch (tf.getType()) { + case "not_used": + break; + case "boolean": + Mockito.when(rs.getBoolean(tf.getField())).thenReturn(false); + break; + case "date": + Mockito.when(rs.getDate(tf.getField())).thenReturn(null); + break; + case "int": + Mockito.when(rs.getInt(tf.getField())).thenReturn(0); + break; + case "double": + Mockito.when(rs.getDouble(tf.getField())).thenReturn(0.0); + break; + case "array": + Mockito.when(rs.getArray(tf.getField())).thenReturn(null); + break; + case "string": + default: + Mockito.when(rs.getString(tf.getField())).thenReturn(null); + break; + } + } else { + switch (tf.getType()) { + case "not_used": + break; + case "boolean": + Mockito.when(rs.getBoolean(tf.getField())) + .thenReturn(Boolean.parseBoolean(tf.getValue().toString())); + break; + case "date": + Mockito.when(rs.getDate(tf.getField())) + .thenReturn(Date.valueOf(tf.getValue().toString())); + break; + case "int": + Mockito.when(rs.getInt(tf.getField())) + .thenReturn(new Integer(tf.getValue().toString())); + break; + case "double": + Mockito.when(rs.getDouble(tf.getField())) + .thenReturn(new Double(tf.getValue().toString())); + break; + case "array": + final Array arr = Mockito.mock(Array.class); + final String[] values = + ((List) tf.getValue()) + .stream() + .filter(Objects::nonNull) + .map(o -> o.toString()) + .toArray(String[]::new); - private String getValueAsString(final String name, final List fields) { - return fields.stream() - .filter(f -> f.getField().equals(name)) - .map(TypedField::getValue) - .filter(Objects::nonNull) - .map(o -> o.toString()) - .findFirst() - .get(); - } + Mockito.when(arr.getArray()).thenReturn(values); + Mockito.when(rs.getArray(tf.getField())).thenReturn(arr); + break; + case "string": + default: + Mockito.when(rs.getString(tf.getField())) + .thenReturn(tf.getValue().toString()); + break; + } + } + } + + return list; + } + + private void verifyMocks(final List list) throws SQLException { + for (final TypedField tf : list) { + + switch (tf.getType()) { + case "not_used": + break; + case "boolean": + Mockito.verify(rs, Mockito.atLeastOnce()).getBoolean(tf.getField()); + break; + case "date": + Mockito.verify(rs, Mockito.atLeastOnce()).getDate(tf.getField()); + break; + case "int": + Mockito.verify(rs, Mockito.atLeastOnce()).getInt(tf.getField()); + break; + case "double": + Mockito.verify(rs, Mockito.atLeastOnce()).getDouble(tf.getField()); + break; + case "array": + Mockito.verify(rs, Mockito.atLeastOnce()).getArray(tf.getField()); + break; + case "string": + default: + Mockito.verify(rs, Mockito.atLeastOnce()).getString(tf.getField()); + break; + } + } + } + + private void assertValidId(final String id) { + assertEquals(49, id.length()); + assertEquals('|', id.charAt(2)); + assertEquals(':', id.charAt(15)); + assertEquals(':', id.charAt(16)); + } + + private String getValueAsString(final String name, final List fields) { + return fields.stream() + .filter(f -> f.getField().equals(name)) + .map(TypedField::getValue) + .filter(Objects::nonNull) + .map(o -> o.toString()) + .findFirst() + .get(); + } } class TypedField { - private String field; - private String type; - private Object value; + private String field; + private String type; + private Object value; - public String getField() { - return field; - } + public String getField() { + return field; + } - public void setField(final String field) { - this.field = field; - } + public void setField(final String field) { + this.field = field; + } - public String getType() { - return type; - } + public String getType() { + return type; + } - public void setType(final String type) { - this.type = type; - } + public void setType(final String type) { + this.type = type; + } - public Object getValue() { - return value; - } + public Object getValue() { + return value; + } - public void setValue(final Object value) { - this.value = value; - } + public void setValue(final Object value) { + this.value = value; + } } From 25307965d20b3fc7ba4ba22ebcc18addacc63bcb Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 20 Apr 2020 09:43:27 +0200 Subject: [PATCH 06/19] add a default datainfo if missing --- .../raw/AbstractMdRecordToOafMapper.java | 857 +++++++++--------- 1 file changed, 426 insertions(+), 431 deletions(-) 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 f1058db38..29d17d1ce 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 @@ -1,443 +1,438 @@ 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 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; import org.dom4j.DocumentHelper; import org.dom4j.Node; +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; + public abstract class AbstractMdRecordToOafMapper { - protected final Map code2name; - - protected static final Qualifier MAIN_TITLE_QUALIFIER = - qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); - - protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER = - qualifier( - "publication", - "publication", - "dnet:result_typologies", - "dnet:result_typologies"); - protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER = - qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies"); - protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = - 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 AbstractMdRecordToOafMapper(final Map code2name) { - this.code2name = code2name; - } - - public List processMdRecord(final String xml) { - try { - final Map nsContext = new HashMap<>(); - nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); - nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); - nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); - nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); - nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); - nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); - nsContext.put("datacite", "http://datacite.org/schema/kernel-3"); - DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); - - final Document doc = - DocumentHelper.parseText( - xml.replaceAll( - "http://datacite.org/schema/kernel-4", - "http://datacite.org/schema/kernel-3")); - - final String type = doc.valueOf("//dr:CobjCategory/@type"); - final KeyValue collectedFrom = - keyValue( - doc.valueOf("//oaf:collectedFrom/@id"), - doc.valueOf("//oaf:collectedFrom/@name")); - final KeyValue hostedBy = - StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) - ? collectedFrom - : keyValue( - doc.valueOf("//oaf:hostedBy/@id"), - doc.valueOf("//oaf:hostedBy/@name")); - - final DataInfo info = prepareDataInfo(doc); - final long lastUpdateTimestamp = new Date().getTime(); - - return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - protected List createOafs( - final Document doc, - final String type, - final KeyValue collectedFrom, - final KeyValue hostedBy, - final DataInfo info, - final long lastUpdateTimestamp) { - - final List oafs = new ArrayList<>(); - - switch (type.toLowerCase()) { - case "": - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER); - p.setJournal(prepareJournal(doc, info)); - oafs.add(p); - break; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - d.setResulttype(DATASET_RESULTTYPE_QUALIFIER); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - oafs.add(d); - break; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - oafs.add(s); - break; - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - o.setResulttype(OTHER_RESULTTYPE_QUALIFIER); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - oafs.add(o); - break; - } - - if (!oafs.isEmpty()) { - oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp)); - oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp)); - } - - return oafs; - } - - private List addProjectRels( - final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { - - final List res = new ArrayList<>(); - - final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); - - for (final Object o : doc.selectNodes("//oaf:projectid")) { - final String projectId = createOpenaireId(40, ((Node) o).getText(), true); - - final Relation r1 = new Relation(); - r1.setRelType("resultProject"); - r1.setSubRelType("outcome"); - r1.setRelClass("isProducedBy"); - r1.setSource(docId); - r1.setTarget(projectId); - r1.setCollectedFrom(Arrays.asList(collectedFrom)); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r1); - - final Relation r2 = new Relation(); - r2.setRelType("resultProject"); - r2.setSubRelType("outcome"); - r2.setRelClass("produces"); - r2.setSource(projectId); - r2.setTarget(docId); - r2.setCollectedFrom(Arrays.asList(collectedFrom)); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r2); - } - - return res; - } - - protected abstract List addOtherResultRels( - final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp); - - private void populateResultFields( - final Result r, - final Document doc, - final KeyValue collectedFrom, - final KeyValue hostedBy, - final DataInfo info, - final long lastUpdateTimestamp) { - r.setDataInfo(info); - r.setLastupdatetimestamp(lastUpdateTimestamp); - r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); - r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); - r.setCollectedfrom(Arrays.asList(collectedFrom)); - r.setPid( - prepareListStructProps( - doc, - "//oaf:identifier", - "@identifierType", - "dnet:pid_types", - "dnet:pid_types", - info)); - r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); - r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); - r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setOaiprovenance(prepareOAIprovenance(doc)); - r.setAuthor(prepareAuthors(doc, info)); - r.setLanguage(prepareLanguages(doc)); - r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setSubject(prepareSubjects(doc, info)); - r.setTitle(prepareTitles(doc, info)); - r.setRelevantdate(prepareRelevantDates(doc, info)); - r.setDescription(prepareDescriptions(doc, info)); - r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); - r.setPublisher(preparePublisher(doc, info)); - r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); - r.setSource(prepareSources(doc, info)); - r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setFormat(prepareFormats(doc, info)); - r.setContributor(prepareContributors(doc, info)); - r.setResourcetype(prepareResourceType(doc, info)); - r.setCoverage(prepareCoverages(doc, info)); - r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy)); - } - - protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); - - protected abstract List prepareInstances( - Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby); - - protected abstract List> prepareSources(Document doc, DataInfo info); - - protected abstract List prepareRelevantDates(Document doc, DataInfo info); - - protected abstract List> prepareCoverages(Document doc, DataInfo info); - - protected abstract List> prepareContributors(Document doc, DataInfo info); - - protected abstract List> prepareFormats(Document doc, DataInfo info); - - protected abstract Field preparePublisher(Document doc, DataInfo info); - - protected abstract List> prepareDescriptions(Document doc, DataInfo info); - - protected abstract List prepareTitles(Document doc, DataInfo info); - - protected abstract List prepareSubjects(Document doc, DataInfo info); - - protected abstract Qualifier prepareLanguages(Document doc); - - protected abstract List prepareAuthors(Document doc, DataInfo info); - - protected abstract List> prepareOtherResearchProductTools( - Document doc, DataInfo info); - - protected abstract List> prepareOtherResearchProductContactGroups( - Document doc, DataInfo info); - - protected abstract List> prepareOtherResearchProductContactPersons( - Document doc, DataInfo info); - - protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); - - protected abstract Field prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); - - protected abstract List prepareSoftwareLicenses( - Document doc, DataInfo info); - - protected abstract List> prepareSoftwareDocumentationUrls( - Document doc, DataInfo info); - - protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); - - protected abstract Field prepareDatasetMetadataVersionNumber( - Document doc, DataInfo info); - - protected abstract Field prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); - - protected abstract Field prepareDatasetVersion(Document doc, DataInfo info); - - protected abstract Field prepareDatasetSize(Document doc, DataInfo info); - - protected abstract Field prepareDatasetDevice(Document doc, DataInfo info); - - protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); - - private Journal prepareJournal(final Document doc, final DataInfo info) { - final Node n = doc.selectSingleNode("//oaf:journal"); - if (n != null) { - final String name = n.getText(); - final String issnPrinted = n.valueOf("@issn"); - final String issnOnline = n.valueOf("@eissn"); - final String issnLinking = n.valueOf("@lissn"); - final String ep = n.valueOf("@ep"); - final String iss = n.valueOf("@iss"); - final String sp = n.valueOf("@sp"); - final String vol = n.valueOf("@vol"); - final String edition = n.valueOf("@edition"); - if (StringUtils.isNotBlank(name)) { - return journal( - name, - issnPrinted, - issnOnline, - issnLinking, - ep, - iss, - sp, - vol, - edition, - null, - null, - info); - } - } - return null; - } - - protected Qualifier prepareQualifier( - final Node node, final String xpath, final String schemeId, final String schemeName) { - final String classId = node.valueOf(xpath); - final String className = code2name.get(classId); - return qualifier(classId, className, schemeId, schemeName); - } - - protected List prepareListStructProps( - final Node node, - final String xpath, - final String xpathClassId, - final String schemeId, - final String schemeName, - final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - final String classId = n.valueOf(xpathClassId); - final String className = code2name.get(classId); - res.add( - structuredProperty( - n.getText(), classId, className, schemeId, schemeName, info)); - } - return res; - } - - protected List prepareListStructProps( - final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res.add(structuredProperty(n.getText(), qualifier, info)); - } - return res; - } - - protected List prepareListStructProps( - final Node node, final String xpath, final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res.add( - structuredProperty( - n.getText(), - n.valueOf("@classid"), - n.valueOf("@classname"), - n.valueOf("@schemeid"), - n.valueOf("@schemename"), - info)); - } - return res; - } - - protected OAIProvenance prepareOAIprovenance(final Document doc) { - final Node n = - doc.selectSingleNode( - "//*[local-name()='provenance']/*[local-name()='originDescription']"); - - if (n == null) { - return null; - } - - final String identifier = n.valueOf("./*[local-name()='identifier']"); - final String baseURL = n.valueOf("./*[local-name()='baseURL']"); - ; - final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']"); - ; - final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); - final String datestamp = n.valueOf("./*[local-name()='datestamp']"); - ; - final String harvestDate = n.valueOf("@harvestDate"); - ; - - return oaiIProvenance( - identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); - } - - protected DataInfo prepareDataInfo(final Document doc) { - final Node n = doc.selectSingleNode("//oaf:datainfo"); - - if (n == null) { - return null; - } - - final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); - final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); - final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); - final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename"); - - final boolean deletedbyinference = - Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); - final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance"); - final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); - final String trust = n.valueOf("./oaf:trust"); - - return dataInfo( - deletedbyinference, - inferenceprovenance, - inferred, - false, - qualifier(paClassId, paClassName, paSchemeId, paSchemeName), - trust); - } - - protected Field prepareField(final Node node, final String xpath, final DataInfo info) { - return field(node.valueOf(xpath), info); - } - - protected List> prepareListFields( - final Node node, final String xpath, final DataInfo info) { - return listFields(info, prepareListString(node, xpath)); - } - - protected List prepareListString(final Node node, final String xpath) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final String s = ((Node) o).getText().trim(); - if (StringUtils.isNotBlank(s)) { - res.add(s); - } - } - return res; - } + protected final Map code2name; + + protected static final Qualifier MAIN_TITLE_QUALIFIER = + qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + + protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER = + qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies"); + protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER = + qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies"); + protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = + 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; + } + + public List processMdRecord(final String xml) { + try { + final Map nsContext = new HashMap<>(); + nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); + nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); + nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); + nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); + nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); + nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); + nsContext.put("datacite", "http://datacite.org/schema/kernel-3"); + DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); + + final Document doc = + DocumentHelper.parseText(xml.replaceAll("http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3")); + + final String type = doc.valueOf("//dr:CobjCategory/@type"); + final KeyValue collectedFrom = + keyValue(doc.valueOf("//oaf:collectedFrom/@id"), doc.valueOf("//oaf:collectedFrom/@name")); + final KeyValue hostedBy = + StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) + ? collectedFrom + : keyValue(doc.valueOf("//oaf:hostedBy/@id"), doc.valueOf("//oaf:hostedBy/@name")); + + final DataInfo info = prepareDataInfo(doc); + final long lastUpdateTimestamp = new Date().getTime(); + + return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + protected List createOafs( + final Document doc, + final String type, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { + + final List oafs = new ArrayList<>(); + + switch (type.toLowerCase()) { + case "": + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER); + p.setJournal(prepareJournal(doc, info)); + oafs.add(p); + break; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + d.setResulttype(DATASET_RESULTTYPE_QUALIFIER); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + oafs.add(d); + break; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + oafs.add(s); + break; + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + o.setResulttype(OTHER_RESULTTYPE_QUALIFIER); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + oafs.add(o); + break; + } + + if (!oafs.isEmpty()) { + oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp)); + oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp)); + } + + return oafs; + } + + private List addProjectRels( + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + + final List res = new ArrayList<>(); + + final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); + + for (final Object o : doc.selectNodes("//oaf:projectid")) { + final String projectId = createOpenaireId(40, ((Node) o).getText(), true); + + final Relation r1 = new Relation(); + r1.setRelType("resultProject"); + r1.setSubRelType("outcome"); + r1.setRelClass("isProducedBy"); + r1.setSource(docId); + r1.setTarget(projectId); + r1.setCollectedFrom(Arrays.asList(collectedFrom)); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r1); + + final Relation r2 = new Relation(); + r2.setRelType("resultProject"); + r2.setSubRelType("outcome"); + r2.setRelClass("produces"); + r2.setSource(projectId); + r2.setTarget(docId); + r2.setCollectedFrom(Arrays.asList(collectedFrom)); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r2); + } + + return res; + } + + protected abstract List addOtherResultRels( + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp); + + private void populateResultFields( + final Result r, + final Document doc, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { + r.setDataInfo(info); + r.setLastupdatetimestamp(lastUpdateTimestamp); + r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); + r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); + r.setCollectedfrom(Arrays.asList(collectedFrom)); + r.