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Integrate EOSC services mining with IIS primary workflow #1398
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2ba28b7
Closes #1049: Perform test mining for EOSC services
marekhorst f63873a
Closes #1393: Remove obsolete DeduplicationMappingConverter
marekhorst 324b6a8
Closes #1394: Integrate EOSC services mining with IIS primary workflow
marekhorst c9a93e4
Closes #1394: Integrate EOSC services mining with IIS primary workflow
marekhorst eb577b0
Closes #1394: Integrate EOSC services mining with IIS primary workflow
marekhorst 1325e29
Closes #1394: Integrate EOSC services mining with IIS primary workflow
marekhorst c785566
Closes #1394: Integrate EOSC services mining with IIS primary workflow
marekhorst 476a378
Closes #1394: Integrate EOSC services mining with IIS primary workflow
marekhorst 48a9c5b
Closes #1394: Integrate EOSC services mining with IIS primary workflow
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18 changes: 18 additions & 0 deletions
18
iis-schemas/src/main/avro/eu/dnetlib/iis/importer/Service.avdl
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| @namespace("eu.dnetlib.iis.importer.schemas") | ||
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| protocol IIS { | ||
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| record Service { | ||
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| // InformationSpace service identifier | ||
| string id; | ||
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| // service name | ||
| union {null , string} name; | ||
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| // service url | ||
| string url; | ||
| } | ||
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| } |
15 changes: 15 additions & 0 deletions
15
...mas/src/main/avro/eu/dnetlib/iis/referenceextraction/datasource/DocumentToDatasource.avdl
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| Original file line number | Diff line number | Diff line change |
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| @namespace("eu.dnetlib.iis.referenceextraction.datasource.schemas") | ||
| protocol IIS{ | ||
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| record DocumentToDatasource { | ||
| // document identifier, foreign key: DocumentWithBasicMetadata.id ("document basic metadata" data store) | ||
| string documentId; | ||
| // identifier of the referenced datasource, | ||
| // foreign key: Datasource.id | ||
| string datasourceId; | ||
| // Find more details on `confidenceLevel` constraints in eu/dnetlib/iis/README.markdown file. | ||
| float confidenceLevel; | ||
| // text snippet surrounding the matched reference, required mostly for internal debugging and analytics | ||
| union { null , string } textsnippet = null; | ||
| } | ||
| } |
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84 changes: 84 additions & 0 deletions
84
...ib/iis/wf/export/actionmanager/module/DocumentToDatasourceActionBuilderModuleFactory.java
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| @@ -0,0 +1,84 @@ | ||
| package eu.dnetlib.iis.wf.export.actionmanager.module; | ||
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| import java.util.Arrays; | ||
| import java.util.List; | ||
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| import org.apache.hadoop.conf.Configuration; | ||
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| import eu.dnetlib.dhp.schema.action.AtomicAction; | ||
| import eu.dnetlib.dhp.schema.oaf.Relation; | ||
| import eu.dnetlib.iis.referenceextraction.datasource.schemas.DocumentToDatasource; | ||
| import eu.dnetlib.iis.wf.export.actionmanager.OafConstants; | ||
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| /** | ||
| * {@link DocumentToDatasource} based action builder module. | ||
| * | ||
| * @author mhorst | ||
| * | ||
| */ | ||
| public class DocumentToDatasourceActionBuilderModuleFactory extends AbstractActionBuilderFactory<DocumentToDatasource, Relation> { | ||
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| // ------------------------ CONSTRUCTORS -------------------------- | ||
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| public DocumentToDatasourceActionBuilderModuleFactory() { | ||
| super(AlgorithmName.document_referencedDatasources); | ||
| } | ||
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| // ------------------------ LOGIC --------------------------------- | ||
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| @Override | ||