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); + r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); + r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); + r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setOaiprovenance(prepareOAIprovenance(doc)); + r.setAuthor(prepareAuthors(doc, info)); + r.setLanguage(prepareLanguages(doc)); + r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setSubject(prepareSubjects(doc, info)); + r.setTitle(prepareTitles(doc, info)); + r.setRelevantdate(prepareRelevantDates(doc, info)); + r.setDescription(prepareDescriptions(doc, info)); + r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); + r.setPublisher(preparePublisher(doc, info)); + r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); + r.setSource(prepareSources(doc, info)); + r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setFormat(prepareFormats(doc, info)); + r.setContributor(prepareContributors(doc, info)); + r.setResourcetype(prepareResourceType(doc, info)); + r.setCoverage(prepareCoverages(doc, info)); + r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy)); + } + + protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); + + protected abstract List prepareInstances( + Document doc, + DataInfo info, + KeyValue collectedfrom, + KeyValue hostedby); + + protected abstract List> prepareSources(Document doc, DataInfo info); + + protected abstract List prepareRelevantDates(Document doc, DataInfo info); + + protected abstract List> prepareCoverages(Document doc, DataInfo info); + + protected abstract List> prepareContributors(Document doc, DataInfo info); + + protected abstract List> prepareFormats(Document doc, DataInfo info); + + protected abstract Field preparePublisher(Document doc, DataInfo info); + + protected abstract List> prepareDescriptions(Document doc, DataInfo info); + + protected abstract List prepareTitles(Document doc, DataInfo info); + + protected abstract List prepareSubjects(Document doc, DataInfo info); + + protected abstract Qualifier prepareLanguages(Document doc); + + protected abstract List prepareAuthors(Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductTools( + Document doc, + DataInfo info); + + protected abstract List> prepareOtherResearchProductContactGroups( + Document doc, + DataInfo info); + + protected abstract List> prepareOtherResearchProductContactPersons( + Document doc, + DataInfo info); + + protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); + + protected abstract Field prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); + + protected abstract List prepareSoftwareLicenses( + Document doc, + DataInfo info); + + protected abstract List> prepareSoftwareDocumentationUrls( + Document doc, + DataInfo info); + + protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); + + protected abstract Field prepareDatasetMetadataVersionNumber( + Document doc, + DataInfo info); + + protected abstract Field prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); + + protected abstract Field prepareDatasetVersion(Document doc, DataInfo info); + + protected abstract Field prepareDatasetSize(Document doc, DataInfo info); + + protected abstract Field prepareDatasetDevice(Document doc, DataInfo info); + + protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); + + private Journal prepareJournal(final Document doc, final DataInfo info) { + final Node n = doc.selectSingleNode("//oaf:journal"); + if (n != null) { + final String name = n.getText(); + final String issnPrinted = n.valueOf("@issn"); + final String issnOnline = n.valueOf("@eissn"); + final String issnLinking = n.valueOf("@lissn"); + final String ep = n.valueOf("@ep"); + final String iss = n.valueOf("@iss"); + final String sp = n.valueOf("@sp"); + final String vol = n.valueOf("@vol"); + final String edition = n.valueOf("@edition"); + if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } + } + return null; + } + + protected Qualifier prepareQualifier( + final Node node, + final String xpath, + final String schemeId, + final String schemeName) { + final String classId = node.valueOf(xpath); + final String className = code2name.get(classId); + return qualifier(classId, className, schemeId, schemeName); + } + + protected List prepareListStructProps( + final Node node, + final String xpath, + final String xpathClassId, + final String schemeId, + final String schemeName, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + final String classId = n.valueOf(xpathClassId); + final String className = code2name.get(classId); + res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info)); + } + return res; + } + + protected List prepareListStructProps( + final Node node, + final String xpath, + final Qualifier qualifier, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res.add(structuredProperty(n.getText(), qualifier, info)); + } + return res; + } + + protected List prepareListStructProps( + final Node node, + final String xpath, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info)); + } + return res; + } + + protected OAIProvenance prepareOAIprovenance(final Document doc) { + final Node n = + doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); + + if (n == null) { return null; } + + final String identifier = n.valueOf("./*[local-name()='identifier']"); + final String baseURL = n.valueOf("./*[local-name()='baseURL']");; + final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");; + final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); + final String datestamp = n.valueOf("./*[local-name()='datestamp']");; + final String harvestDate = n.valueOf("@harvestDate");; + + return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); + } + + protected DataInfo prepareDataInfo(final Document doc) { + final Node n = doc.selectSingleNode("//oaf:datainfo"); + + if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9"); } + + final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); + final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); + final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); + final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename"); + + final boolean deletedbyinference = + Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); + final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance"); + final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); + final String trust = n.valueOf("./oaf:trust"); + + return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); + } + + protected Field prepareField(final Node node, final String xpath, final DataInfo info) { + return field(node.valueOf(xpath), info); + } + + protected List> prepareListFields( + final Node node, + final String xpath, + final DataInfo info) { + return listFields(info, prepareListString(node, xpath)); + } + + protected List prepareListString(final Node node, final String xpath) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final String s = ((Node) o).getText().trim(); + if (StringUtils.isNotBlank(s)) { + res.add(s); + } + } + return res; + } } From 8ff7facfa3c93009939a12d1dcc3b5b2b25bd4e7 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 20 Apr 2020 11:09:27 +0200 Subject: [PATCH 07/19] fixed collectedFrom ID --- .../raw/AbstractMdRecordToOafMapper.java | 4 +- .../raw/MigrateDbEntitiesApplication.java | 988 +++++++++--------- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 5 + .../raw/MigrateDbEntitiesApplicationTest.java | 17 +- 4 files changed, 504 insertions(+), 510 deletions(-) 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 29d17d1ce..01a426567 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 @@ -80,11 +80,11 @@ public abstract class AbstractMdRecordToOafMapper { final String type = doc.valueOf("//dr:CobjCategory/@type"); final KeyValue collectedFrom = - keyValue(doc.valueOf("//oaf:collectedFrom/@id"), doc.valueOf("//oaf:collectedFrom/@name")); + keyValue(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"), doc.valueOf("//oaf:hostedBy/@name")); + : keyValue(createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), doc.valueOf("//oaf:hostedBy/@name")); final DataInfo info = prepareDataInfo(doc); final long lastUpdateTimestamp = new Date().getTime(); 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 6de7303c3..f0d4c62c5 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 +1,15 @@ 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 java.io.Closeable; import java.io.IOException; import java.sql.Array; @@ -17,510 +21,484 @@ import java.util.Date; import java.util.List; import java.util.function.Consumer; import java.util.function.Function; + import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +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; + public class MigrateDbEntitiesApplication extends AbstractMigrationApplication - implements Closeable { - - private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = - qualifier( - "sysimport:crosswalk:entityregistry", - "sysimport:crosswalk:entityregistry", - "dnet:provenance_actions", - "dnet:provenance_actions"); - - private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); - - private final DbClient dbClient; - - private final long lastUpdateTimestamp; - - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = - new ArgumentApplicationParser( - IOUtils.toString( - MigrateDbEntitiesApplication.class.getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json"))); - - parser.parseArgument(args); - - final String dbUrl = parser.get("postgresUrl"); - final String dbUser = parser.get("postgresUser"); - final String dbPassword = parser.get("postgresPassword"); - - final String hdfsPath = parser.get("hdfsPath"); - - final boolean processClaims = - parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims"); - - try (final MigrateDbEntitiesApplication smdbe = - new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser, dbPassword)) { - if (processClaims) { - log.info("Processing claims..."); - smdbe.execute("queryClaims.sql", smdbe::processClaims); - } else { - log.info("Processing datasources..."); - smdbe.execute("queryDatasources.sql", smdbe::processDatasource); - - log.info("Processing projects..."); - smdbe.execute("queryProjects.sql", smdbe::processProject); - - log.info("Processing orgs..."); - smdbe.execute("queryOrganizations.sql", smdbe::processOrganization); - - log.info("Processing relations ds <-> orgs ..."); - smdbe.execute( - "queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization); - - log.info("Processing projects <-> orgs ..."); - smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization); - } - log.info("All done."); - } - } - - protected MigrateDbEntitiesApplication() { // ONLY FOR UNIT TEST - super(); - this.dbClient = null; - this.lastUpdateTimestamp = new Date().getTime(); - } - - public MigrateDbEntitiesApplication( - final String hdfsPath, final String dbUrl, final String dbUser, final String dbPassword) - throws Exception { - super(hdfsPath); - this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); - this.lastUpdateTimestamp = new Date().getTime(); - } - - public void execute(final String sqlFile, final Function> producer) - throws Exception { - final String sql = - IOUtils.toString( - getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile)); - - final Consumer consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf)); - - dbClient.processResults(sql, consumer); - } - - public List processDatasource(final ResultSet rs) { - - try { - - final DataInfo info = prepareDataInfo(rs); - - final Datasource ds = new Datasource(); - - ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); - ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); - ds.setCollectedfrom( - listKeyValues( - 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 - ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB - ds.setOaiprovenance(null); // Values not present in the DB - ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); - ds.setOpenairecompatibility( - prepareQualifierSplitting(rs.getString("openairecompatibility"))); - ds.setOfficialname(field(rs.getString("officialname"), info)); - ds.setEnglishname(field(rs.getString("englishname"), info)); - ds.setWebsiteurl(field(rs.getString("websiteurl"), info)); - ds.setLogourl(field(rs.getString("logourl"), info)); - ds.setContactemail(field(rs.getString("contactemail"), info)); - ds.setNamespaceprefix(field(rs.getString("namespaceprefix"), info)); - ds.setLatitude(field(Double.toString(rs.getDouble("latitude")), info)); - ds.setLongitude(field(Double.toString(rs.getDouble("longitude")), info)); - ds.setDateofvalidation(field(asString(rs.getDate("dateofvalidation")), info)); - ds.setDescription(field(rs.getString("description"), info)); - ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); - ds.setOdnumberofitems(field(Double.toString(rs.getInt("odnumberofitems")), info)); - ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info)); - ds.setOdpolicies(field(rs.getString("odpolicies"), info)); - ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); - ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); - ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); - ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); - ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info)); - ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info)); - ds.setDataprovider(field(rs.getBoolean("dataprovider"), info)); - ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info)); - ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info)); - ds.setDatauploadtype(field(rs.getString("datauploadtype"), info)); - ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); - ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info)); - ds.setVersioning(field(rs.getBoolean("versioning"), info)); - ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info)); - ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info)); - ds.setPidsystems(field(rs.getString("pidsystems"), info)); - ds.setCertificates(field(rs.getString("certificates"), info)); - ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array - ds.setJournal( - prepareJournal( - rs.getString("officialname"), - rs.getString("journal"), - info)); // Journal - ds.setDataInfo(info); - ds.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(ds); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processProject(final ResultSet rs) { - try { - - final DataInfo info = prepareDataInfo(rs); - - final Project p = new Project(); - - p.setId(createOpenaireId(40, rs.getString("projectid"), true)); - p.setOriginalId(Arrays.asList(rs.getString("projectid"))); - p.setCollectedfrom( - listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname"))); - p.setPid(new ArrayList<>()); - p.setDateofcollection(asString(rs.getDate("dateofcollection"))); - p.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); - p.setExtraInfo(new ArrayList<>()); // Values not present in the DB - p.setOaiprovenance(null); // Values not present in the DB - p.setWebsiteurl(field(rs.getString("websiteurl"), info)); - p.setCode(field(rs.getString("code"), info)); - p.setAcronym(field(rs.getString("acronym"), info)); - p.setTitle(field(rs.getString("title"), info)); - p.setStartdate(field(asString(rs.getDate("startdate")), info)); - p.setEnddate(field(asString(rs.getDate("enddate")), info)); - p.setCallidentifier(field(rs.getString("callidentifier"), info)); - p.setKeywords(field(rs.getString("keywords"), info)); - p.setDuration(field(Integer.toString(rs.getInt("duration")), info)); - p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info)); - p.setOamandatepublications( - field(Boolean.toString(rs.getBoolean("oamandatepublications")), info)); - p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info)); - p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); - p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info)); - p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype"))); - p.setOptional1(field(rs.getString("optional1"), info)); - p.setOptional2(field(rs.getString("optional2"), info)); - p.setJsonextrainfo(field(rs.getString("jsonextrainfo"), info)); - p.setContactfullname(field(rs.getString("contactfullname"), info)); - p.setContactfax(field(rs.getString("contactfax"), info)); - p.setContactphone(field(rs.getString("contactphone"), info)); - p.setContactemail(field(rs.getString("contactemail"), info)); - p.setSummary(field(rs.getString("summary"), info)); - p.setCurrency(field(rs.getString("currency"), info)); - p.setTotalcost(new Float(rs.getDouble("totalcost"))); - p.setFundedamount(new Float(rs.getDouble("fundedamount"))); - p.setDataInfo(info); - p.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(p); - - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processOrganization(final ResultSet rs) { - - try { - - final DataInfo info = prepareDataInfo(rs); - - final Organization o = new Organization(); - - o.setId(createOpenaireId(20, rs.getString("organizationid"), true)); - o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); - o.setCollectedfrom( - listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname"))); - o.setPid(new ArrayList<>()); - o.setDateofcollection(asString(rs.getDate("dateofcollection"))); - o.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); - o.setExtraInfo(new ArrayList<>()); // Values not present in the DB - o.setOaiprovenance(null); // Values not present in the DB - o.setLegalshortname(field(rs.getString("legalshortname"), info)); - o.setLegalname(field(rs.getString("legalname"), info)); - o.setAlternativeNames(new ArrayList<>()); // Values not returned by the SQL query - o.setWebsiteurl(field(rs.getString("websiteurl"), info)); - o.setLogourl(field(rs.getString("logourl"), info)); - o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info)); - o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info)); - o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info)); - o.setEcresearchorganization( - field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info)); - o.setEchighereducation( - field(Boolean.toString(rs.getBoolean("echighereducation")), info)); - o.setEcinternationalorganizationeurinterests( - field( - Boolean.toString( - rs.getBoolean("ecinternationalorganizationeurinterests")), - info)); - o.setEcinternationalorganization( - field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info)); - o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info)); - o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info)); - o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info)); - o.setCountry(prepareQualifierSplitting(rs.getString("country"))); - o.setDataInfo(info); - o.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(o); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processDatasourceOrganization(final ResultSet rs) { - try { - final DataInfo info = prepareDataInfo(rs); - final String orgId = createOpenaireId(20, rs.getString("organization"), true); - final String dsId = createOpenaireId(10, rs.getString("datasource"), true); - final List collectedFrom = - listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname")); - - final Relation r1 = new Relation(); - r1.setRelType("datasourceOrganization"); - r1.setSubRelType("provision"); - r1.setRelClass("isProvidedBy"); - r1.setSource(dsId); - r1.setTarget(orgId); - r1.setCollectedFrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - final Relation r2 = new Relation(); - r2.setRelType("datasourceOrganization"); - r2.setSubRelType("provision"); - r2.setRelClass("provides"); - r2.setSource(orgId); - r2.setTarget(dsId); - r2.setCollectedFrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(r1, r2); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processProjectOrganization(final ResultSet rs) { - try { - final DataInfo info = prepareDataInfo(rs); - final String orgId = createOpenaireId(20, rs.getString("resporganization"), true); - final String projectId = createOpenaireId(40, rs.getString("project"), true); - final List collectedFrom = - listKeyValues( - rs.getString("collectedfromid"), rs.getString("collectedfromname")); - - final Relation r1 = new Relation(); - r1.setRelType("projectOrganization"); - r1.setSubRelType("participation"); - r1.setRelClass("isParticipant"); - r1.setSource(projectId); - r1.setTarget(orgId); - r1.setCollectedFrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - final Relation r2 = new Relation(); - r2.setRelType("projectOrganization"); - r2.setSubRelType("participation"); - r2.setRelClass("hasParticipant"); - r2.setSource(orgId); - r2.setTarget(projectId); - r2.setCollectedFrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(r1, r2); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processClaims(final ResultSet rs) { - - final DataInfo info = - dataInfo( - false, - null, - false, - false, - qualifier( - "user:claim", - "user:claim", - "dnet:provenanceActions", - "dnet:provenanceActions"), - "0.9"); - - try { - - if (rs.getString("source_type").equals("context")) { - final Result r; - - if (rs.getString("target_type").equals("dataset")) { - r = new Dataset(); - } else if (rs.getString("target_type").equals("software")) { - r = new Software(); - } else if (rs.getString("target_type").equals("other")) { - r = new OtherResearchProduct(); - } else { - r = new Publication(); - } - r.setId(createOpenaireId(50, rs.getString("target_id"), false)); - r.setLastupdatetimestamp(lastUpdateTimestamp); - r.setContext(prepareContext(rs.getString("source_id"), info)); - r.setDataInfo(info); - - return Arrays.asList(r); - } else { - final String sourceId = - createOpenaireId( - rs.getString("source_type"), rs.getString("source_id"), false); - final String targetId = - createOpenaireId( - rs.getString("target_type"), rs.getString("target_id"), false); - - final Relation r1 = new Relation(); - final Relation r2 = new Relation(); - - if (rs.getString("source_type").equals("project")) { - r1.setRelType("resultProject"); - r1.setSubRelType("outcome"); - r1.setRelClass("produces"); - - r2.setRelType("resultProject"); - r2.setSubRelType("outcome"); - r2.setRelClass("isProducedBy"); - } else { - r1.setRelType("resultResult"); - r1.setSubRelType("relationship"); - r1.setRelClass("isRelatedTo"); - - r2.setRelType("resultResult"); - r2.setSubRelType("relationship"); - r2.setRelClass("isRelatedTo"); - } - - r1.setSource(sourceId); - r1.setTarget(targetId); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - r2.setSource(targetId); - r2.setTarget(sourceId); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(r1, r2); - } - - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - private List prepareContext(final String id, final DataInfo dataInfo) { - final Context context = new Context(); - context.setId(id); - context.setDataInfo(Arrays.asList(dataInfo)); - return Arrays.asList(context); - } - - private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException { - final Boolean deletedbyinference = rs.getBoolean("deletedbyinference"); - final String inferenceprovenance = rs.getString("inferenceprovenance"); - final Boolean inferred = rs.getBoolean("inferred"); - final String trust = rs.getString("trust"); - return dataInfo( - deletedbyinference, - inferenceprovenance, - inferred, - false, - ENTITYREGISTRY_PROVENANCE_ACTION, - trust); - } - - private Qualifier prepareQualifierSplitting(final String s) { - if (StringUtils.isBlank(s)) { - return null; - } - final String[] arr = s.split("@@@"); - return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null; - } - - private List> prepareListFields(final Array array, final DataInfo info) { - try { - return array != null - ? listFields(info, (String[]) array.getArray()) - : new ArrayList<>(); - } catch (final SQLException e) { - throw new RuntimeException("Invalid SQL array", e); - } - } - - private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) { - if (StringUtils.isBlank(s)) { - return null; - } - final String[] parts = s.split("###"); - if (parts.length == 2) { - final String value = parts[0]; - final String[] arr = parts[1].split("@@@"); - if (arr.length == 4) { - return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); - } - } - return null; - } - - private List prepareListOfStructProps( - final Array array, final DataInfo dataInfo) throws SQLException { - final List res = new ArrayList<>(); - if (array != null) { - for (final String s : (String[]) array.getArray()) { - final StructuredProperty sp = prepareStructProp(s, dataInfo); - if (sp != null) { - res.add(sp); - } - } - } - - return res; - } - - private Journal prepareJournal(final String name, final String sj, final DataInfo info) { - if (StringUtils.isNotBlank(sj)) { - final String[] arr = sj.split("@@@"); - if (arr.length == 3) { - final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null; - final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null; - ; - final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null; - ; - if (issn != null || eissn != null || lissn != null) { - return journal( - name, issn, eissn, eissn, null, null, null, null, null, null, null, - info); - } - } - } - return null; - } - - @Override - public void close() throws IOException { - super.close(); - dbClient.close(); - } + implements Closeable { + + private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = + qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenance_actions", "dnet:provenance_actions"); + + private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); + + private final DbClient dbClient; + + private final long lastUpdateTimestamp; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString(MigrateDbEntitiesApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json"))); + + parser.parseArgument(args); + + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); + + final String hdfsPath = parser.get("hdfsPath"); + + final boolean processClaims = + parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims"); + + try (final MigrateDbEntitiesApplication smdbe = + new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser, dbPassword)) { + if (processClaims) { + log.info("Processing claims..."); + smdbe.execute("queryClaims.sql", smdbe::processClaims); + } else { + log.info("Processing datasources..."); + smdbe.execute("queryDatasources.sql", smdbe::processDatasource); + + log.info("Processing projects..."); + smdbe.execute("queryProjects.sql", smdbe::processProject); + + log.info("Processing orgs..."); + smdbe.execute("queryOrganizations.sql", smdbe::processOrganization); + + log.info("Processing relations ds <-> orgs ..."); + smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization); + + log.info("Processing projects <-> orgs ..."); + smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization); + } + log.info("All done."); + } + } + + protected MigrateDbEntitiesApplication() { // ONLY FOR UNIT TEST + super(); + this.dbClient = null; + this.lastUpdateTimestamp = new Date().getTime(); + } + + public MigrateDbEntitiesApplication( + final String hdfsPath, final String dbUrl, final String dbUser, final String dbPassword) + throws Exception { + super(hdfsPath); + this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); + this.lastUpdateTimestamp = new Date().getTime(); + } + + public void execute(final String sqlFile, final Function> producer) + throws Exception { + final String sql = + IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile)); + + final Consumer consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf)); + + dbClient.processResults(sql, consumer); + } + + public List processDatasource(final ResultSet rs) { + + try { + + final DataInfo info = prepareDataInfo(rs); + + final Datasource ds = new Datasource(); + + ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); + ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); + ds.setCollectedfrom(listKeyValues(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 + ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB + ds.setOaiprovenance(null); // Values not present in the DB + ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); + ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility"))); + ds.setOfficialname(field(rs.getString("officialname"), info)); + ds.setEnglishname(field(rs.getString("englishname"), info)); + ds.setWebsiteurl(field(rs.getString("websiteurl"), info)); + ds.setLogourl(field(rs.getString("logourl"), info)); + ds.setContactemail(field(rs.getString("contactemail"), info)); + ds.setNamespaceprefix(field(rs.getString("namespaceprefix"), info)); + ds.setLatitude(field(Double.toString(rs.getDouble("latitude")), info)); + ds.setLongitude(field(Double.toString(rs.getDouble("longitude")), info)); + ds.setDateofvalidation(field(asString(rs.getDate("dateofvalidation")), info)); + ds.setDescription(field(rs.getString("description"), info)); + ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); + ds.setOdnumberofitems(field(Double.toString(rs.getInt("odnumberofitems")), info)); + ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info)); + ds.setOdpolicies(field(rs.getString("odpolicies"), info)); + ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); + ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); + ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); + ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); + ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info)); + ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info)); + ds.setDataprovider(field(rs.getBoolean("dataprovider"), info)); + ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info)); + ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info)); + ds.setDatauploadtype(field(rs.getString("datauploadtype"), info)); + ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); + ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info)); + ds.setVersioning(field(rs.getBoolean("versioning"), info)); + ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info)); + ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info)); + ds.setPidsystems(field(rs.getString("pidsystems"), info)); + ds.setCertificates(field(rs.getString("certificates"), info)); + ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array + ds.setJournal(prepareJournal(rs.getString("officialname"), rs.getString("journal"), info)); // Journal + ds.setDataInfo(info); + ds.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(ds); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processProject(final ResultSet rs) { + try { + + final DataInfo info = prepareDataInfo(rs); + + final Project p = new Project(); + + p.setId(createOpenaireId(40, rs.getString("projectid"), true)); + p.setOriginalId(Arrays.asList(rs.getString("projectid"))); + p.setCollectedfrom(listKeyValues(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"))); + p.setExtraInfo(new ArrayList<>()); // Values not present in the DB + p.setOaiprovenance(null); // Values not present in the DB + p.setWebsiteurl(field(rs.getString("websiteurl"), info)); + p.setCode(field(rs.getString("code"), info)); + p.setAcronym(field(rs.getString("acronym"), info)); + p.setTitle(field(rs.getString("title"), info)); + p.setStartdate(field(asString(rs.getDate("startdate")), info)); + p.setEnddate(field(asString(rs.getDate("enddate")), info)); + p.setCallidentifier(field(rs.getString("callidentifier"), info)); + p.setKeywords(field(rs.getString("keywords"), info)); + p.setDuration(field(Integer.toString(rs.getInt("duration")), info)); + p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info)); + p.setOamandatepublications(field(Boolean.toString(rs.getBoolean("oamandatepublications")), info)); + p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info)); + p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); + p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info)); + p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype"))); + p.setOptional1(field(rs.getString("optional1"), info)); + p.setOptional2(field(rs.getString("optional2"), info)); + p.setJsonextrainfo(field(rs.getString("jsonextrainfo"), info)); + p.setContactfullname(field(rs.getString("contactfullname"), info)); + p.setContactfax(field(rs.getString("contactfax"), info)); + p.setContactphone(field(rs.getString("contactphone"), info)); + p.setContactemail(field(rs.getString("contactemail"), info)); + p.setSummary(field(rs.getString("summary"), info)); + p.setCurrency(field(rs.getString("currency"), info)); + p.setTotalcost(new Float(rs.getDouble("totalcost"))); + p.setFundedamount(new Float(rs.getDouble("fundedamount"))); + p.setDataInfo(info); + p.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(p); + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processOrganization(final ResultSet rs) { + + try { + + final DataInfo info = prepareDataInfo(rs); + + final Organization o = new Organization(); + + o.setId(createOpenaireId(20, rs.getString("organizationid"), true)); + o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); + o.setCollectedfrom(listKeyValues(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"))); + o.setExtraInfo(new ArrayList<>()); // Values not present in the DB + o.setOaiprovenance(null); // Values not present in the DB + o.setLegalshortname(field(rs.getString("legalshortname"), info)); + o.setLegalname(field(rs.getString("legalname"), info)); + o.setAlternativeNames(new ArrayList<>()); // Values not returned by the SQL query + o.setWebsiteurl(field(rs.getString("websiteurl"), info)); + o.setLogourl(field(rs.getString("logourl"), info)); + o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info)); + o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info)); + o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info)); + o.setEcresearchorganization(field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info)); + o.setEchighereducation(field(Boolean.toString(rs.getBoolean("echighereducation")), info)); + o.setEcinternationalorganizationeurinterests(field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info)); + o.setEcinternationalorganization(field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info)); + o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info)); + o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info)); + o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info)); + o.setCountry(prepareQualifierSplitting(rs.getString("country"))); + o.setDataInfo(info); + o.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(o); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processDatasourceOrganization(final ResultSet rs) { + try { + final DataInfo info = prepareDataInfo(rs); + final String orgId = createOpenaireId(20, rs.getString("organization"), true); + final String dsId = createOpenaireId(10, rs.getString("datasource"), true); + final List collectedFrom = + listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); + + final Relation r1 = new Relation(); + r1.setRelType("datasourceOrganization"); + r1.setSubRelType("provision"); + r1.setRelClass("isProvidedBy"); + r1.setSource(dsId); + r1.setTarget(orgId); + r1.setCollectedFrom(collectedFrom); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + + final Relation r2 = new Relation(); + r2.setRelType("datasourceOrganization"); + r2.setSubRelType("provision"); + r2.setRelClass("provides"); + r2.setSource(orgId); + r2.setTarget(dsId); + r2.setCollectedFrom(collectedFrom); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(r1, r2); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processProjectOrganization(final ResultSet rs) { + try { + final DataInfo info = prepareDataInfo(rs); + final String orgId = createOpenaireId(20, rs.getString("resporganization"), true); + final String projectId = createOpenaireId(40, rs.getString("project"), true); + final List collectedFrom = + listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); + + final Relation r1 = new Relation(); + r1.setRelType("projectOrganization"); + r1.setSubRelType("participation"); + r1.setRelClass("isParticipant"); + r1.setSource(projectId); + r1.setTarget(orgId); + r1.setCollectedFrom(collectedFrom); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + + final Relation r2 = new Relation(); + r2.setRelType("projectOrganization"); + r2.setSubRelType("participation"); + r2.setRelClass("hasParticipant"); + r2.setSource(orgId); + r2.setTarget(projectId); + r2.setCollectedFrom(collectedFrom); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(r1, r2); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processClaims(final ResultSet rs) { + + final DataInfo info = + dataInfo(false, null, false, false, qualifier("user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"), "0.9"); + + final List collectedFrom = listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE"); + + try { + + if (rs.getString("source_type").equals("context")) { + final Result r; + + if (rs.getString("target_type").equals("dataset")) { + r = new Dataset(); + } else if (rs.getString("target_type").equals("software")) { + r = new Software(); + } else if (rs.getString("target_type").equals("other")) { + r = new OtherResearchProduct(); + } else { + r = new Publication(); + } + r.setId(createOpenaireId(50, rs.getString("target_id"), false)); + r.setLastupdatetimestamp(lastUpdateTimestamp); + r.setContext(prepareContext(rs.getString("source_id"), info)); + r.setDataInfo(info); + r.setCollectedfrom(collectedFrom); + + return Arrays.asList(r); + } else { + final String sourceId = + createOpenaireId(rs.getString("source_type"), rs.getString("source_id"), false); + final String targetId = + createOpenaireId(rs.getString("target_type"), rs.getString("target_id"), false); + + final Relation r1 = new Relation(); + 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"); + } + + r1.setSource(sourceId); + r1.setTarget(targetId); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + + r2.setSource(targetId); + r2.setTarget(sourceId); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(r1, r2); + } + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + private List prepareContext(final String id, final DataInfo dataInfo) { + final Context context = new Context(); + context.setId(id); + context.setDataInfo(Arrays.asList(dataInfo)); + return Arrays.asList(context); + } + + private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException { + final Boolean deletedbyinference = rs.getBoolean("deletedbyinference"); + final String inferenceprovenance = rs.getString("inferenceprovenance"); + final Boolean inferred = rs.getBoolean("inferred"); + final String trust = rs.getString("trust"); + return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust); + } + + private Qualifier prepareQualifierSplitting(final String s) { + if (StringUtils.isBlank(s)) { return null; } + final String[] arr = s.split("@@@"); + return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null; + } + + private List> prepareListFields(final Array array, final DataInfo info) { + try { + return array != null + ? listFields(info, (String[]) array.getArray()) + : new ArrayList<>(); + } catch (final SQLException e) { + throw new RuntimeException("Invalid SQL array", e); + } + } + + private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) { + if (StringUtils.isBlank(s)) { return null; } + final String[] parts = s.split("###"); + if (parts.length == 2) { + final String value = parts[0]; + final String[] arr = parts[1].split("@@@"); + if (arr.length == 4) { return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); } + } + return null; + } + + private List prepareListOfStructProps( + final Array array, + final DataInfo dataInfo) throws SQLException { + final List res = new ArrayList<>(); + if (array != null) { + for (final String s : (String[]) array.getArray()) { + final StructuredProperty sp = prepareStructProp(s, dataInfo); + if (sp != null) { + res.add(sp); + } + } + } + + return res; + } + + private Journal prepareJournal(final String name, final String sj, final DataInfo info) { + if (StringUtils.isNotBlank(sj)) { + final String[] arr = sj.split("@@@"); + if (arr.length == 3) { + final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null; + final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;; + final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;; + if (issn != null || eissn != null || lissn != null) { + return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info); + } + } + } + return null; + } + + @Override + public void close() throws IOException { + super.close(); + dbClient.close(); + } } 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 3fc1d72d6..b0b8aba3c 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 @@ -51,6 +51,7 @@ 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); @@ -61,6 +62,8 @@ public class MappersTest { 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()); @@ -92,6 +95,7 @@ public class MappersTest { 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); @@ -124,6 +128,7 @@ 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 69a13fb81..b0802f662 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 @@ -29,6 +29,7 @@ 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; @ExtendWith(MockitoExtension.class) public class MigrateDbEntitiesApplicationTest { @@ -53,12 +54,12 @@ 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)); } @@ -72,10 +73,11 @@ 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)); + } @Test @@ -90,6 +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)); @@ -97,7 +100,6 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]); assertEquals(o.getCountry().getSchemeid(), getValueAsString("country", fields).split("@@@")[2]); 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)); } @@ -133,6 +135,8 @@ 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 @@ -142,8 +146,12 @@ 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 @@ -176,6 +184,9 @@ public class MigrateDbEntitiesApplicationTest { 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)); } From d714bfb4d45a08ccca71a7f5ad5759e57aaf7f91 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 20 Apr 2020 12:25:19 +0200 Subject: [PATCH 08/19] collectedfrom field moved in common parent class Oaf.java --- .../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 | 850 ++++++++------- .../raw/MigrateDbEntitiesApplication.java | 997 ++++++++++-------- .../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 | 197 ++-- .../raw/MigrateDbEntitiesApplicationTest.java | 541 +++++----- .../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 +++--- 23 files changed, 1873 insertions(+), 1774 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 7a7a9a89c..79138d641 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 86f4ff616..6db3b7f74 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 9d211d058..aaeecb871 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/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 bc65230a8..36d3fdd27 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"} 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+{"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 b5d027c03..5188cf55a 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 bb310050c..3c3a63ca4 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 @@ -14,7 +14,9 @@ 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; @@ -24,6 +26,9 @@ 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); @@ -84,8 +89,29 @@ abstract class AbstractSparkAction implements Serializable { return SparkSession.builder().config(conf).getOrCreate(); } - protected static void save(Dataset dataset, String outPath, SaveMode mode) { - dataset.write().option("compression", "gzip").mode(mode).json(outPath); + 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 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 127a19139..a4e69e6db 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 @@ -11,8 +11,6 @@ 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; @@ -71,14 +69,11 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { Class clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); - DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf) - .map( - (MapFunction) - value -> OBJECT_MAPPER.writeValueAsString(value), - Encoders.STRING()) - .write() - .mode(SaveMode.Overwrite) - .json(outputPath); + save( + DedupRecordFactory.createDedupRecord( + spark, mergeRelPath, entityPath, clazz, dedupConf), + outputPath, + SaveMode.Overwrite); } } } 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 ca6d04d49..cfd541f29 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 @@ -6,7 +6,6 @@ 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; @@ -35,9 +34,7 @@ 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); @@ -148,22 +145,13 @@ public class SparkCreateMergeRels extends AbstractSparkAction { r.setRelClass(relClass); r.setSubRelType("dedup"); - DataInfo info = new DataInfo(); - info.setDeletedbyinference(false); - info.setInferred(true); - info.setInvisible(false); + DataInfo info = getDataInfo(); 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(info); + r.setDataInfo(getDataInfo()); 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 2fd807ccb..186b21ef2 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 @@ -2,7 +2,6 @@ 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; @@ -115,7 +114,7 @@ public class SparkCreateSimRels extends AbstractSparkAction { r.setTarget(target); r.setSubRelType("dedupSimilarity"); r.setRelClass("isSimilarTo"); - r.setDataInfo(new DataInfo()); + r.setDataInfo(getDataInfo()); 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 17c99c002..b983f5a29 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -4,7 +4,6 @@ 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; @@ -125,7 +124,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { return value -> { final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class); if (rel.getDataInfo() == null) { - rel.setDataInfo(new DataInfo()); + rel.setDataInfo(getDataInfo()); } return rel; }; @@ -149,7 +148,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { Relation r = value._1()._2(); String id = value._2()._2(); if (r.getDataInfo() == null) { - r.setDataInfo(new DataInfo()); + r.setDataInfo(getDataInfo()); } r.getDataInfo().setDeletedbyinference(false); switch (type) { @@ -173,7 +172,7 @@ public class SparkPropagateRelation extends AbstractSparkAction { if (value._2() != null) { Relation r = value._1()._2(); if (r.getDataInfo() == null) { - r.setDataInfo(new DataInfo()); + r.setDataInfo(getDataInfo()); } 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 50e71c366..b9b9c22ba 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", 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"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|erc_________::8511e17e153877fecd5a9a4ea8eb0969", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::07c370987d51b8273071fedf5931acf6"} {"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|erc_________::67b1c4d6876a12e265e965c1451a7f36", "lastupdatetimestamp": 0, "relType": "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 01a426567..a7aa600cf 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 @@ -10,19 +10,6 @@ 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 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; -import org.dom4j.DocumentHelper; -import org.dom4j.Node; - import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Dataset; @@ -40,399 +27,452 @@ 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; +import org.dom4j.DocumentHelper; +import org.dom4j.Node; public abstract class AbstractMdRecordToOafMapper { - protected final Map code2name; - - protected static final Qualifier MAIN_TITLE_QUALIFIER = - qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); - - protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER = - qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies"); - protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER = - qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies"); - protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = - 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; - } - - public List processMdRecord(final String xml) { - try { - final Map nsContext = new HashMap<>(); - nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); - nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); - nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); - nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); - nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); - nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); - nsContext.put("datacite", "http://datacite.org/schema/kernel-3"); - DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); - - final Document doc = - DocumentHelper.parseText(xml.replaceAll("http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3")); - - final String type = doc.valueOf("//dr:CobjCategory/@type"); - final KeyValue collectedFrom = - keyValue(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(createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), doc.valueOf("//oaf:hostedBy/@name")); - - final DataInfo info = prepareDataInfo(doc); - final long lastUpdateTimestamp = new Date().getTime(); - - return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - protected List createOafs( - final Document doc, - final String type, - final KeyValue collectedFrom, - final KeyValue hostedBy, - final DataInfo info, - final long lastUpdateTimestamp) { - - final List oafs = new ArrayList<>(); - - switch (type.toLowerCase()) { - case "": - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER); - p.setJournal(prepareJournal(doc, info)); - oafs.add(p); - break; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - d.setResulttype(DATASET_RESULTTYPE_QUALIFIER); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - oafs.add(d); - break; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - oafs.add(s); - break; - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - o.setResulttype(OTHER_RESULTTYPE_QUALIFIER); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - oafs.add(o); - break; - } - - if (!oafs.isEmpty()) { - oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp)); - oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp)); - } - - return oafs; - } - - private List addProjectRels( - final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { - - final List res = new ArrayList<>(); - - final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); - - for (final Object o : doc.selectNodes("//oaf:projectid")) { - final String projectId = createOpenaireId(40, ((Node) o).getText(), true); - - final Relation r1 = new Relation(); - r1.setRelType("resultProject"); - r1.setSubRelType("outcome"); - r1.setRelClass("isProducedBy"); - r1.setSource(docId); - r1.setTarget(projectId); - r1.setCollectedFrom(Arrays.asList(collectedFrom)); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r1); - - final Relation r2 = new Relation(); - r2.setRelType("resultProject"); - r2.setSubRelType("outcome"); - r2.setRelClass("produces"); - r2.setSource(projectId); - r2.setTarget(docId); - r2.setCollectedFrom(Arrays.asList(collectedFrom)); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - res.add(r2); - } - - return res; - } - - protected abstract List addOtherResultRels( - final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp); - - private void populateResultFields( - final Result r, - final Document doc, - final KeyValue collectedFrom, - final KeyValue hostedBy, - final DataInfo info, - final long lastUpdateTimestamp) { - r.setDataInfo(info); - r.setLastupdatetimestamp(lastUpdateTimestamp); - r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); - r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); - r.setCollectedfrom(Arrays.asList(collectedFrom)); - r.