| public ActionBuilderModule<DocumentToDatasource, Relation> instantiate(Configuration config) { | ||
| return new DocumentToDatasourceActionBuilderModule(provideTrustLevelThreshold(config)); | ||
| } | ||
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| // ------------------------ INNER CLASS -------------------------- | ||
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| class DocumentToDatasourceActionBuilderModule extends AbstractBuilderModule<DocumentToDatasource, Relation> { | ||
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| // ------------------------ CONSTRUCTORS -------------------------- | ||
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| /** | ||
| * @param trustLevelThreshold trust level threshold or null when all records should be exported | ||
| */ | ||
| public DocumentToDatasourceActionBuilderModule(Float trustLevelThreshold) { | ||
| super(trustLevelThreshold, buildInferenceProvenance()); | ||
| } | ||
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| // ------------------------ LOGIC -------------------------- | ||
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| @Override | ||
| public List<AtomicAction<Relation>> build(DocumentToDatasource object) throws TrustLevelThresholdExceededException { | ||
| return Arrays.asList( | ||
| createAction(object.getDocumentId().toString(), object.getDatasourceId().toString(), | ||
| object.getConfidenceLevel(), OafConstants.REL_CLASS_REFERENCES), | ||
| createAction(object.getDatasourceId().toString(), object.getDocumentId().toString(), | ||
| object.getConfidenceLevel(), OafConstants.REL_CLASS_IS_REFERENCED_BY)); | ||
| } | ||
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| // ------------------------ PRIVATE -------------------------- | ||
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| /** | ||
| * Creates similarity related actions. | ||
| */ | ||
| private AtomicAction<Relation> createAction(String source, String target, float confidenceLevel, | ||
| String relClass) throws TrustLevelThresholdExceededException { | ||
| AtomicAction<Relation> action = new AtomicAction<>(); | ||
| action.setClazz(Relation.class); | ||
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| Relation relation = new Relation(); | ||
| relation.setSource(source); | ||
| relation.setTarget(target); | ||
| relation.setRelType(OafConstants.REL_TYPE_RESULT_DATASOURCE); | ||
| relation.setSubRelType(OafConstants.SUBREL_TYPE_RELATIONSHIP); | ||
| relation.setRelClass(relClass); | ||
| relation.setDataInfo(buildInference(confidenceLevel)); | ||
| relation.setLastupdatetimestamp(System.currentTimeMillis()); | ||
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| action.setPayload(relation); | ||
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| return action; | ||
| } | ||
| } | ||
| } | ||
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85 changes: 85 additions & 0 deletions
85
...is/wf/export/actionmanager/module/DocumentToDatasourceActionBuilderModuleFactoryTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,85 @@ | ||
| package eu.dnetlib.iis.wf.export.actionmanager.module; | ||
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| import eu.dnetlib.dhp.schema.action.AtomicAction; | ||
| import eu.dnetlib.dhp.schema.oaf.Relation; | ||
| import eu.dnetlib.iis.referenceextraction.datasource.schemas.DocumentToDatasource; | ||
| import eu.dnetlib.iis.wf.export.actionmanager.OafConstants; | ||
| import eu.dnetlib.iis.wf.export.actionmanager.module.VerificationUtils.Expectations; | ||
| import org.junit.jupiter.api.Test; | ||
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| import java.util.List; | ||
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| import static eu.dnetlib.iis.wf.export.actionmanager.module.VerificationUtils.assertOafRel; | ||
| import static org.junit.jupiter.api.Assertions.*; | ||
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| /** | ||
| * @author mhorst | ||
| * | ||
| */ | ||
| public class DocumentToDatasourceActionBuilderModuleFactoryTest extends AbstractActionBuilderModuleFactoryTest<DocumentToDatasource, Relation> { | ||
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| // ----------------------- CONSTRUCTORS ------------------- | ||
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| public DocumentToDatasourceActionBuilderModuleFactoryTest() throws Exception { | ||
| super(DocumentToDatasourceActionBuilderModuleFactory.class, AlgorithmName.document_referencedDatasources); | ||