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); - r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); - r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); - r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setOaiprovenance(prepareOAIprovenance(doc)); - r.setAuthor(prepareAuthors(doc, info)); - r.setLanguage(prepareLanguages(doc)); - r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setSubject(prepareSubjects(doc, info)); - r.setTitle(prepareTitles(doc, info)); - r.setRelevantdate(prepareRelevantDates(doc, info)); - r.setDescription(prepareDescriptions(doc, info)); - r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); - r.setPublisher(preparePublisher(doc, info)); - r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); - r.setSource(prepareSources(doc, info)); - r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setFormat(prepareFormats(doc, info)); - r.setContributor(prepareContributors(doc, info)); - r.setResourcetype(prepareResourceType(doc, info)); - r.setCoverage(prepareCoverages(doc, info)); - r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy)); - } - - protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); - - protected abstract List prepareInstances( - Document doc, - DataInfo info, - KeyValue collectedfrom, - KeyValue hostedby); - - protected abstract List> prepareSources(Document doc, DataInfo info); - - protected abstract List prepareRelevantDates(Document doc, DataInfo info); - - protected abstract List> prepareCoverages(Document doc, DataInfo info); - - protected abstract List> prepareContributors(Document doc, DataInfo info); - - protected abstract List> prepareFormats(Document doc, DataInfo info); - - protected abstract Field preparePublisher(Document doc, DataInfo info); - - protected abstract List> prepareDescriptions(Document doc, DataInfo info); - - protected abstract List prepareTitles(Document doc, DataInfo info); - - protected abstract List prepareSubjects(Document doc, DataInfo info); - - protected abstract Qualifier prepareLanguages(Document doc); - - protected abstract List prepareAuthors(Document doc, DataInfo info); - - protected abstract List> prepareOtherResearchProductTools( - Document doc, - DataInfo info); - - protected abstract List> prepareOtherResearchProductContactGroups( - Document doc, - DataInfo info); - - protected abstract List> prepareOtherResearchProductContactPersons( - Document doc, - DataInfo info); - - protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); - - protected abstract Field prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); - - protected abstract List prepareSoftwareLicenses( - Document doc, - DataInfo info); - - protected abstract List> prepareSoftwareDocumentationUrls( - Document doc, - DataInfo info); - - protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); - - protected abstract Field prepareDatasetMetadataVersionNumber( - Document doc, - DataInfo info); - - protected abstract Field prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); - - protected abstract Field prepareDatasetVersion(Document doc, DataInfo info); - - protected abstract Field prepareDatasetSize(Document doc, DataInfo info); - - protected abstract Field prepareDatasetDevice(Document doc, DataInfo info); - - protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); - - private Journal prepareJournal(final Document doc, final DataInfo info) { - final Node n = doc.selectSingleNode("//oaf:journal"); - if (n != null) { - final String name = n.getText(); - final String issnPrinted = n.valueOf("@issn"); - final String issnOnline = n.valueOf("@eissn"); - final String issnLinking = n.valueOf("@lissn"); - final String ep = n.valueOf("@ep"); - final String iss = n.valueOf("@iss"); - final String sp = n.valueOf("@sp"); - final String vol = n.valueOf("@vol"); - final String edition = n.valueOf("@edition"); - if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } - } - return null; - } - - protected Qualifier prepareQualifier( - final Node node, - final String xpath, - final String schemeId, - final String schemeName) { - final String classId = node.valueOf(xpath); - final String className = code2name.get(classId); - return qualifier(classId, className, schemeId, schemeName); - } - - protected List prepareListStructProps( - final Node node, - final String xpath, - final String xpathClassId, - final String schemeId, - final String schemeName, - final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - final String classId = n.valueOf(xpathClassId); - final String className = code2name.get(classId); - res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info)); - } - return res; - } - - protected List prepareListStructProps( - final Node node, - final String xpath, - final Qualifier qualifier, - final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res.add(structuredProperty(n.getText(), qualifier, info)); - } - return res; - } - - protected List prepareListStructProps( - final Node node, - final String xpath, - final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info)); - } - return res; - } - - protected OAIProvenance prepareOAIprovenance(final Document doc) { - final Node n = - doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - - if (n == null) { return null; } - - final String identifier = n.valueOf("./*[local-name()='identifier']"); - final String baseURL = n.valueOf("./*[local-name()='baseURL']");; - final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");; - final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); - final String datestamp = n.valueOf("./*[local-name()='datestamp']");; - final String harvestDate = n.valueOf("@harvestDate");; - - return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); - } - - protected DataInfo prepareDataInfo(final Document doc) { - final Node n = doc.selectSingleNode("//oaf:datainfo"); - - if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9"); } - - final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); - final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); - final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); - final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename"); - - final boolean deletedbyinference = - Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); - final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance"); - final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); - final String trust = n.valueOf("./oaf:trust"); - - return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); - } - - protected Field prepareField(final Node node, final String xpath, final DataInfo info) { - return field(node.valueOf(xpath), info); - } - - protected List> prepareListFields( - final Node node, - final String xpath, - final DataInfo info) { - return listFields(info, prepareListString(node, xpath)); - } - - protected List prepareListString(final Node node, final String xpath) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final String s = ((Node) o).getText().trim(); - if (StringUtils.isNotBlank(s)) { - res.add(s); - } - } - return res; - } + protected final Map code2name; + + protected static final Qualifier MAIN_TITLE_QUALIFIER = + qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + + protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER = + qualifier( + "publication", + "publication", + "dnet:result_typologies", + "dnet:result_typologies"); + protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER = + qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies"); + protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = + 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; + } + + public List processMdRecord(final String xml) { + try { + final Map nsContext = new HashMap<>(); + nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); + nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); + nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); + nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); + nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); + nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); + nsContext.put("datacite", "http://datacite.org/schema/kernel-3"); + DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); + + final Document doc = + DocumentHelper.parseText( + xml.replaceAll( + "http://datacite.org/schema/kernel-4", + "http://datacite.org/schema/kernel-3")); + + final String type = doc.valueOf("//dr:CobjCategory/@type"); + final KeyValue collectedFrom = + keyValue( + 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( + createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), + doc.valueOf("//oaf:hostedBy/@name")); + + final DataInfo info = prepareDataInfo(doc); + final long lastUpdateTimestamp = new Date().getTime(); + + return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + protected List createOafs( + final Document doc, + final String type, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { + + final List oafs = new ArrayList<>(); + + switch (type.toLowerCase()) { + case "": + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER); + p.setJournal(prepareJournal(doc, info)); + oafs.add(p); + break; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + d.setResulttype(DATASET_RESULTTYPE_QUALIFIER); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + oafs.add(d); + break; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + oafs.add(s); + break; + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + o.setResulttype(OTHER_RESULTTYPE_QUALIFIER); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + oafs.add(o); + break; + } + + if (!oafs.isEmpty()) { + oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp)); + oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp)); + } + + return oafs; + } + + private List addProjectRels( + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + + final List res = new ArrayList<>(); + + final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); + + for (final Object o : doc.selectNodes("//oaf:projectid")) { + final String projectId = createOpenaireId(40, ((Node) o).getText(), true); + + final Relation r1 = new Relation(); + r1.setRelType("resultProject"); + r1.setSubRelType("outcome"); + r1.setRelClass("isProducedBy"); + r1.setSource(docId); + r1.setTarget(projectId); + r1.setCollectedfrom(Arrays.asList(collectedFrom)); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r1); + + final Relation r2 = new Relation(); + r2.setRelType("resultProject"); + r2.setSubRelType("outcome"); + r2.setRelClass("produces"); + r2.setSource(projectId); + r2.setTarget(docId); + r2.setCollectedfrom(Arrays.asList(collectedFrom)); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r2); + } + + return res; + } + + protected abstract List addOtherResultRels( + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp); + + private void populateResultFields( + final Result r, + final Document doc, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { + r.setDataInfo(info); + r.setLastupdatetimestamp(lastUpdateTimestamp); + r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); + r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); + r.setCollectedfrom(Arrays.asList(collectedFrom)); + r.setPid( + prepareListStructProps( + doc, + "//oaf:identifier", + "@identifierType", + "dnet:pid_types", + "dnet:pid_types", + info)); + r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); + r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); + r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setOaiprovenance(prepareOAIprovenance(doc)); + r.setAuthor(prepareAuthors(doc, info)); + r.setLanguage(prepareLanguages(doc)); + r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setSubject(prepareSubjects(doc, info)); + r.setTitle(prepareTitles(doc, info)); + r.setRelevantdate(prepareRelevantDates(doc, info)); + r.setDescription(prepareDescriptions(doc, info)); + r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); + r.setPublisher(preparePublisher(doc, info)); + r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); + r.setSource(prepareSources(doc, info)); + r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setFormat(prepareFormats(doc, info)); + r.setContributor(prepareContributors(doc, info)); + r.setResourcetype(prepareResourceType(doc, info)); + r.setCoverage(prepareCoverages(doc, info)); + r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy)); + } + + protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); + + protected abstract List prepareInstances( + Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby); + + protected abstract List> prepareSources(Document doc, DataInfo info); + + protected abstract List prepareRelevantDates(Document doc, DataInfo info); + + protected abstract List> prepareCoverages(Document doc, DataInfo info); + + protected abstract List> prepareContributors(Document doc, DataInfo info); + + protected abstract List> prepareFormats(Document doc, DataInfo info); + + protected abstract Field preparePublisher(Document doc, DataInfo info); + + protected abstract List> prepareDescriptions(Document doc, DataInfo info); + + protected abstract List prepareTitles(Document doc, DataInfo info); + + protected abstract List prepareSubjects(Document doc, DataInfo info); + + protected abstract Qualifier prepareLanguages(Document doc); + + protected abstract List prepareAuthors(Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductTools( + Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductContactGroups( + Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductContactPersons( + Document doc, DataInfo info); + + protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); + + protected abstract Field prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); + + protected abstract List prepareSoftwareLicenses( + Document doc, DataInfo info); + + protected abstract List> prepareSoftwareDocumentationUrls( + Document doc, DataInfo info); + + protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); + + protected abstract Field prepareDatasetMetadataVersionNumber( + Document doc, DataInfo info); + + protected abstract Field prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); + + protected abstract Field prepareDatasetVersion(Document doc, DataInfo info); + + protected abstract Field prepareDatasetSize(Document doc, DataInfo info); + + protected abstract Field prepareDatasetDevice(Document doc, DataInfo info); + + protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); + + private Journal prepareJournal(final Document doc, final DataInfo info) { + final Node n = doc.selectSingleNode("//oaf:journal"); + if (n != null) { + final String name = n.getText(); + final String issnPrinted = n.valueOf("@issn"); + final String issnOnline = n.valueOf("@eissn"); + final String issnLinking = n.valueOf("@lissn"); + final String ep = n.valueOf("@ep"); + final String iss = n.valueOf("@iss"); + final String sp = n.valueOf("@sp"); + final String vol = n.valueOf("@vol"); + final String edition = n.valueOf("@edition"); + if (StringUtils.isNotBlank(name)) { + return journal( + name, + issnPrinted, + issnOnline, + issnLinking, + ep, + iss, + sp, + vol, + edition, + null, + null, + info); + } + } + return null; + } + + protected Qualifier prepareQualifier( + final Node node, final String xpath, final String schemeId, final String schemeName) { + final String classId = node.valueOf(xpath); + final String className = code2name.get(classId); + return qualifier(classId, className, schemeId, schemeName); + } + + protected List prepareListStructProps( + final Node node, + final String xpath, + final String xpathClassId, + final String schemeId, + final String schemeName, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + final String classId = n.valueOf(xpathClassId); + final String className = code2name.get(classId); + res.add( + structuredProperty( + n.getText(), classId, className, schemeId, schemeName, info)); + } + return res; + } + + protected List prepareListStructProps( + final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res.add(structuredProperty(n.getText(), qualifier, info)); + } + return res; + } + + protected List prepareListStructProps( + final Node node, final String xpath, final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res.add( + structuredProperty( + n.getText(), + n.valueOf("@classid"), + n.valueOf("@classname"), + n.valueOf("@schemeid"), + n.valueOf("@schemename"), + info)); + } + return res; + } + + protected OAIProvenance prepareOAIprovenance(final Document doc) { + final Node n = + doc.selectSingleNode( + "//*[local-name()='provenance']/*[local-name()='originDescription']"); + + if (n == null) { + return null; + } + + final String identifier = n.valueOf("./*[local-name()='identifier']"); + final String baseURL = n.valueOf("./*[local-name()='baseURL']"); + ; + final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']"); + ; + final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); + final String datestamp = n.valueOf("./*[local-name()='datestamp']"); + ; + final String harvestDate = n.valueOf("@harvestDate"); + ; + + return oaiIProvenance( + identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); + } + + protected DataInfo prepareDataInfo(final Document doc) { + final Node n = doc.selectSingleNode("//oaf:datainfo"); + + if (n == null) { + return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9"); + } + + final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); + final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); + final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); + final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename"); + + final boolean deletedbyinference = + Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); + final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance"); + final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); + final String trust = n.valueOf("./oaf:trust"); + + return dataInfo( + deletedbyinference, + inferenceprovenance, + inferred, + false, + qualifier(paClassId, paClassName, paSchemeId, paSchemeName), + trust); + } + + protected Field prepareField(final Node node, final String xpath, final DataInfo info) { + return field(node.valueOf(xpath), info); + } + + protected List> prepareListFields( + final Node node, final String xpath, final DataInfo info) { + return listFields(info, prepareListString(node, xpath)); + } + + protected List prepareListString(final Node node, final String xpath) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final String s = ((Node) o).getText().trim(); + if (StringUtils.isNotBlank(s)) { + res.add(s); + } + } + return res; + } } 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 f0d4c62c5..476e617d7 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 @@ -10,23 +10,6 @@ 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 java.io.Closeable; -import java.io.IOException; -import java.sql.Array; -import java.sql.ResultSet; -import java.sql.SQLException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Date; -import java.util.List; -import java.util.function.Consumer; -import java.util.function.Function; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; @@ -47,458 +30,534 @@ 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; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Date; +import java.util.List; +import java.util.function.Consumer; +import java.util.function.Function; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; public class MigrateDbEntitiesApplication extends AbstractMigrationApplication - implements Closeable { - - private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = - qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenance_actions", "dnet:provenance_actions"); - - private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); - - private final DbClient dbClient; - - private final long lastUpdateTimestamp; - - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = - new ArgumentApplicationParser( - IOUtils.toString(MigrateDbEntitiesApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json"))); - - parser.parseArgument(args); - - final String dbUrl = parser.get("postgresUrl"); - final String dbUser = parser.get("postgresUser"); - final String dbPassword = parser.get("postgresPassword"); - - final String hdfsPath = parser.get("hdfsPath"); - - final boolean processClaims = - parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims"); - - try (final MigrateDbEntitiesApplication smdbe = - new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser, dbPassword)) { - if (processClaims) { - log.info("Processing claims..."); - smdbe.execute("queryClaims.sql", smdbe::processClaims); - } else { - log.info("Processing datasources..."); - smdbe.execute("queryDatasources.sql", smdbe::processDatasource); - - log.info("Processing projects..."); - smdbe.execute("queryProjects.sql", smdbe::processProject); - - log.info("Processing orgs..."); - smdbe.execute("queryOrganizations.sql", smdbe::processOrganization); - - log.info("Processing relations ds <-> orgs ..."); - smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization); - - log.info("Processing projects <-> orgs ..."); - smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization); - } - log.info("All done."); - } - } - - protected MigrateDbEntitiesApplication() { // ONLY FOR UNIT TEST - super(); - this.dbClient = null; - this.lastUpdateTimestamp = new Date().getTime(); - } - - public MigrateDbEntitiesApplication( - final String hdfsPath, final String dbUrl, final String dbUser, final String dbPassword) - throws Exception { - super(hdfsPath); - this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); - this.lastUpdateTimestamp = new Date().getTime(); - } - - public void execute(final String sqlFile, final Function> producer) - throws Exception { - final String sql = - IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile)); - - final Consumer consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf)); - - dbClient.processResults(sql, consumer); - } - - public List processDatasource(final ResultSet rs) { - - try { - - final DataInfo info = prepareDataInfo(rs); - - final Datasource ds = new Datasource(); - - ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); - ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); - ds.setCollectedfrom(listKeyValues(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 - ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB - ds.setOaiprovenance(null); // Values not present in the DB - ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); - ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility"))); - ds.setOfficialname(field(rs.getString("officialname"), info)); - ds.setEnglishname(field(rs.getString("englishname"), info)); - ds.setWebsiteurl(field(rs.getString("websiteurl"), info)); - ds.setLogourl(field(rs.getString("logourl"), info)); - ds.setContactemail(field(rs.getString("contactemail"), info)); - ds.setNamespaceprefix(field(rs.getString("namespaceprefix"), info)); - ds.setLatitude(field(Double.toString(rs.getDouble("latitude")), info)); - ds.setLongitude(field(Double.toString(rs.getDouble("longitude")), info)); - ds.setDateofvalidation(field(asString(rs.getDate("dateofvalidation")), info)); - ds.setDescription(field(rs.getString("description"), info)); - ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); - ds.setOdnumberofitems(field(Double.toString(rs.getInt("odnumberofitems")), info)); - ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info)); - ds.setOdpolicies(field(rs.getString("odpolicies"), info)); - ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); - ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); - ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); - ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); - ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info)); - ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info)); - ds.setDataprovider(field(rs.getBoolean("dataprovider"), info)); - ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info)); - ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info)); - ds.setDatauploadtype(field(rs.getString("datauploadtype"), info)); - ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); - ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info)); - ds.setVersioning(field(rs.getBoolean("versioning"), info)); - ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info)); - ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info)); - ds.setPidsystems(field(rs.getString("pidsystems"), info)); - ds.setCertificates(field(rs.getString("certificates"), info)); - ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array - ds.setJournal(prepareJournal(rs.getString("officialname"), rs.getString("journal"), info)); // Journal - ds.setDataInfo(info); - ds.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(ds); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processProject(final ResultSet rs) { - try { - - final DataInfo info = prepareDataInfo(rs); - - final Project p = new Project(); - - p.setId(createOpenaireId(40, rs.getString("projectid"), true)); - p.setOriginalId(Arrays.asList(rs.getString("projectid"))); - p.setCollectedfrom(listKeyValues(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"))); - p.setExtraInfo(new ArrayList<>()); // Values not present in the DB - p.setOaiprovenance(null); // Values not present in the DB - p.setWebsiteurl(field(rs.getString("websiteurl"), info)); - p.setCode(field(rs.getString("code"), info)); - p.setAcronym(field(rs.getString("acronym"), info)); - p.setTitle(field(rs.getString("title"), info)); - p.setStartdate(field(asString(rs.getDate("startdate")), info)); - p.setEnddate(field(asString(rs.getDate("enddate")), info)); - p.setCallidentifier(field(rs.getString("callidentifier"), info)); - p.setKeywords(field(rs.getString("keywords"), info)); - p.setDuration(field(Integer.toString(rs.getInt("duration")), info)); - p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info)); - p.setOamandatepublications(field(Boolean.toString(rs.getBoolean("oamandatepublications")), info)); - p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info)); - p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); - p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info)); - p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype"))); - p.setOptional1(field(rs.getString("optional1"), info)); - p.setOptional2(field(rs.getString("optional2"), info)); - p.setJsonextrainfo(field(rs.getString("jsonextrainfo"), info)); - p.setContactfullname(field(rs.getString("contactfullname"), info)); - p.setContactfax(field(rs.getString("contactfax"), info)); - p.setContactphone(field(rs.getString("contactphone"), info)); - p.setContactemail(field(rs.getString("contactemail"), info)); - p.setSummary(field(rs.getString("summary"), info)); - p.setCurrency(field(rs.getString("currency"), info)); - p.setTotalcost(new Float(rs.getDouble("totalcost"))); - p.setFundedamount(new Float(rs.getDouble("fundedamount"))); - p.setDataInfo(info); - p.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(p); - - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processOrganization(final ResultSet rs) { - - try { - - final DataInfo info = prepareDataInfo(rs); - - final Organization o = new Organization(); - - o.setId(createOpenaireId(20, rs.getString("organizationid"), true)); - o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); - o.setCollectedfrom(listKeyValues(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"))); - o.setExtraInfo(new ArrayList<>()); // Values not present in the DB - o.setOaiprovenance(null); // Values not present in the DB - o.setLegalshortname(field(rs.getString("legalshortname"), info)); - o.setLegalname(field(rs.getString("legalname"), info)); - o.setAlternativeNames(new ArrayList<>()); // Values not returned by the SQL query - o.setWebsiteurl(field(rs.getString("websiteurl"), info)); - o.setLogourl(field(rs.getString("logourl"), info)); - o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info)); - o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info)); - o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info)); - o.setEcresearchorganization(field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info)); - o.setEchighereducation(field(Boolean.toString(rs.getBoolean("echighereducation")), info)); - o.setEcinternationalorganizationeurinterests(field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info)); - o.setEcinternationalorganization(field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info)); - o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info)); - o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info)); - o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info)); - o.setCountry(prepareQualifierSplitting(rs.getString("country"))); - o.setDataInfo(info); - o.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(o); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processDatasourceOrganization(final ResultSet rs) { - try { - final DataInfo info = prepareDataInfo(rs); - final String orgId = createOpenaireId(20, rs.getString("organization"), true); - final String dsId = createOpenaireId(10, rs.getString("datasource"), true); - final List collectedFrom = - listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - - final Relation r1 = new Relation(); - r1.setRelType("datasourceOrganization"); - r1.setSubRelType("provision"); - r1.setRelClass("isProvidedBy"); - r1.setSource(dsId); - r1.setTarget(orgId); - r1.setCollectedFrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - final Relation r2 = new Relation(); - r2.setRelType("datasourceOrganization"); - r2.setSubRelType("provision"); - r2.setRelClass("provides"); - r2.setSource(orgId); - r2.setTarget(dsId); - r2.setCollectedFrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(r1, r2); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processProjectOrganization(final ResultSet rs) { - try { - final DataInfo info = prepareDataInfo(rs); - final String orgId = createOpenaireId(20, rs.getString("resporganization"), true); - final String projectId = createOpenaireId(40, rs.getString("project"), true); - final List collectedFrom = - listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - - final Relation r1 = new Relation(); - r1.setRelType("projectOrganization"); - r1.setSubRelType("participation"); - r1.setRelClass("isParticipant"); - r1.setSource(projectId); - r1.setTarget(orgId); - r1.setCollectedFrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - final Relation r2 = new Relation(); - r2.setRelType("projectOrganization"); - r2.setSubRelType("participation"); - r2.setRelClass("hasParticipant"); - r2.setSource(orgId); - r2.setTarget(projectId); - r2.setCollectedFrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(r1, r2); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - public List processClaims(final ResultSet rs) { - - final DataInfo info = - dataInfo(false, null, false, false, qualifier("user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"), "0.9"); - - final List collectedFrom = listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE"); - - try { - - if (rs.getString("source_type").equals("context")) { - final Result r; - - if (rs.getString("target_type").equals("dataset")) { - r = new Dataset(); - } else if (rs.getString("target_type").equals("software")) { - r = new Software(); - } else if (rs.getString("target_type").equals("other")) { - r = new OtherResearchProduct(); - } else { - r = new Publication(); - } - r.setId(createOpenaireId(50, rs.getString("target_id"), false)); - r.setLastupdatetimestamp(lastUpdateTimestamp); - r.setContext(prepareContext(rs.getString("source_id"), info)); - r.setDataInfo(info); - r.setCollectedfrom(collectedFrom); - - return Arrays.asList(r); - } else { - final String sourceId = - createOpenaireId(rs.getString("source_type"), rs.getString("source_id"), false); - final String targetId = - createOpenaireId(rs.getString("target_type"), rs.getString("target_id"), false); - - final Relation r1 = new Relation(); - 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"); - } - - r1.setSource(sourceId); - r1.setTarget(targetId); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - r2.setSource(targetId); - r2.setTarget(sourceId); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(r1, r2); - } - - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - private List prepareContext(final String id, final DataInfo dataInfo) { - final Context context = new Context(); - context.setId(id); - context.setDataInfo(Arrays.asList(dataInfo)); - return Arrays.asList(context); - } - - private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException { - final Boolean deletedbyinference = rs.getBoolean("deletedbyinference"); - final String inferenceprovenance = rs.getString("inferenceprovenance"); - final Boolean inferred = rs.getBoolean("inferred"); - final String trust = rs.getString("trust"); - return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust); - } - - private Qualifier prepareQualifierSplitting(final String s) { - if (StringUtils.isBlank(s)) { return null; } - final String[] arr = s.split("@@@"); - return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null; - } - - private List> prepareListFields(final Array array, final DataInfo info) { - try { - return array != null - ? listFields(info, (String[]) array.getArray()) - : new ArrayList<>(); - } catch (final SQLException e) { - throw new RuntimeException("Invalid SQL array", e); - } - } - - private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) { - if (StringUtils.isBlank(s)) { return null; } - final String[] parts = s.split("###"); - if (parts.length == 2) { - final String value = parts[0]; - final String[] arr = parts[1].split("@@@"); - if (arr.length == 4) { return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); } - } - return null; - } - - private List prepareListOfStructProps( - final Array array, - final DataInfo dataInfo) throws SQLException { - final List res = new ArrayList<>(); - if (array != null) { - for (final String s : (String[]) array.getArray()) { - final StructuredProperty sp = prepareStructProp(s, dataInfo); - if (sp != null) { - res.add(sp); - } - } - } - - return res; - } - - private Journal prepareJournal(final String name, final String sj, final DataInfo info) { - if (StringUtils.isNotBlank(sj)) { - final String[] arr = sj.split("@@@"); - if (arr.length == 3) { - final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null; - final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;; - final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;; - if (issn != null || eissn != null || lissn != null) { - return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info); - } - } - } - return null; - } - - @Override - public void close() throws IOException { - super.close(); - dbClient.close(); - } + implements Closeable { + + private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = + qualifier( + "sysimport:crosswalk:entityregistry", + "sysimport:crosswalk:entityregistry", + "dnet:provenance_actions", + "dnet:provenance_actions"); + + private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); + + private final DbClient dbClient; + + private final long lastUpdateTimestamp; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + MigrateDbEntitiesApplication.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json"))); + + parser.parseArgument(args); + + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); + + final String hdfsPath = parser.get("hdfsPath"); + + final boolean processClaims = + parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims"); + + try (final MigrateDbEntitiesApplication smdbe = + new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser, dbPassword)) { + if (processClaims) { + log.info("Processing claims..."); + smdbe.execute("queryClaims.sql", smdbe::processClaims); + } else { + log.info("Processing datasources..."); + smdbe.execute("queryDatasources.sql", smdbe::processDatasource); + + log.info("Processing projects..."); + smdbe.execute("queryProjects.sql", smdbe::processProject); + + log.info("Processing orgs..."); + smdbe.execute("queryOrganizations.sql", smdbe::processOrganization); + + log.info("Processing relations ds <-> orgs ..."); + smdbe.execute( + "queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization); + + log.info("Processing projects <-> orgs ..."); + smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization); + } + log.info("All done."); + } + } + + protected MigrateDbEntitiesApplication() { // ONLY FOR UNIT TEST + super(); + this.dbClient = null; + this.lastUpdateTimestamp = new Date().getTime(); + } + + public MigrateDbEntitiesApplication( + final String hdfsPath, final String dbUrl, final String dbUser, final String dbPassword) + throws Exception { + super(hdfsPath); + this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); + this.lastUpdateTimestamp = new Date().getTime(); + } + + public void execute(final String sqlFile, final Function> producer) + throws Exception { + final String sql = + IOUtils.toString( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile)); + + final Consumer consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf)); + + dbClient.processResults(sql, consumer); + } + + public List processDatasource(final ResultSet rs) { + + try { + + final DataInfo info = prepareDataInfo(rs); + + final Datasource ds = new Datasource(); + + ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); + ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); + ds.setCollectedfrom( + listKeyValues( + 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 + ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB + ds.setOaiprovenance(null); // Values not present in the DB + ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); + ds.setOpenairecompatibility( + prepareQualifierSplitting(rs.getString("openairecompatibility"))); + ds.setOfficialname(field(rs.getString("officialname"), info)); + ds.setEnglishname(field(rs.getString("englishname"), info)); + ds.setWebsiteurl(field(rs.getString("websiteurl"), info)); + ds.setLogourl(field(rs.getString("logourl"), info)); + ds.setContactemail(field(rs.getString("contactemail"), info)); + ds.setNamespaceprefix(field(rs.getString("namespaceprefix"), info)); + ds.setLatitude(field(Double.toString(rs.getDouble("latitude")), info)); + ds.setLongitude(field(Double.toString(rs.getDouble("longitude")), info)); + ds.setDateofvalidation(field(asString(rs.getDate("dateofvalidation")), info)); + ds.setDescription(field(rs.getString("description"), info)); + ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); + ds.setOdnumberofitems(field(Double.toString(rs.getInt("odnumberofitems")), info)); + ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info)); + ds.setOdpolicies(field(rs.getString("odpolicies"), info)); + ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); + ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); + ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); + ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); + ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info)); + ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info)); + ds.setDataprovider(field(rs.getBoolean("dataprovider"), info)); + ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info)); + ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info)); + ds.setDatauploadtype(field(rs.getString("datauploadtype"), info)); + ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); + ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info)); + ds.setVersioning(field(rs.getBoolean("versioning"), info)); + ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info)); + ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info)); + ds.setPidsystems(field(rs.getString("pidsystems"), info)); + ds.setCertificates(field(rs.getString("certificates"), info)); + ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array + ds.setJournal( + prepareJournal( + rs.getString("officialname"), + rs.getString("journal"), + info)); // Journal + ds.setDataInfo(info); + ds.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(ds); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processProject(final ResultSet rs) { + try { + + final DataInfo info = prepareDataInfo(rs); + + final Project p = new Project(); + + p.setId(createOpenaireId(40, rs.getString("projectid"), true)); + p.setOriginalId(Arrays.asList(rs.getString("projectid"))); + p.setCollectedfrom( + listKeyValues( + 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"))); + p.setExtraInfo(new ArrayList<>()); // Values not present in the DB + p.setOaiprovenance(null); // Values not present in the DB + p.setWebsiteurl(field(rs.getString("websiteurl"), info)); + p.setCode(field(rs.getString("code"), info)); + p.setAcronym(field(rs.getString("acronym"), info)); + p.setTitle(field(rs.getString("title"), info)); + p.setStartdate(field(asString(rs.getDate("startdate")), info)); + p.setEnddate(field(asString(rs.getDate("enddate")), info)); + p.setCallidentifier(field(rs.getString("callidentifier"), info)); + p.setKeywords(field(rs.getString("keywords"), info)); + p.setDuration(field(Integer.toString(rs.getInt("duration")), info)); + p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info)); + p.setOamandatepublications( + field(Boolean.toString(rs.getBoolean("oamandatepublications")), info)); + p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info)); + p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); + p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info)); + p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype"))); + p.setOptional1(field(rs.getString("optional1"), info)); + p.setOptional2(field(rs.getString("optional2"), info)); + p.setJsonextrainfo(field(rs.getString("jsonextrainfo"), info)); + p.setContactfullname(field(rs.getString("contactfullname"), info)); + p.setContactfax(field(rs.getString("contactfax"), info)); + p.setContactphone(field(rs.getString("contactphone"), info)); + p.setContactemail(field(rs.getString("contactemail"), info)); + p.setSummary(field(rs.getString("summary"), info)); + p.setCurrency(field(rs.getString("currency"), info)); + p.setTotalcost(new Float(rs.getDouble("totalcost"))); + p.setFundedamount(new Float(rs.getDouble("fundedamount"))); + p.setDataInfo(info); + p.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(p); + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processOrganization(final ResultSet rs) { + + try { + + final DataInfo info = prepareDataInfo(rs); + + final Organization o = new Organization(); + + o.setId(createOpenaireId(20, rs.getString("organizationid"), true)); + o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); + o.setCollectedfrom( + listKeyValues( + 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"))); + o.setExtraInfo(new ArrayList<>()); // Values not present in the DB + o.setOaiprovenance(null); // Values not present in the DB + o.setLegalshortname(field(rs.getString("legalshortname"), info)); + o.setLegalname(field(rs.getString("legalname"), info)); + o.setAlternativeNames(new ArrayList<>()); // Values not returned by the SQL query + o.setWebsiteurl(field(rs.getString("websiteurl"), info)); + o.setLogourl(field(rs.getString("logourl"), info)); + o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info)); + o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info)); + o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info)); + o.setEcresearchorganization( + field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info)); + o.setEchighereducation( + field(Boolean.toString(rs.getBoolean("echighereducation")), info)); + o.setEcinternationalorganizationeurinterests( + field( + Boolean.toString( + rs.getBoolean("ecinternationalorganizationeurinterests")), + info)); + o.setEcinternationalorganization( + field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info)); + o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info)); + o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info)); + o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info)); + o.setCountry(prepareQualifierSplitting(rs.getString("country"))); + o.setDataInfo(info); + o.