| } | ||
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| // ----------------------- TESTS -------------------------- | ||
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| @Test | ||
| public void testBuildBelowThreshold() { | ||
| // given | ||
| DocumentToDatasource documentToDataset = buildDocumentToDataset("documentId", "datasourceId", 0.4f); | ||
| ActionBuilderModule<DocumentToDatasource, Relation> module = factory.instantiate(config); | ||
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| // execute | ||
| assertThrows(TrustLevelThresholdExceededException.class, () -> module.build(documentToDataset)); | ||
| } | ||
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| @Test | ||
| public void testBuild() throws Exception { | ||
| // given | ||
| String docId = "documentId"; | ||
| String datasourceId = "datasourceId"; | ||
| float matchStrength = 0.9f; | ||
| ActionBuilderModule<DocumentToDatasource, Relation> module = factory.instantiate(config); | ||
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| // execute | ||
| List<AtomicAction<Relation>> actions = module.build(buildDocumentToDataset(docId, datasourceId, matchStrength)); | ||
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| // assert | ||
| assertNotNull(actions); | ||
| assertEquals(2, actions.size()); | ||
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| AtomicAction<Relation> action = actions.get(0); | ||
| assertNotNull(action); | ||
| assertEquals(Relation.class, action.getClazz()); | ||
| Expectations expectations = new Expectations(docId, datasourceId, matchStrength, | ||
| OafConstants.REL_TYPE_RESULT_DATASOURCE, OafConstants.SUBREL_TYPE_RELATIONSHIP, | ||
| OafConstants.REL_CLASS_REFERENCES); | ||
| assertOafRel(action.getPayload(), expectations); | ||
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| // checking backward relation | ||
| action = actions.get(1); | ||
| assertNotNull(action); | ||
| assertEquals(Relation.class, action.getClazz()); | ||
| expectations.setSource(datasourceId); | ||
| expectations.setTarget(docId); | ||
| expectations.setRelationClass(OafConstants.REL_CLASS_IS_REFERENCED_BY); | ||
| assertOafRel(action.getPayload(), expectations); | ||
| } | ||
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| // ----------------------- PRIVATE -------------------------- | ||
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| private static DocumentToDatasource buildDocumentToDataset(String docId, String datasourceId, | ||
| float confidenceLevel) { | ||
| DocumentToDatasource.Builder builder = DocumentToDatasource.newBuilder(); | ||
| builder.setDocumentId(docId); | ||
| builder.setDatasourceId(datasourceId); | ||
| builder.setConfidenceLevel(confidenceLevel); | ||
| return builder.build(); | ||
| } | ||
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| } |
1 change: 1 addition & 0 deletions
1
...wf/export/actionmanager/sequencefile/sampledataproducer/input/document_to_datasource.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| {"documentId":"id-10","datasourceId":"dsid-1","confidenceLevel":0.8164966, "textsnippet": null} |
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15 changes: 15 additions & 0 deletions
15
.../actionmanager/sequencefile/sampledataproducer/output/document_to_datasource_1.properties
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| Original file line number | Diff line number | Diff line change |
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| clazz.canonicalName=eu.dnetlib.dhp.schema.oaf.Relation | ||
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| payload.relType=resultDatasource | ||
| payload.subRelType=relationship | ||
| payload.relClass=References | ||
| payload.source=id-10 | ||
| payload.target=dsid-1 | ||
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| payload.dataInfo.inferred=true | ||
| payload.dataInfo.trust=0.7348 | ||
| payload.dataInfo.inferenceprovenance=iis::document_referencedDatasources | ||
| payload.dataInfo.provenanceaction.classid=iis | ||
| payload.dataInfo.provenanceaction.classname=iis | ||
| payload.dataInfo.provenanceaction.schemeid=dnet:provenanceActions | ||
| payload.dataInfo.provenanceaction.schemename=dnet:provenanceActions |
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I'm probably missing something, but is this code related to similarity?
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Right, this is probably some copy/paste leftover. Fixed.