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(o); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processDatasourceOrganization(final ResultSet rs) { + try { + final DataInfo info = prepareDataInfo(rs); + final String orgId = createOpenaireId(20, rs.getString("organization"), true); + final String dsId = createOpenaireId(10, rs.getString("datasource"), true); + final List collectedFrom = + listKeyValues( + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname")); + + final Relation r1 = new Relation(); + r1.setRelType("datasourceOrganization"); + r1.setSubRelType("provision"); + r1.setRelClass("isProvidedBy"); + r1.setSource(dsId); + r1.setTarget(orgId); + r1.setCollectedfrom(collectedFrom); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + + final Relation r2 = new Relation(); + r2.setRelType("datasourceOrganization"); + r2.setSubRelType("provision"); + r2.setRelClass("provides"); + r2.setSource(orgId); + r2.setTarget(dsId); + r2.setCollectedfrom(collectedFrom); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(r1, r2); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processProjectOrganization(final ResultSet rs) { + try { + final DataInfo info = prepareDataInfo(rs); + final String orgId = createOpenaireId(20, rs.getString("resporganization"), true); + final String projectId = createOpenaireId(40, rs.getString("project"), true); + final List collectedFrom = + listKeyValues( + createOpenaireId(10, rs.getString("collectedfromid"), true), + rs.getString("collectedfromname")); + + final Relation r1 = new Relation(); + r1.setRelType("projectOrganization"); + r1.setSubRelType("participation"); + r1.setRelClass("isParticipant"); + r1.setSource(projectId); + r1.setTarget(orgId); + r1.setCollectedfrom(collectedFrom); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + + final Relation r2 = new Relation(); + r2.setRelType("projectOrganization"); + r2.setSubRelType("participation"); + r2.setRelClass("hasParticipant"); + r2.setSource(orgId); + r2.setTarget(projectId); + r2.setCollectedfrom(collectedFrom); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(r1, r2); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public List processClaims(final ResultSet rs) { + + final DataInfo info = + dataInfo( + false, + null, + false, + false, + qualifier( + "user:claim", + "user:claim", + "dnet:provenanceActions", + "dnet:provenanceActions"), + "0.9"); + + final List collectedFrom = + listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE"); + + try { + + if (rs.getString("source_type").equals("context")) { + final Result r; + + if (rs.getString("target_type").equals("dataset")) { + r = new Dataset(); + } else if (rs.getString("target_type").equals("software")) { + r = new Software(); + } else if (rs.getString("target_type").equals("other")) { + r = new OtherResearchProduct(); + } else { + r = new Publication(); + } + r.setId(createOpenaireId(50, rs.getString("target_id"), false)); + r.setLastupdatetimestamp(lastUpdateTimestamp); + r.setContext(prepareContext(rs.getString("source_id"), info)); + r.setDataInfo(info); + r.setCollectedfrom(collectedFrom); + + return Arrays.asList(r); + } else { + final String sourceId = + createOpenaireId( + rs.getString("source_type"), rs.getString("source_id"), false); + final String targetId = + createOpenaireId( + rs.getString("target_type"), rs.getString("target_id"), false); + + final Relation r1 = new Relation(); + 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"); + } + + r1.setSource(sourceId); + r1.setTarget(targetId); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + + r2.setSource(targetId); + r2.setTarget(sourceId); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(r1, r2); + } + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + private List prepareContext(final String id, final DataInfo dataInfo) { + final Context context = new Context(); + context.setId(id); + context.setDataInfo(Arrays.asList(dataInfo)); + return Arrays.asList(context); + } + + private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException { + final Boolean deletedbyinference = rs.getBoolean("deletedbyinference"); + final String inferenceprovenance = rs.getString("inferenceprovenance"); + final Boolean inferred = rs.getBoolean("inferred"); + final String trust = rs.getString("trust"); + return dataInfo( + deletedbyinference, + inferenceprovenance, + inferred, + false, + ENTITYREGISTRY_PROVENANCE_ACTION, + trust); + } + + private Qualifier prepareQualifierSplitting(final String s) { + if (StringUtils.isBlank(s)) { + return null; + } + final String[] arr = s.split("@@@"); + return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null; + } + + private List> prepareListFields(final Array array, final DataInfo info) { + try { + return array != null + ? listFields(info, (String[]) array.getArray()) + : new ArrayList<>(); + } catch (final SQLException e) { + throw new RuntimeException("Invalid SQL array", e); + } + } + + private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) { + if (StringUtils.isBlank(s)) { + return null; + } + final String[] parts = s.split("###"); + if (parts.length == 2) { + final String value = parts[0]; + final String[] arr = parts[1].split("@@@"); + if (arr.length == 4) { + return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); + } + } + return null; + } + + private List prepareListOfStructProps( + final Array array, final DataInfo dataInfo) throws SQLException { + final List res = new ArrayList<>(); + if (array != null) { + for (final String s : (String[]) array.getArray()) { + final StructuredProperty sp = prepareStructProp(s, dataInfo); + if (sp != null) { + res.add(sp); + } + } + } + + return res; + } + + private Journal prepareJournal(final String name, final String sj, final DataInfo info) { + if (StringUtils.isNotBlank(sj)) { + final String[] arr = sj.split("@@@"); + if (arr.length == 3) { + final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null; + final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null; + ; + final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null; + ; + if (issn != null || eissn != null || lissn != null) { + return journal( + name, issn, eissn, eissn, null, null, null, null, null, null, null, + info); + } + } + } + return null; + } + + @Override + public void close() throws IOException { + super.close(); + dbClient.close(); + } } 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 e77b1f87f..6b304c9b0 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 5e6462417..f6fab499b 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 bfd5d5c7f..4d3cb02d6 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 b0b8aba3c..b09c5d638 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 @@ -6,10 +6,14 @@ 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 java.io.IOException; import java.util.List; import java.util.Map; - import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; @@ -18,126 +22,119 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -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; - @ExtendWith(MockitoExtension.class) public class MappersTest { - @Mock - private Map code2name; + @Mock private Map code2name; - @BeforeEach - public void setUp() throws Exception { - when(code2name.get(anyString())).thenAnswer(invocation -> invocation.getArgument(0)); - } + @BeforeEach + public void setUp() throws Exception { + when(code2name.get(anyString())).thenAnswer(invocation -> invocation.getArgument(0)); + } - @Test - void testPublication() throws IOException { - final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml")); + @Test + void testPublication() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml")); - final List list = new OafToOafMapper(code2name).processMdRecord(xml); + final List list = new OafToOafMapper(code2name).processMdRecord(xml); - assertEquals(3, list.size()); - assertTrue(list.get(0) instanceof Publication); - assertTrue(list.get(1) instanceof Relation); - assertTrue(list.get(2) instanceof Relation); + assertEquals(3, list.size()); + assertTrue(list.get(0) instanceof Publication); + assertTrue(list.get(1) instanceof Relation); + assertTrue(list.get(2) instanceof Relation); - final Publication p = (Publication) list.get(0); - final Relation r1 = (Relation) list.get(1); - final Relation r2 = (Relation) list.get(2); + final Publication p = (Publication) list.get(0); + final Relation r1 = (Relation) list.get(1); + 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); - assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); - assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); + 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); + assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); + 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())); + 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)); - } + // System.out.println(new ObjectMapper().writeValueAsString(r1)); + // System.out.println(new ObjectMapper().writeValueAsString(r2)); + } - @Test - void testDataset() throws IOException { - final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml")); + @Test + void testDataset() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml")); - final List list = new OdfToOafMapper(code2name).processMdRecord(xml); + final List list = new OdfToOafMapper(code2name).processMdRecord(xml); - assertEquals(3, list.size()); - assertTrue(list.get(0) instanceof Dataset); - assertTrue(list.get(1) instanceof Relation); - assertTrue(list.get(2) instanceof Relation); + 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); + 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(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())); - } + 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 - void testSoftware() throws IOException { - final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml")); + @Test + void testSoftware() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml")); - final List list = new OdfToOafMapper(code2name).processMdRecord(xml); + final List list = new OdfToOafMapper(code2name).processMdRecord(xml); - assertEquals(1, list.size()); - assertTrue(list.get(0) instanceof Software); + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Software); - final Software s = (Software) list.get(0); + 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); - } + 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); + } - private void assertValidId(final String id) { - assertEquals(49, id.length()); - assertEquals('|', id.charAt(2)); - assertEquals(':', id.charAt(15)); - assertEquals(':', id.charAt(16)); - } + private void assertValidId(final String id) { + assertEquals(49, id.length()); + assertEquals('|', id.charAt(2)); + assertEquals(':', id.charAt(15)); + assertEquals(':', id.charAt(16)); + } } 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 b0802f662..b88731ba2 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 @@ -4,6 +4,14 @@ 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 java.io.IOException; import java.sql.Array; import java.sql.Date; @@ -11,7 +19,6 @@ import java.sql.ResultSet; 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; @@ -21,325 +28,325 @@ import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; -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; - @ExtendWith(MockitoExtension.class) public class MigrateDbEntitiesApplicationTest { - private MigrateDbEntitiesApplication app; + private MigrateDbEntitiesApplication app; - @Mock - private ResultSet rs; + @Mock private ResultSet rs; - @BeforeEach - public void setUp() { - this.app = new MigrateDbEntitiesApplication(); - } + @BeforeEach + public void setUp() { + this.app = new MigrateDbEntitiesApplication(); + } - @Test - public void testProcessDatasource() throws Exception { - final List fields = prepareMocks("datasources_resultset_entry.json"); + @Test + public void testProcessDatasource() throws Exception { + final List fields = prepareMocks("datasources_resultset_entry.json"); - final List list = app.processDatasource(rs); - assertEquals(1, list.size()); - verifyMocks(fields); + final List list = app.processDatasource(rs); + assertEquals(1, list.size()); + verifyMocks(fields); - 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).getValue(), getValueAsString("collectedfromname", fields)); - } + 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).getValue(), + getValueAsString("collectedfromname", fields)); + } - @Test - public void testProcessProject() throws Exception { - final List fields = prepareMocks("projects_resultset_entry.json"); + @Test + public void testProcessProject() throws Exception { + final List fields = prepareMocks("projects_resultset_entry.json"); - final List list = app.processProject(rs); - assertEquals(1, list.size()); - verifyMocks(fields); + final List list = app.processProject(rs); + assertEquals(1, list.size()); + verifyMocks(fields); - 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).getValue(), getValueAsString("collectedfromname", fields)); + 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).getValue(), + getValueAsString("collectedfromname", fields)); + } - } + @Test + public void testProcessOrganization() throws Exception { + final List fields = prepareMocks("organizations_resultset_entry.json"); - @Test - public void testProcessOrganization() throws Exception { - final List fields = prepareMocks("organizations_resultset_entry.json"); + final List list = app.processOrganization(rs); - final List list = app.processOrganization(rs); + assertEquals(1, list.size()); - assertEquals(1, list.size()); + verifyMocks(fields); - verifyMocks(fields); + 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)); + assertEquals( + o.getCountry().getClassid(), getValueAsString("country", fields).split("@@@")[0]); + assertEquals( + o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]); + assertEquals( + o.getCountry().getSchemeid(), getValueAsString("country", fields).split("@@@")[2]); + assertEquals( + o.getCountry().getSchemename(), + getValueAsString("country", fields).split("@@@")[3]); + assertEquals( + o.getCollectedfrom().get(0).getValue(), + getValueAsString("collectedfromname", fields)); + } - 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)); - assertEquals(o.getCountry().getClassid(), getValueAsString("country", fields).split("@@@")[0]); - assertEquals(o.getCountry().getClassname(), getValueAsString("country", fields).split("@@@")[1]); - assertEquals(o.getCountry().getSchemeid(), getValueAsString("country", fields).split("@@@")[2]); - assertEquals(o.getCountry().getSchemename(), getValueAsString("country", fields).split("@@@")[3]); - assertEquals(o.getCollectedfrom().get(0).getValue(), getValueAsString("collectedfromname", fields)); - } + @Test + public void testProcessDatasourceOrganization() throws Exception { + final List fields = prepareMocks("datasourceorganization_resultset_entry.json"); - @Test - public void testProcessDatasourceOrganization() throws Exception { - final List fields = prepareMocks("datasourceorganization_resultset_entry.json"); + final List list = app.processDatasourceOrganization(rs); - final List list = app.processDatasourceOrganization(rs); + assertEquals(2, list.size()); + verifyMocks(fields); - assertEquals(2, list.size()); - verifyMocks(fields); + final Relation r1 = (Relation) list.get(0); + final Relation r2 = (Relation) list.get(1); + assertValidId(r1.getSource()); + assertValidId(r2.getSource()); + assertEquals(r1.getSource(), r2.getTarget()); + assertEquals(r2.getSource(), r1.getTarget()); + } - final Relation r1 = (Relation) list.get(0); - final Relation r2 = (Relation) list.get(1); - assertValidId(r1.getSource()); - assertValidId(r2.getSource()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - } + @Test + public void testProcessProjectOrganization() throws Exception { + final List fields = prepareMocks("projectorganization_resultset_entry.json"); - @Test - public void testProcessProjectOrganization() throws Exception { - final List fields = prepareMocks("projectorganization_resultset_entry.json"); + final List list = app.processProjectOrganization(rs); - final List list = app.processProjectOrganization(rs); + assertEquals(2, list.size()); + verifyMocks(fields); - assertEquals(2, list.size()); - verifyMocks(fields); + final Relation r1 = (Relation) list.get(0); + final Relation r2 = (Relation) list.get(1); + assertValidId(r1.getSource()); + 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()); + } - final Relation r1 = (Relation) list.get(0); - final Relation r2 = (Relation) list.get(1); - assertValidId(r1.getSource()); - 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 + public void testProcessClaims_context() throws Exception { + final List fields = prepareMocks("claimscontext_resultset_entry.json"); - @Test - public void testProcessClaims_context() throws Exception { - final List fields = prepareMocks("claimscontext_resultset_entry.json"); + final List list = app.processClaims(rs); - final List list = app.processClaims(rs); + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Result); + final Result r = (Result) list.get(0); - assertEquals(1, list.size()); - assertTrue(list.get(0) instanceof Result); - final Result r = (Result) list.get(0); + verifyMocks(fields); - verifyMocks(fields); + assertValidId(r.getCollectedfrom().get(0).getKey()); + } - assertValidId(r.getCollectedfrom().get(0).getKey()); - } + @Test + public void testProcessClaims_rels() throws Exception { + final List fields = prepareMocks("claimsrel_resultset_entry.json"); - @Test - public void testProcessClaims_rels() throws Exception { - final List fields = prepareMocks("claimsrel_resultset_entry.json"); + final List list = app.processClaims(rs); - final List list = app.processClaims(rs); + assertEquals(2, list.size()); + verifyMocks(fields); - assertEquals(2, list.size()); - verifyMocks(fields); + assertTrue(list.get(0) instanceof Relation); + assertTrue(list.get(1) instanceof Relation); - 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); - 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.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()); - 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)); + } - // System.out.println(new ObjectMapper().writeValueAsString(r1)); - // System.out.println(new ObjectMapper().writeValueAsString(r2)); - } + private List prepareMocks(final String jsonFile) throws IOException, SQLException { + final String json = IOUtils.toString(getClass().getResourceAsStream(jsonFile)); + final ObjectMapper mapper = new ObjectMapper(); + final List list = + mapper.readValue(json, new TypeReference>() {}); - private List prepareMocks(final String jsonFile) throws IOException, SQLException { - final String json = IOUtils.toString(getClass().getResourceAsStream(jsonFile)); - final ObjectMapper mapper = new ObjectMapper(); - final List list = - mapper.readValue(json, new TypeReference>() {}); + for (final TypedField tf : list) { + if (tf.getValue() == null) { + switch (tf.getType()) { + case "not_used": + break; + case "boolean": + Mockito.when(rs.getBoolean(tf.getField())).thenReturn(false); + break; + case "date": + Mockito.when(rs.getDate(tf.getField())).thenReturn(null); + break; + case "int": + Mockito.when(rs.getInt(tf.getField())).thenReturn(0); + break; + case "double": + Mockito.when(rs.getDouble(tf.getField())).thenReturn(0.0); + break; + case "array": + Mockito.when(rs.getArray(tf.getField())).thenReturn(null); + break; + case "string": + default: + Mockito.when(rs.getString(tf.getField())).thenReturn(null); + break; + } + } else { + switch (tf.getType()) { + case "not_used": + break; + case "boolean": + Mockito.when(rs.getBoolean(tf.getField())) + .thenReturn(Boolean.parseBoolean(tf.getValue().toString())); + break; + case "date": + Mockito.when(rs.getDate(tf.getField())) + .thenReturn(Date.valueOf(tf.getValue().toString())); + break; + case "int": + Mockito.when(rs.getInt(tf.getField())) + .thenReturn(new Integer(tf.getValue().toString())); + break; + case "double": + Mockito.when(rs.getDouble(tf.getField())) + .thenReturn(new Double(tf.getValue().toString())); + break; + case "array": + final Array arr = Mockito.mock(Array.class); + final String[] values = + ((List) tf.getValue()) + .stream() + .filter(Objects::nonNull) + .map(o -> o.toString()) + .toArray(String[]::new); - for (final TypedField tf : list) { - if (tf.getValue() == null) { - switch (tf.getType()) { - case "not_used": - break; - case "boolean": - Mockito.when(rs.getBoolean(tf.getField())).thenReturn(false); - break; - case "date": - Mockito.when(rs.getDate(tf.getField())).thenReturn(null); - break; - case "int": - Mockito.when(rs.getInt(tf.getField())).thenReturn(0); - break; - case "double": - Mockito.when(rs.getDouble(tf.getField())).thenReturn(0.0); - break; - case "array": - Mockito.when(rs.getArray(tf.getField())).thenReturn(null); - break; - case "string": - default: - Mockito.when(rs.getString(tf.getField())).thenReturn(null); - break; - } - } else { - switch (tf.getType()) { - case "not_used": - break; - case "boolean": - Mockito.when(rs.getBoolean(tf.getField())) - .thenReturn(Boolean.parseBoolean(tf.getValue().toString())); - break; - case "date": - Mockito.when(rs.getDate(tf.getField())) - .thenReturn(Date.valueOf(tf.getValue().toString())); - break; - case "int": - Mockito.when(rs.getInt(tf.getField())) - .thenReturn(new Integer(tf.getValue().toString())); - break; - case "double": - Mockito.when(rs.getDouble(tf.getField())) - .thenReturn(new Double(tf.getValue().toString())); - break; - case "array": - final Array arr = Mockito.mock(Array.class); - final String[] values = - ((List) tf.getValue()) - .stream() - .filter(Objects::nonNull) - .map(o -> o.toString()) - .toArray(String[]::new); + Mockito.when(arr.getArray()).thenReturn(values); + Mockito.when(rs.getArray(tf.getField())).thenReturn(arr); + break; + case "string": + default: + Mockito.when(rs.getString(tf.getField())) + .thenReturn(tf.getValue().toString()); + break; + } + } + } - Mockito.when(arr.getArray()).thenReturn(values); - Mockito.when(rs.getArray(tf.getField())).thenReturn(arr); - break; - case "string": - default: - Mockito.when(rs.getString(tf.getField())) - .thenReturn(tf.getValue().toString()); - break; - } - } - } + return list; + } - return list; - } + private void verifyMocks(final List list) throws SQLException { + for (final TypedField tf : list) { - private void verifyMocks(final List list) throws SQLException { - for (final TypedField tf : list) { + switch (tf.getType()) { + case "not_used": + break; + case "boolean": + Mockito.verify(rs, Mockito.atLeastOnce()).getBoolean(tf.getField()); + break; + case "date": + Mockito.verify(rs, Mockito.atLeastOnce()).getDate(tf.getField()); + break; + case "int": + Mockito.verify(rs, Mockito.atLeastOnce()).getInt(tf.getField()); + break; + case "double": + Mockito.verify(rs, Mockito.atLeastOnce()).getDouble(tf.getField()); + break; + case "array": + Mockito.verify(rs, Mockito.atLeastOnce()).getArray(tf.getField()); + break; + case "string": + default: + Mockito.verify(rs, Mockito.atLeastOnce()).getString(tf.getField()); + break; + } + } + } - switch (tf.getType()) { - case "not_used": - break; - case "boolean": - Mockito.verify(rs, Mockito.atLeastOnce()).getBoolean(tf.getField()); - break; - case "date": - Mockito.verify(rs, Mockito.atLeastOnce()).getDate(tf.getField()); - break; - case "int": - Mockito.verify(rs, Mockito.atLeastOnce()).getInt(tf.getField()); - break; - case "double": - Mockito.verify(rs, Mockito.atLeastOnce()).getDouble(tf.getField()); - break; - case "array": - Mockito.verify(rs, Mockito.atLeastOnce()).getArray(tf.getField()); - break; - case "string": - default: - Mockito.verify(rs, Mockito.atLeastOnce()).getString(tf.getField()); - break; - } - } - } + private void assertValidId(final String id) { + assertEquals(49, id.length()); + assertEquals('|', id.charAt(2)); + assertEquals(':', id.charAt(15)); + assertEquals(':', id.charAt(16)); + } - private void assertValidId(final String id) { - assertEquals(49, id.length()); - assertEquals('|', id.charAt(2)); - assertEquals(':', id.charAt(15)); - assertEquals(':', id.charAt(16)); - } - - private String getValueAsString(final String name, final List fields) { - return fields.stream() - .filter(f -> f.getField().equals(name)) - .map(TypedField::getValue) - .filter(Objects::nonNull) - .map(o -> o.toString()) - .findFirst() - .get(); - } + private String getValueAsString(final String name, final List fields) { + return fields.stream() + .filter(f -> f.getField().equals(name)) + .map(TypedField::getValue) + .filter(Objects::nonNull) + .map(o -> o.toString()) + .findFirst() + .get(); + } } class TypedField { - private String field; - private String type; - private Object value; + private String field; + private String type; + private Object value; - public String getField() { - return field; - } + public String getField() { + return field; + } - public void setField(final String field) { - this.field = field; - } + public void setField(final String field) { + this.field = field; + } - public String getType() { - return type; - } + public String getType() { + return type; + } - public void setType(final String type) { - this.type = type; - } + public void setType(final String type) { + this.type = type; + } - public Object getValue() { - return value; - } + public Object getValue() { + return value; + } - public void setValue(final Object value) { - this.value = value; - } + public void setValue(final Object value) { + this.value = value; + } } diff --git 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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 e029ddf62..3cca6e370 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 a6c261ec7..b663a8082 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 3455cb5f3..874c34c09 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) { From 9147af7fedd046eaada90a15edc8235338d17f4d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 20 Apr 2020 15:24:33 +0200 Subject: [PATCH 09/19] actionsets migration workflow moved in dhp-workflows/dhp-actionmanager --- dhp-workflows/dhp-actionmanager/pom.xml | 48 ++++ .../migration}/LicenseComparator.java | 2 +- .../migration}/MigrateActionSet.java | 34 ++- .../migration}/ProtoConverter.java | 7 +- .../migration/TransformActions.java | 174 ++++++++++++++ .../migrate_actionsets_parameters.json | 56 +++++ .../transform_actionsets_parameters.json | 20 ++ .../migration}/oozie_app/config-default.xml | 0 .../wf/migration}/oozie_app/workflow.xml | 56 +++-- .../migration/actions/TransformActions.java | 213 ------------------ .../migrate_actionsets_parameters.json | 10 - .../transform_actionsets_parameters.json | 5 - 12 files changed, 357 insertions(+), 268 deletions(-) rename dhp-workflows/{dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions => dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration}/LicenseComparator.java (96%) rename dhp-workflows/{dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions => dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration}/MigrateActionSet.java (88%) rename dhp-workflows/{dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions => dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration}/ProtoConverter.java (98%) create mode 100644 dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java create mode 100644 dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json create mode 100644 dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json rename dhp-workflows/{dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions => dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration}/oozie_app/config-default.xml (100%) rename dhp-workflows/{dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions => dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration}/oozie_app/workflow.xml (63%) delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/TransformActions.java delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index aa2078be5..22ca7504d 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -47,6 +47,16 @@ jaxen + + org.apache.hadoop + hadoop-distcp + + + + eu.dnetlib + dnet-openaire-data-protos + + eu.dnetlib.dhp dhp-schemas @@ -57,6 +67,44 @@ eu.dnetlib dnet-actionmanager-api + + eu.dnetlib + dnet-actionmanager-common + + + eu.dnetlib + dnet-openaireplus-mapping-utils + + + saxonica + saxon + + + saxonica + saxon-dom + + + jgrapht + jgrapht + + + net.sf.ehcache + ehcache + + + org.springframework + spring-test + + + org.apache.* + * + + + apache + * + + + diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/LicenseComparator.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/LicenseComparator.java similarity index 96% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/LicenseComparator.java rename to dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/LicenseComparator.java index 126a97e39..8998a090d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/LicenseComparator.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/LicenseComparator.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.migration.actions; +package eu.dnetlib.dhp.actionmanager.migration; import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier; import java.util.Comparator; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/MigrateActionSet.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java similarity index 88% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/MigrateActionSet.java rename to dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java index 680f7759c..db1bed48a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/MigrateActionSet.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.migration.actions; +package eu.dnetlib.dhp.actionmanager.migration; import com.google.common.base.Splitter; import com.google.common.collect.Lists; @@ -9,35 +9,36 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import java.io.File; import java.io.FileOutputStream; import java.io.OutputStream; -import java.util.*; +import java.util.ArrayList; +import java.util.LinkedList; +import java.util.List; +import java.util.Properties; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.tools.DistCp; import org.apache.hadoop.tools.DistCpOptions; import org.apache.hadoop.util.ToolRunner; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; public class MigrateActionSet { - private static final Log log = LogFactory.getLog(MigrateActionSet.class); + private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class); private static final String SEPARATOR = "/"; private static final String TARGET_PATHS = "target_paths"; private static final String RAWSET_PREFIX = "rawset_"; - private static Boolean DEFAULT_TRANSFORM_ONLY = false; - public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils.toString( MigrateActionSet.class.getResourceAsStream( - "/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json"))); + "/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json"))); parser.parseArgument(args); new MigrateActionSet().run(parser); @@ -56,11 +57,11 @@ public class MigrateActionSet { final String transform_only_s = parser.get("transform_only"); - log.info("transform only param: " + transform_only_s); + log.info("transform only param: {}", transform_only_s); final Boolean transformOnly = Boolean.valueOf(parser.get("transform_only")); - log.info("transform only: " + transformOnly); + log.info("transform only: {}", transformOnly); ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); @@ -79,22 +80,19 @@ public class MigrateActionSet { final List sourcePaths = getSourcePaths(sourceNN, isLookUp); log.info( - String.format( - "paths to process:\n%s", - sourcePaths.stream() - .map(p -> p.toString()) - .collect(Collectors.joining("\n")))); + "paths to process:\n{}", + sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n"))); for (Path source : sourcePaths) { if (!sourceFS.exists(source)) { - log.warn(String.format("skipping unexisting path: %s", source)); + log.warn("skipping unexisting path: {}", source); } else { LinkedList pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath())); final String rawSet = pathQ.pollLast(); - log.info(String.format("got RAWSET: %s", rawSet)); + log.info("got RAWSET: {}", rawSet); if (StringUtils.isNotBlank(rawSet) && rawSet.startsWith(RAWSET_PREFIX)) { @@ -109,7 +107,7 @@ public class MigrateActionSet { + SEPARATOR + rawSet); - log.info(String.format("using TARGET PATH: %s", targetPath)); + log.info("using TARGET PATH: {}", targetPath); if (!transformOnly) { if (targetFS.exists(targetPath)) { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java similarity index 98% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java rename to dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java index 5188cf55a..adeffa9fc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/ProtoConverter.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java @@ -1,4 +1,9 @@ -package eu.dnetlib.dhp.migration.actions; +package eu.dnetlib.dhp.actionmanager.migration; + +import static eu.dnetlib.data.proto.KindProtos.Kind.entity; +import static eu.dnetlib.data.proto.KindProtos.Kind.relation; +import static eu.dnetlib.data.proto.TypeProtos.*; +import static eu.dnetlib.data.proto.TypeProtos.Type.*; import com.google.common.collect.Lists; import com.googlecode.protobuf.format.JsonFormat; diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java new file mode 100644 index 000000000..5001cff25 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java @@ -0,0 +1,174 @@ +package eu.dnetlib.dhp.actionmanager.migration; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.base.Splitter; +import com.google.common.collect.Lists; +import com.google.protobuf.InvalidProtocolBufferException; +import eu.dnetlib.data.proto.OafProtos; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import java.io.IOException; +import java.io.Serializable; +import java.util.LinkedList; +import java.util.Optional; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import scala.Tuple2; + +public class TransformActions implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(TransformActions.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final String SEPARATOR = "/"; + + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser parser = + new ArgumentApplicationParser( + IOUtils.toString( + MigrateActionSet.class.getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json"))); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = + Optional.ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final String inputPaths = parser.get("inputPaths"); + + if (StringUtils.isBlank(inputPaths)) { + throw new RuntimeException("empty inputPaths"); + } + log.info("inputPaths: {}", inputPaths); + + final String targetBaseDir = getTargetBaseDir(isLookupUrl); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> transformActions(inputPaths, targetBaseDir, spark)); + } + + private static void transformActions( + String inputPaths, String targetBaseDir, SparkSession spark) throws IOException { + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration()); + + for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) { + + LinkedList pathQ = + Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath)); + + final String rawset = pathQ.pollLast(); + final String actionSetDirectory = pathQ.pollLast(); + + final Path targetDirectory = + new Path(targetBaseDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawset); + + if (fs.exists(targetDirectory)) { + log.info("found target directory '{}", targetDirectory); + fs.delete(targetDirectory, true); + log.info("deleted target directory '{}", targetDirectory); + } + + log.info("transforming actions from '{}' to '{}'", sourcePath, targetDirectory); + + sc.sequenceFile(sourcePath, Text.class, Text.class) + .map( + a -> + eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON( + a._2().toString())) + .map(a -> doTransform(a)) + // .filter(Objects::isNull) + // .filter(a -> a.getPayload() == null) + .mapToPair( + a -> + new Tuple2<>( + a.getClazz().toString(), + OBJECT_MAPPER.writeValueAsString(a))) + .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) + .saveAsNewAPIHadoopFile( + targetDirectory.toString(), + Text.class, + Text.class, + SequenceFileOutputFormat.class, + sc.hadoopConfiguration()); + } + } + + private static AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa) + throws InvalidProtocolBufferException { + final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue()); + final Oaf oaf = ProtoConverter.convert(proto_oaf); + switch (proto_oaf.getKind()) { + case entity: + switch (proto_oaf.getEntity().getType()) { + case datasource: + return new AtomicAction<>(Datasource.class, (Datasource) oaf); + case organization: + return new AtomicAction<>(Organization.class, (Organization) oaf); + case project: + return new AtomicAction<>(Project.class, (Project) oaf); + case result: + final String resulttypeid = + proto_oaf + .getEntity() + .getResult() + .getMetadata() + .getResulttype() + .getClassid(); + switch (resulttypeid) { + case "publication": + return new AtomicAction<>(Publication.class, (Publication) oaf); + case "software": + return new AtomicAction<>(Software.class, (Software) oaf); + case "other": + return new AtomicAction<>( + OtherResearchProduct.class, (OtherResearchProduct) oaf); + case "dataset": + return new AtomicAction<>(Dataset.class, (Dataset) oaf); + default: + // can be an update, where the resulttype is not specified + return new AtomicAction<>(Result.class, (Result) oaf); + } + default: + throw new IllegalArgumentException( + "invalid entity type: " + proto_oaf.getEntity().getType()); + } + case relation: + return new AtomicAction<>(Relation.class, (Relation) oaf); + default: + throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind()); + } + } + + private static String getTargetBaseDir(String isLookupUrl) throws ISLookUpException { + ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); + String XQUERY = + "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()"; + return isLookUp.getResourceProfileByQuery(XQUERY); + } +} diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json new file mode 100644 index 000000000..c7b931c44 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json @@ -0,0 +1,56 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "is", + "paramLongName": "isLookupUrl", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + }, + { + "paramName": "sn", + "paramLongName": "sourceNameNode", + "paramDescription": "nameNode of the source cluster", + "paramRequired": true + }, + { + "paramName": "tn", + "paramLongName": "targetNameNode", + "paramDescription": "namoNode of the target cluster", + "paramRequired": true + }, + { + "paramName": "w", + "paramLongName": "workingDirectory", + "paramDescription": "working directory", + "paramRequired": true + }, + { + "paramName": "nm", + "paramLongName": "distcp_num_maps", + "paramDescription": "maximum number of map tasks used in the distcp process", + "paramRequired": true + }, + { + "paramName": "mm", + "paramLongName": "distcp_memory_mb", + "paramDescription": "memory for distcp action copying actionsets from remote cluster", + "paramRequired": true + }, + { + "paramName": "tt", + "paramLongName": "distcp_task_timeout", + "paramDescription": "timeout for distcp copying actions from remote cluster", + "paramRequired": true + }, + { + "paramName": "tr", + "paramLongName": "transform_only", + "paramDescription": "activate tranform-only mode. Only apply transformation step", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json new file mode 100644 index 000000000..85c39c5b3 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "is", + "paramLongName": "isLookupUrl", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "inputPaths", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions/oozie_app/config-default.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions/oozie_app/config-default.xml rename to dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration/oozie_app/workflow.xml similarity index 63% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions/oozie_app/workflow.xml rename to dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration/oozie_app/workflow.xml index ed01c8de4..d8888de9d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/actions/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/migration/oozie_app/workflow.xml @@ -10,7 +10,6 @@ workingDirectory - /tmp/actionsets working directory @@ -44,6 +43,20 @@ sparkExecutorCores number of cores used by single executor + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + spark2YarnHistoryServerAddress spark 2.* yarn history server address @@ -66,23 +79,27 @@ oozie.launcher.mapred.job.queue.name ${oozieLauncherQueueName} + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + - + - + - eu.dnetlib.dhp.migration.actions.MigrateActionSet + eu.dnetlib.dhp.actionmanager.migration.MigrateActionSet -Dmapred.task.timeout=${distcp_task_timeout} - -is${isLookupUrl} - -sn${sourceNN} - -tn${nameNode} - -w${workingDirectory} - -nm${distcp_num_maps} - -mm${distcp_memory_mb} - -tt${distcp_task_timeout} - -tr${transform_only} + --isLookupUrl${isLookupUrl} + --sourceNameNode${sourceNN} + --targetNameNode${nameNode} + --workingDirectory${workingDirectory} + --distcp_num_maps${distcp_num_maps} + --distcp_memory_mb${distcp_memory_mb} + --distcp_task_timeout${distcp_task_timeout} + --transform_only${transform_only} @@ -94,19 +111,18 @@ yarn cluster transform_actions - eu.dnetlib.dhp.migration.actions.TransformActions - dhp-aggregation-${projectVersion}.jar + eu.dnetlib.dhp.actionmanager.migration.TransformActions + dhp-actionmanager-${projectVersion}.jar - --executor-cores ${sparkExecutorCores} - --executor-memory ${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - -mtyarn - -is${isLookupUrl} + --isLookupUrl${isLookupUrl} --inputPaths${wf:actionData('migrate_actionsets')['target_paths']} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/TransformActions.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/TransformActions.java deleted file mode 100644 index 81c2e7705..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/actions/TransformActions.java +++ /dev/null @@ -1,213 +0,0 @@ -package eu.dnetlib.dhp.migration.actions; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.common.base.Splitter; -import com.google.common.collect.Lists; -import com.google.protobuf.InvalidProtocolBufferException; -import eu.dnetlib.data.proto.OafProtos; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.action.AtomicAction; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import java.io.IOException; -import java.io.Serializable; -import java.util.LinkedList; -import java.util.Objects; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.io.Text; -import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.SparkSession; - -public class TransformActions implements Serializable { - - private static final Log log = LogFactory.getLog(TransformActions.class); - private static final String SEPARATOR = "/"; - - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = - new ArgumentApplicationParser( - IOUtils.toString( - MigrateActionSet.class.getResourceAsStream( - "/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json"))); - parser.parseArgument(args); - - new TransformActions().run(parser); - } - - private void run(ArgumentApplicationParser parser) throws ISLookUpException, IOException { - - final String isLookupUrl = parser.get("isLookupUrl"); - log.info("isLookupUrl: " + isLookupUrl); - - final String inputPaths = parser.get("inputPaths"); - - if (StringUtils.isBlank(inputPaths)) { - throw new RuntimeException("empty inputPaths"); - } - log.info("inputPaths: " + inputPaths); - - final String targetBaseDir = getTargetBaseDir(isLookupUrl); - - try (SparkSession spark = getSparkSession(parser)) { - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration()); - - for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) { - - LinkedList pathQ = - Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath)); - - final String rawset = pathQ.pollLast(); - final String actionSetDirectory = pathQ.pollLast(); - - final Path targetDirectory = - new Path( - targetBaseDir - + SEPARATOR - + actionSetDirectory - + SEPARATOR - + rawset); - - if (fs.exists(targetDirectory)) { - log.info(String.format("found target directory '%s", targetDirectory)); - fs.delete(targetDirectory, true); - log.info(String.format("deleted target directory '%s", targetDirectory)); - } - - log.info( - String.format( - "transforming actions from '%s' to '%s'", - sourcePath, targetDirectory)); - - sc.sequenceFile(sourcePath, Text.class, Text.class) - .map( - a -> - eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON( - a._2().toString())) - .map(a -> doTransform(a)) - .filter(Objects::isNull) - .filter(a -> a.getPayload() == null) - .map(a -> new ObjectMapper().writeValueAsString(a)) - .saveAsTextFile(targetDirectory.toString(), GzipCodec.class); - } - } - } - - private Text transformAction(eu.dnetlib.actionmanager.actions.AtomicAction aa) - throws InvalidProtocolBufferException, JsonProcessingException { - final Text out = new Text(); - final ObjectMapper mapper = new ObjectMapper(); - if (aa.getTargetValue() != null && aa.getTargetValue().length > 0) { - out.set(mapper.writeValueAsString(doTransform(aa))); - } - return out; - } - - private AtomicAction getRelationAtomicAction(String atomicaActionId) { - final String[] splitId = atomicaActionId.split("@"); - - String source = splitId[0]; - String target = splitId[2]; - - String[] relSemantic = splitId[1].split("_"); - - Relation rel = new Relation(); - rel.setSource(source); - rel.setTarget(target); - rel.setRelType(relSemantic[0]); - rel.setSubRelType(relSemantic[1]); - rel.setRelClass(relSemantic[2]); - - DataInfo d = new DataInfo(); - d.setDeletedbyinference(false); - d.setInferenceprovenance("deduplication"); - d.setInferred(true); - d.setInvisible(false); - Qualifier provenanceaction = new Qualifier(); - - provenanceaction.setClassid("deduplication"); - provenanceaction.setClassname("deduplication"); - provenanceaction.setSchemeid("dnet:provenanceActions"); - provenanceaction.setSchemename("dnet:provenanceActions"); - - d.setProvenanceaction(provenanceaction); - - rel.setDataInfo(d); - - return new AtomicAction<>(Relation.class, rel); - } - - private AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa) - throws InvalidProtocolBufferException { - final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue()); - final Oaf oaf = ProtoConverter.convert(proto_oaf); - switch (proto_oaf.getKind()) { - case entity: - switch (proto_oaf.getEntity().getType()) { - case datasource: - return new AtomicAction<>(Datasource.class, (Datasource) oaf); - case organization: - return new AtomicAction<>(Organization.class, (Organization) oaf); - case project: - return new AtomicAction<>(Project.class, (Project) oaf); - case result: - final String resulttypeid = - proto_oaf - .getEntity() - .getResult() - .getMetadata() - .getResulttype() - .getClassid(); - switch (resulttypeid) { - case "publication": - return new AtomicAction<>(Publication.class, (Publication) oaf); - case "software": - return new AtomicAction<>(Software.class, (Software) oaf); - case "other": - return new AtomicAction<>( - OtherResearchProduct.class, (OtherResearchProduct) oaf); - case "dataset": - return new AtomicAction<>(Dataset.class, (Dataset) oaf); - default: - // can be an update, where the resulttype is not specified - return new AtomicAction<>(Result.class, (Result) oaf); - } - default: - throw new IllegalArgumentException( - "invalid entity type: " + proto_oaf.getEntity().getType()); - } - case relation: - return new AtomicAction<>(Relation.class, (Relation) oaf); - default: - throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind()); - } - } - - private String getTargetBaseDir(String isLookupUrl) throws ISLookUpException { - ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); - String XQUERY = - "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()"; - return isLookUp.getResourceProfileByQuery(XQUERY); - } - - private static SparkSession getSparkSession(ArgumentApplicationParser parser) { - SparkConf conf = new SparkConf(); - - return SparkSession.builder() - .appName(TransformActions.class.getSimpleName()) - .master(parser.get("master")) - .config(conf) - .enableHiveSupport() - .getOrCreate(); - } -} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json deleted file mode 100644 index c4910ec61..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json +++ /dev/null @@ -1,10 +0,0 @@ -[ - {"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true}, - {"paramName":"sn", "paramLongName":"sourceNameNode", "paramDescription": "nameNode of the source cluster", "paramRequired": true}, - {"paramName":"tn", "paramLongName":"targetNameNode", "paramDescription": "namoNode of the target cluster", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workingDirectory", "paramDescription": "working directory", "paramRequired": true}, - {"paramName":"nm", "paramLongName":"distcp_num_maps", "paramDescription": "maximum number of map tasks used in the distcp process", "paramRequired": true}, - {"paramName":"mm", "paramLongName":"distcp_memory_mb", "paramDescription": "memory for distcp action copying actionsets from remote cluster", "paramRequired": true}, - {"paramName":"tt", "paramLongName":"distcp_task_timeout", "paramDescription": "timeout for distcp copying actions from remote cluster", "paramRequired": true}, - {"paramName":"tr", "paramLongName":"transform_only", "paramDescription": "activate tranform-only mode. Only apply transformation step", "paramRequired": true} -] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json deleted file mode 100644 index ce72f53ca..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json +++ /dev/null @@ -1,5 +0,0 @@ -[ - {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true}, - {"paramName":"i", "paramLongName":"inputPaths", "paramDescription": "URL of the isLookUp Service", "paramRequired": true} -] From 4da13e457040ca406ca00cf2605c055ba3ab080e Mon Sep 17 00:00:00 2001 From: miconis Date: Mon, 20 Apr 2020 16:04:49 +0200 Subject: [PATCH 10/19] 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 79138d641..7a7a9a89c 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 6db3b7f74..86f4ff616 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 aaeecb871..9d211d058 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 36d3fdd27..bc65230a8 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 5188cf55a..b5d027c03 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 3c3a63ca4..bb310050c 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 a4e69e6db..127a19139 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 cfd541f29..ca6d04d49 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 186b21ef2..2fd807ccb 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 b983f5a29..17c99c002 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 b9b9c22ba..50e71c366 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 a7aa600cf..f1058db38 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 476e617d7..6de7303c3 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 6b304c9b0..e77b1f87f 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 f6fab499b..5e6462417 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 4d3cb02d6..bfd5d5c7f 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 b09c5d638..6af314d76 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 b88731ba2..3c7bc684d 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 94dc802fa..0c36e8686 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| z#Y!Bt)@HBq6+&7MLPPEuDGoXF44a*EXijrm(FwQ>d)9SZ_+Ll&ROGw|W9kAG^0|=f 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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 3cca6e370..e029ddf62 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 b663a8082..a6c261ec7 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 874c34c09..3455cb5f3 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 667d23c58bb535a89fbdef9c0e10d76a1abb5b8c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 20 Apr 2020 16:45:21 +0200 Subject: [PATCH 11/19] finalising Actionset migration workflow --- .../dhp/actionmanager/migration/TransformActions.java | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java index 5001cff25..3226361cb 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java @@ -16,6 +16,7 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import java.io.IOException; import java.io.Serializable; import java.util.LinkedList; +import java.util.Objects; import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; @@ -101,9 +102,8 @@ public class TransformActions implements Serializable { a -> eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON( a._2().toString())) - .map(a -> doTransform(a)) - // .filter(Objects::isNull) - // .filter(a -> a.getPayload() == null) + .map(TransformActions::doTransform) + .filter(Objects::nonNull) .mapToPair( a -> new Tuple2<>( @@ -121,6 +121,11 @@ public class TransformActions implements Serializable { private static AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa) throws InvalidProtocolBufferException { + + // dedup similarity relations had empty target value, don't migrate them + if (aa.getTargetValue().length == 0) { + return null; + } final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue()); final Oaf oaf = ProtoConverter.convert(proto_oaf); switch (proto_oaf.getKind()) { From 1102e3246263c4687715490907206e01b897ff99 Mon Sep 17 00:00:00 2001 From: miconis Date: Mon, 20 Apr 2020 16:49:01 +0200 Subject: [PATCH 12/19] 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 7ad2f6d17..ce0be4f91 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 7e34ad133..1a0ef251a 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": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}, 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"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": ""}, "country": {"classid": "FR", "classname": "France", "schemename": "dnet:countries", "schemeid": "dnet:countries"}, "extraInfo": [], "originalId": ["re3data_____::da767b97e147aa12c82325ad9f6469b6"], "ecsmevalidated": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}} {"eclegalbody": {"dataInfo": 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"sysimport:crosswalk:entityregistry", "schemename": "dnet:provenance_actions", "schemeid": "dnet:provenance_actions"}, "inferred": true, "inferenceprovenance": "dedup-similarity-organization-simple", "invisible": false, "trust": "0.9"}, "alternativeNames": [], "echighereducation": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}, "id": "20|re3data_____::bae667dcb5add10a573824e32dbbed5f", "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": "2019-04-23", "dateoftransformation": "2019-04-23", "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": ""}, "country": {"classid": "FR", "classname": "France", "schemename": "dnet:countries", "schemeid": "dnet:countries"}, "extraInfo": [], "originalId": ["re3data_____::9f1b4503c8ae13797b69d2305bdb3cfa"], "ecsmevalidated": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}} {"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": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}, "legalname": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "\\u00c9cole polytechnique f\\u00e9d\\u00e9rale de Lausanne"}, "pid": [], "websiteurl": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "https://www.epfl.ch/index.en.html"}, "ecnutscode": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "false"}, "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": "Registry of Research Data Repository", "key": "10|openaire____::21f8a223b9925c2f87c404096080b046"}], "dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemename": "dnet:provenance_actions", "schemeid": "dnet:provenance_actions"}, "inferred": true, "inferenceprovenance": "dedup-similarity-organization-simple", "invisible": false, "trust": ""}, "alternativeNames": [], "echighereducation": {"dataInfo": {"deletedbyinference": false, "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 13/19] 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 1cb04d02f..e5c8a4606 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 127a19139..d442d73a8 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 ce0be4f91..8fd7a0ec9 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 14/19] 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 7a7a9a89c..79138d641 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 86f4ff616..6db3b7f74 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 9d211d058..aaeecb871 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 c56ded145..adeffa9fc 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 bc65230a8..36d3fdd27 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 f1058db38..a7aa600cf 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 6de7303c3..476e617d7 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 e77b1f87f..6b304c9b0 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 5e6462417..f6fab499b 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 bfd5d5c7f..4d3cb02d6 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 6af314d76..b09c5d638 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 3c7bc684d..b88731ba2 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 0c36e8686..94dc802fa 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 e029ddf62..3cca6e370 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 a6c261ec7..b663a8082 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 3455cb5f3..874c34c09 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) { From 5c9ef08a8e0afc0f6b99ece47930e3d8e9e332ed Mon Sep 17 00:00:00 2001 From: miconis Date: Tue, 21 Apr 2020 10:19:04 +0200 Subject: [PATCH 15/19] spark dedup test fixed --- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) 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 8fd7a0ec9..695498a6e 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 @@ -272,7 +272,17 @@ public class SparkDedupTest implements Serializable { .distinct() .count(); - assertEquals(831, publications); + long mergedSw = + spark.read() + .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); + + assertEquals(897, publications); assertEquals(835, organizations); assertEquals(100, projects); assertEquals(100, datasource); @@ -288,8 +298,14 @@ public class SparkDedupTest implements Serializable { .filter(this::isDeletedByInference) .count(); + long deletedSw = + jsc.textFile(testDedupGraphBasePath + "/software") + .filter(this::isDeletedByInference) + .count(); + assertEquals(mergedOrgs, deletedOrgs); assertEquals(mergedPubs, deletedPubs); + assertEquals(mergedSw, deletedSw); } @Test From 91e72a69447ceb318c25e36381eb8654ae69d91b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 21 Apr 2020 12:06:08 +0200 Subject: [PATCH 16/19] Dataset based implementation for SparkCreateDedupRecord phase, fixed datasource entity dump supplementing dedup unit tests --- .../dhp/oa/dedup/SparkCreateDedupRecord.java | 7 +- .../dhp/oa/dedup/SparkUpdateEntity.java | 19 +- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 6 +- .../eu/dnetlib/dhp/dedup/entities/datasource | 200 +++++++++--------- 4 files changed, 112 insertions(+), 120 deletions(-) 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 d442d73a8..c46464ffd 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 @@ -11,8 +11,6 @@ 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; @@ -72,12 +70,9 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { Class clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz) - .map( - (MapFunction) - value -> OBJECT_MAPPER.writeValueAsString(value), - Encoders.STRING()) .write() .mode(SaveMode.Overwrite) + .option("compression", "gzip") .json(outputPath); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java index fde5dd75f..ee13eff6b 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java @@ -33,7 +33,7 @@ public class SparkUpdateEntity extends AbstractSparkAction { private static final Logger log = LoggerFactory.getLogger(SparkUpdateEntity.class); - final String IDJSONPATH = "$.id"; + private static final String IDJSONPATH = "$.id"; public SparkUpdateEntity(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); @@ -65,27 +65,25 @@ public class SparkUpdateEntity extends AbstractSparkAction { log.info("workingPath: '{}'", workingPath); log.info("dedupGraphPath: '{}'", dedupGraphPath); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); // for each entity ModelSupport.entityTypes.forEach( - (entity, clazz) -> { - final String outputPath = dedupGraphPath + "/" + entity; + (type, clazz) -> { + final String outputPath = dedupGraphPath + "/" + type; removeOutputDir(spark, outputPath); JavaRDD sourceEntity = sc.textFile( - DedupUtility.createEntityPath( - graphBasePath, entity.toString())); + DedupUtility.createEntityPath(graphBasePath, type.toString())); - if (mergeRelExists(workingPath, entity.toString())) { + if (mergeRelExists(workingPath, type.toString())) { final String mergeRelPath = - DedupUtility.createMergeRelPath( - workingPath, "*", entity.toString()); + DedupUtility.createMergeRelPath(workingPath, "*", type.toString()); final String dedupRecordPath = DedupUtility.createDedupRecordPath( - workingPath, "*", entity.toString()); + workingPath, "*", type.toString()); final Dataset rel = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class)); @@ -107,7 +105,6 @@ public class SparkUpdateEntity extends AbstractSparkAction { MapDocumentUtil.getJPathString( IDJSONPATH, s), s)); - JavaRDD map = entitiesWithId .leftOuterJoin(mergedIds) 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 695498a6e..5979fc9b7 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 @@ -72,7 +72,7 @@ public class SparkDedupTest implements Serializable { spark = SparkSession.builder() - .appName(SparkCreateSimRels.class.getSimpleName()) + .appName(SparkDedupTest.class.getSimpleName()) .master("local[*]") .config(new SparkConf()) .getOrCreate(); @@ -300,8 +300,8 @@ public class SparkDedupTest implements Serializable { long deletedSw = jsc.textFile(testDedupGraphBasePath + "/software") - .filter(this::isDeletedByInference) - .count(); + .filter(this::isDeletedByInference) + .count(); assertEquals(mergedOrgs, deletedOrgs); assertEquals(mergedPubs, deletedPubs); 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00:00:00 2001 From: Claudio Atzori Date: Tue, 21 Apr 2020 16:12:20 +0200 Subject: [PATCH 17/19] added extra spark options to graph to hive workflow --- .../dhp/oa/graph/hive/oozie_app/workflow.xml | 39 ++++++++++++++++--- 1 file changed, 33 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml index 271c7040f..67ca6a64a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml @@ -21,6 +21,28 @@ sparkExecutorCores number of cores used by single executor + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + @@ -35,6 +57,10 @@ oozie.launcher.mapred.job.queue.name ${oozieLauncherQueueName} + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + @@ -52,14 +78,15 @@ eu.dnetlib.dhp.oa.graph.GraphHiveImporterJob dhp-graph-mapper-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} - --executor-cores ${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" - --conf spark.sql.warehouse.dir="/user/hive/warehouse" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - -mt yarn-cluster --sourcePath${sourcePath} --hive_db_name${hive_db_name} --hive_metastore_uris${hive_metastore_uris} From 88fbb3a3538b225d8d2ec1fde9dc394b2b04b2d3 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 21 Apr 2020 16:13:43 +0200 Subject: [PATCH 18/19] added sparkSqlWarehouseDir to the default extra spark options passed to each workflow --- dhp-workflows/pom.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index ce0e28112..767674e1c 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -260,7 +260,8 @@ sparkDriverMemory,sparkExecutorMemory,sparkExecutorCores, oozie.wf.application.path,projectVersion,oozie.use.system.libpath, oozieActionShareLibForSpark1,spark1YarnHistoryServerAddress,spark1EventLogDir, - oozieActionShareLibForSpark2,spark2YarnHistoryServerAddress,spark2EventLogDir + oozieActionShareLibForSpark2,spark2YarnHistoryServerAddress,spark2EventLogDir, + sparkSqlWarehouseDir true From 0b55795d4da257aea5a60d2f9886cdfa49c300d4 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 21 Apr 2020 16:15:04 +0200 Subject: [PATCH 19/19] small adjustments in the provisioning workflow --- .../CreateRelatedEntitiesJob_phase1.java | 96 ++++++++++++++++--- .../dhp/oa/provision/PrepareRelationsJob.java | 23 +---- .../oa/provision/utils/GraphMappingUtils.java | 81 ---------------- .../dhp/oa/provision/oozie_app/workflow.xml | 1 + 4 files changed, 89 insertions(+), 112 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java index 6b1dd52ce..df5b8779a 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java @@ -11,11 +11,13 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; import eu.dnetlib.dhp.oa.provision.model.SortableRelation; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.*; +import java.util.List; +import java.util.Objects; import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -104,16 +106,12 @@ public class CreateRelatedEntitiesJob_phase1 { SparkSession spark, String inputRelationsPath, String inputEntityPath, - Class entityClazz, + Class clazz, String outputPath) { Dataset> relsByTarget = readPathRelation(spark, inputRelationsPath) - .filter( - (FilterFunction) - value -> - value.getDataInfo().getDeletedbyinference() - == false) + .filter("dataInfo.deletedbyinference == false") .map( (MapFunction>) r -> new Tuple2<>(r.getTarget(), r), @@ -122,10 +120,11 @@ public class CreateRelatedEntitiesJob_phase1 { .cache(); Dataset> entities = - readPathEntity(spark, inputEntityPath, entityClazz) + readPathEntity(spark, inputEntityPath, clazz) + .filter("dataInfo.invisible == false") .map( (MapFunction) - value -> asRelatedEntity(value, entityClazz), + value -> asRelatedEntity(value, clazz), Encoders.bean(RelatedEntity.class)) .map( (MapFunction>) @@ -146,7 +145,7 @@ public class CreateRelatedEntitiesJob_phase1 { Encoders.bean(EntityRelEntity.class)) .write() .mode(SaveMode.Overwrite) - .parquet(outputPath + "/" + EntityType.fromClass(entityClazz)); + .parquet(outputPath + "/" + EntityType.fromClass(clazz)); } private static Dataset readPathEntity( @@ -161,6 +160,81 @@ public class CreateRelatedEntitiesJob_phase1 { Encoders.bean(entityClazz)); } + public static RelatedEntity asRelatedEntity(E entity, Class clazz) { + + final RelatedEntity re = new RelatedEntity(); + re.setId(entity.getId()); + re.setType(EntityType.fromClass(clazz).name()); + + re.setPid(entity.getPid()); + re.setCollectedfrom(entity.getCollectedfrom()); + + switch (EntityType.fromClass(clazz)) { + case publication: + case dataset: + case otherresearchproduct: + case software: + Result result = (Result) entity; + + if (result.getTitle() != null && !result.getTitle().isEmpty()) { + re.setTitle(result.getTitle().stream().findFirst().get()); + } + + re.setDateofacceptance(getValue(result.getDateofacceptance())); + re.setPublisher(getValue(result.getPublisher())); + re.setResulttype(result.getResulttype()); + re.setInstances(result.getInstance()); + + // TODO still to be mapped + // re.setCodeRepositoryUrl(j.read("$.coderepositoryurl")); + + break; + case datasource: + Datasource d = (Datasource) entity; + + re.setOfficialname(getValue(d.getOfficialname())); + re.setWebsiteurl(getValue(d.getWebsiteurl())); + re.setDatasourcetype(d.getDatasourcetype()); + re.setOpenairecompatibility(d.getOpenairecompatibility()); + + break; + case organization: + Organization o = (Organization) entity; + + re.setLegalname(getValue(o.getLegalname())); + re.setLegalshortname(getValue(o.getLegalshortname())); + re.setCountry(o.getCountry()); + re.setWebsiteurl(getValue(o.getWebsiteurl())); + break; + case project: + Project p = (Project) entity; + + re.setProjectTitle(getValue(p.getTitle())); + re.setCode(getValue(p.getCode())); + re.setAcronym(getValue(p.getAcronym())); + re.setContracttype(p.getContracttype()); + + List> f = p.getFundingtree(); + if (!f.isEmpty()) { + re.setFundingtree( + f.stream().map(s -> s.getValue()).collect(Collectors.toList())); + } + break; + } + return re; + } + + private static String getValue(Field field) { + return getFieldValueWithDefault(field, ""); + } + + private static T getFieldValueWithDefault(Field f, T defaultValue) { + return Optional.ofNullable(f) + .filter(Objects::nonNull) + .map(x -> x.getValue()) + .orElse(defaultValue); + } + /** * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline * delimited json text 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 b663a8082..87264df05 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 @@ -76,9 +76,6 @@ public class PrepareRelationsJob { String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - int numPartitions = Integer.parseInt(parser.get("relPartitions")); - log.info("relPartitions: {}", numPartitions); - SparkConf conf = new SparkConf(); runWithSparkSession( @@ -86,27 +83,14 @@ public class PrepareRelationsJob { isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - prepareRelationsFromPaths(spark, inputRelationsPath, outputPath, numPartitions); + prepareRelationsFromPaths(spark, inputRelationsPath, outputPath); }); } private static void prepareRelationsFromPaths( - SparkSession spark, String inputRelationsPath, String outputPath, int numPartitions) { + SparkSession spark, String inputRelationsPath, String outputPath) { 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; - } - }) + .filter("dataInfo.deletedbyinference == false") .groupByKey( (MapFunction) value -> value.getSource(), Encoders.STRING()) @@ -114,7 +98,6 @@ public class PrepareRelationsJob { (FlatMapGroupsFunction) (key, values) -> Iterators.limit(values, MAX_RELS), Encoders.bean(SortableRelation.class)) - .repartition(numPartitions) .write() .mode(SaveMode.Overwrite) .parquet(outputPath); diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java index cea3539bc..ebd33363b 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java @@ -3,14 +3,8 @@ package eu.dnetlib.dhp.oa.provision.utils; import static org.apache.commons.lang3.StringUtils.substringAfter; import com.google.common.collect.Sets; -import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; -import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.oaf.*; -import java.util.List; -import java.util.Objects; -import java.util.Optional; import java.util.Set; -import java.util.stream.Collectors; public class GraphMappingUtils { @@ -18,81 +12,6 @@ public class GraphMappingUtils { public static Set authorPidTypes = Sets.newHashSet("orcid", "magidentifier"); - public static RelatedEntity asRelatedEntity(E entity, Class clazz) { - - final RelatedEntity re = new RelatedEntity(); - re.setId(entity.getId()); - re.setType(EntityType.fromClass(clazz).name()); - - re.setPid(entity.getPid()); - re.setCollectedfrom(entity.getCollectedfrom()); - - switch (EntityType.fromClass(clazz)) { - case publication: - case dataset: - case otherresearchproduct: - case software: - Result result = (Result) entity; - - if (result.getTitle() == null && !result.getTitle().isEmpty()) { - re.setTitle(result.getTitle().stream().findFirst().get()); - } - - re.setDateofacceptance(getValue(result.getDateofacceptance())); - re.setPublisher(getValue(result.getPublisher())); - re.setResulttype(result.getResulttype()); - re.setInstances(result.getInstance()); - - // TODO still to be mapped - // re.setCodeRepositoryUrl(j.read("$.coderepositoryurl")); - - break; - case datasource: - Datasource d = (Datasource) entity; - - re.setOfficialname(getValue(d.getOfficialname())); - re.setWebsiteurl(getValue(d.getWebsiteurl())); - re.setDatasourcetype(d.getDatasourcetype()); - re.setOpenairecompatibility(d.getOpenairecompatibility()); - - break; - case organization: - Organization o = (Organization) entity; - - re.setLegalname(getValue(o.getLegalname())); - re.setLegalshortname(getValue(o.getLegalshortname())); - re.setCountry(o.getCountry()); - re.setWebsiteurl(getValue(o.getWebsiteurl())); - break; - case project: - Project p = (Project) entity; - - re.setProjectTitle(getValue(p.getTitle())); - re.setCode(getValue(p.getCode())); - re.setAcronym(getValue(p.getAcronym())); - re.setContracttype(p.getContracttype()); - - List> f = p.getFundingtree(); - if (!f.isEmpty()) { - re.setFundingtree( - f.stream().map(s -> s.getValue()).collect(Collectors.toList())); - } - break; - } - return re; - } - - private static String getValue(Field field) { - return getFieldValueWithDefault(field, ""); - } - - private static T getFieldValueWithDefault(Field f, T defaultValue) { - return Optional.ofNullable(f) - .filter(Objects::nonNull) - .map(x -> x.getValue()) - .orElse(defaultValue); - } - public static String removePrefix(final String s) { if (s.contains("|")) return substringAfter(s, "|"); return s; diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index e6587ef5e..923f6de69 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -98,6 +98,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 --inputRelationsPath${inputGraphRootPath}/relation --outputPath${workingDir}/relation