From 0c887ca0153690086e1d529c955ae83f51f04261 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 27 Feb 2024 12:35:34 +0100 Subject: [PATCH] [SKG-IF] mapping to version latest in date 27 february 2024 --- .../dnetlib/dhp/skgif/model/Affiliation.java | 20 +- .../eu/dnetlib/dhp/skgif/model/Biblio.java | 20 +- .../dnetlib/dhp/skgif/model/Contribution.java | 10 +- .../dnetlib/dhp/skgif/model/Contributor.java | 14 + .../dnetlib/dhp/skgif/model/Datasource.java | 150 +++ .../eu/dnetlib/dhp/skgif/model/Grant.java | 153 +++ .../eu/dnetlib/dhp/skgif/model/Licence.java | 10 + .../dhp/skgif/model/Manifestation.java | 71 +- .../dnetlib/dhp/skgif/model/Organization.java | 84 ++ .../dhp/skgif/model/OrganizationTypes.java | 20 + .../model/PersistentIdentitySystems.java | 10 + .../eu/dnetlib/dhp/skgif/model/Persons.java | 40 +- .../eu/dnetlib/dhp/skgif/model/Prefixes.java | 31 + .../dnetlib/dhp/skgif/model/RelationType.java | 11 +- .../eu/dnetlib/dhp/skgif/model/Relations.java | 26 +- .../dhp/skgif/model/ResearchProduct.java | 53 +- .../eu/dnetlib/dhp/skgif/model/Venue.java | 102 ++ .../dhp/skgif/model/VenueContribution.java | 30 + .../dhp/skgif/model/VenueIdentifierType.java | 22 + .../eu/dnetlib/dhp/skgif/model/VenueType.java | 21 + dump/nullResearchProduct/._SUCCESS.crc | Bin 0 -> 8 bytes ...8d-4b10-a613-a632f762c6aa-c000.json.gz.crc | Bin 0 -> 12 bytes ...8d-4b10-a613-a632f762c6aa-c000.json.gz.crc | Bin 0 -> 28 bytes dump/nullResearchProduct/_SUCCESS | 0 ...7-dc8d-4b10-a613-a632f762c6aa-c000.json.gz | Bin 0 -> 20 bytes ...7-dc8d-4b10-a613-a632f762c6aa-c000.json.gz | Bin 0 -> 2208 bytes .../dhp/oa/graph/dump/ResultMapper.java | 793 ------------ .../dhp/oa/graph/dump/SaveCommunityMap.java | 91 -- .../dhp/oa/graph/dump/UtilCommunityAPI.java | 203 --- .../eu/dnetlib/dhp/oa/graph/dump/Utils.java | 200 --- .../oa/graph/dump/community/CommunityMap.java | 8 - .../graph/dump/community/CommunitySplit.java | 75 -- .../graph/dump/community/ResultProject.java | 28 - .../community/SparkDumpCommunityProducts.java | 155 --- .../community/SparkPrepareResultProject.java | 206 --- .../community/SparkSplitForCommunity.java | 50 - .../community/SparkUpdateProjectInfo.java | 95 -- .../dhp/oa/graph/dump/complete/Constants.java | 26 - .../oa/graph/dump/complete/ContextInfo.java | 84 -- .../dump/complete/CreateContextEntities.java | 106 -- .../dump/complete/CreateContextRelation.java | 113 -- .../dhp/oa/graph/dump/complete/Extractor.java | 203 --- .../oa/graph/dump/complete/MergedRels.java | 25 - .../graph/dump/complete/OrganizationMap.java | 21 - .../dhp/oa/graph/dump/complete/Process.java | 99 -- .../dump/complete/SparkCollectAndSave.java | 252 ---- .../dump/complete/SparkDumpEntitiesJob.java | 639 ---------- .../dump/complete/SparkDumpRelationJob.java | 132 -- .../SparkExtractRelationFromEntities.java | 54 - .../complete/SparkOrganizationRelation.java | 188 --- .../SparkSelectValidRelationsJob.java | 101 -- .../country/SparkFindResultWithCountry.java | 136 -- .../SparkFindResultsRelatedToCountry.java | 173 --- .../dhp/oa/graph/dump/csv/AuthorResult.java | 102 -- .../dhp/oa/graph/dump/csv/Constants.java | 20 - .../oa/graph/dump/csv/DumpCommunities.java | 96 -- .../oa/graph/dump/csv/SparkDumpResults.java | 362 ------ .../graph/dump/csv/SparkMoveOnSigleDir.java | 133 -- .../SparkSelectResultsAndDumpRelations.java | 227 ---- .../oa/graph/dump/csv/model/CSVAuthor.java | 68 - .../oa/graph/dump/csv/model/CSVCitation.java | 40 - .../dhp/oa/graph/dump/csv/model/CSVPid.java | 50 - .../dump/csv/model/CSVRELCommunityResult.java | 31 - .../oa/graph/dump/csv/model/CSVRelResAut.java | 31 - .../oa/graph/dump/csv/model/CSVResult.java | 113 -- .../CardinalityTooHighException.java | 1 - .../dump/exceptions/MyRuntimeException.java | 30 - .../NoAvailableEntityTypeException.java | 1 - .../funderresults/SparkDumpFunderResults.java | 129 -- .../SparkResultLinkedToProject.java | 120 -- .../SparkDumpOrganizationJob.java | 270 ---- .../ProjectsSubsetSparkJob.java | 87 -- .../SparkSelectResultsAndDumpRelations.java | 241 ---- .../oa/graph/dump/skgif/DumpDatasource.java | 147 +++ .../dhp/oa/graph/dump/skgif/DumpGrant.java | 162 +++ .../oa/graph/dump/skgif/DumpOrganization.java | 110 ++ .../dhp/oa/graph/dump/skgif/DumpResult.java | 394 ++++++ .../dhp/oa/graph/dump/skgif/DumpVenue.java | 156 +++ .../graph/dump}/skgif/EmitFromResults.java | 41 +- .../graph/dump}/skgif/ResultMapper.java | 75 +- .../dhp/oa/graph/dump/skgif/Utils.java | 64 + .../skgif/beans/EmitPerManifestation.java | 2 +- .../skgif/beans/PartialResearchProduct.java | 2 +- .../dump}/skgif/beans/RelationPerProduct.java | 2 +- .../exception/NoAllowedTypeException.java | 2 +- .../exception/NoTitleFoundException.java | 2 +- .../oa/graph/dump/subset/MasterDuplicate.java | 29 - .../subset/ReadMasterDuplicateFromDB.java | 97 -- .../oa/graph/dump/subset/SparkDumpResult.java | 199 --- .../graph/dump/subset/SparkSelectSubset.java | 328 ----- .../dump/subset/SparkSelectValidContext.java | 133 -- .../dump/subset/SparkSelectValidRelation.java | 116 -- .../SparkSelectValidRelationContext.java | 153 --- .../dump/subset/criteria/ContainsVerb.java | 30 - .../criteria/ContainsVerbIgnoreCase.java | 30 - .../graph/dump/subset/criteria/EqualVerb.java | 30 - .../subset/criteria/EqualVerbIgnoreCase.java | 30 - .../dump/subset/criteria/GreatThanVerb.java | 34 - .../subset/criteria/InterfaceAdapter.java | 43 - .../dump/subset/criteria/LessThanVerb.java | 34 - .../dump/subset/criteria/NotContainsVerb.java | 30 - .../criteria/NotContainsVerbIgnoreCase.java | 30 - .../dump/subset/criteria/NotEqualVerb.java | 30 - .../criteria/NotEqualVerbIgnoreCase.java | 30 - .../graph/dump/subset/criteria/Selection.java | 9 - .../graph/dump/subset/criteria/VerbClass.java | 14 - .../dump/subset/criteria/VerbResolver.java | 54 - .../subset/criteria/VerbResolverFactory.java | 13 - .../selectionconstraints/Constraint.java | 53 - .../selectionconstraints/Constraints.java | 65 - .../subset/selectionconstraints/Param.java | 32 - .../subset/selectionconstraints/ProtoMap.java | 15 - .../SelectionConstraints.java | 47 - .../zenodoapi/InputStreamRequestBody.java | 2 +- .../zenodoapi/MissingConceptDoiException.java | 2 +- .../zenodoapi/ZenodoAPIClient.java | 6 +- .../zenodoapi/model/Community.java | 2 +- .../zenodoapi/model/Creator.java | 2 +- .../{common => oa}/zenodoapi/model/File.java | 2 +- .../{common => oa}/zenodoapi/model/Grant.java | 2 +- .../{common => oa}/zenodoapi/model/Links.java | 2 +- .../zenodoapi/model/Metadata.java | 2 +- .../zenodoapi/model/PrereserveDoi.java | 2 +- .../zenodoapi/model/RelatedIdentifier.java | 2 +- .../zenodoapi/model/ZenodoModel.java | 2 +- .../zenodoapi/model/ZenodoModelList.java | 2 +- .../java/eu/dnetlib/dhp/skgif/DumpResult.java | 304 ----- .../eu/dnetlib/dhp/skgif/ExtendResult.java | 134 -- .../dhp/skgif/PrepareResultRelation.java | 106 -- .../main/java/eu/dnetlib/dhp/skgif/Utils.java | 36 - .../oa/graph/dump/copygraph_parameters.json | 21 - .../dump/datasourcemaster_parameters.json | 32 - .../dump/dump_datasource_parameters.json | 27 + .../oa/graph/dump/dump_grant_parameters.json | 27 + .../dump/dump_organization_parameters.json | 22 + .../oa/graph/dump/dump_result_parameters.json | 27 + ...eters.json => emit_biblio_parameters.json} | 4 +- .../dhp/oa/graph/dump/DumpJobTest.java | 1102 ----------------- .../dump/PrepareResultProjectJobTest.java | 347 ------ .../oa/graph/dump/SplitForCommunityTest.java | 167 --- .../oa/graph/dump/UpdateProjectInfoTest.java | 232 ---- .../dhp/oa/graph/dump/ZenodoUploadTest.java | 129 +- .../graph/dump/complete/CreateEntityTest.java | 152 --- .../dump/complete/CreateRelationTest.java | 194 --- ...DumpOrganizationProjectDatasourceTest.java | 267 ---- .../graph/dump/complete/DumpRelationTest.java | 305 ----- .../ExtractRelationFromEntityTest.java | 200 --- .../dump/complete/FunderParsingTest.java | 70 -- .../RelationFromOrganizationTest.java | 123 -- .../dump/complete/SelectRelationTest.java | 95 -- .../FindResultRelatedToCountryTest.java | 96 -- .../country/FindResultWithCountryTest.java | 115 -- .../graph/dump/csv/DumpCommunitiesTest.java | 9 - .../dhp/oa/graph/dump/csv/DumpResultTest.java | 358 ------ .../graph/dump/csv/MoveOnSingleDirTest.java | 119 -- .../csv/SelectResultAndDumpRelationTest.java | 221 ---- .../ResultLinkedToProjectTest.java | 139 --- .../dump/funderresult/SplitPerFunderTest.java | 147 --- .../projectssubset/ProjectSubsetTest.java | 124 -- .../graph/dump/skgif/DumpDatasourceTest.java | 172 +++ .../oa/graph/dump/skgif/DumpGrantTest.java | 118 ++ .../dump/skgif/DumpOrganizationTest.java | 122 ++ .../oa/graph/dump/skgif/DumpResultTest.java | 281 +++++ .../dump/skgif/EmitFromResultJobTest.java | 754 ++--------- .../oa/graph/dump/subset/DumpSubsetTest.java | 522 -------- .../dhp/oa/graph/dump/skgif/graph/dataset | 7 + .../oa/graph/dump/skgif/graph/dataset.json | 90 -- .../dhp/oa/graph/dump/skgif/graph/datasource | 5 + .../oa/graph/dump/skgif/graph/organization | 34 + .../graph/{orp.json => otherresearchproduct} | 2 +- .../dhp/oa/graph/dump/skgif/graph/project | 12 + .../graph/{publication.json => publication} | 2 +- .../dhp/oa/graph/dump/skgif/graph/relation | 31 + .../skgif/graph/{software.json => software} | 4 +- .../skgif/graph_complete_entities/dataset | 0 .../skgif/graph_complete_entities/datasource | 3 + .../otherresearchproduct | 0 .../skgif/graph_complete_entities/publication | 1 + .../relation/publicationrels | 10 + .../skgif/graph_complete_entities/software | 0 ...8-b5e7-482a-ba62-8083ff753e20-c000.json.gz | Bin 0 -> 675 bytes ...7acc-7275-4d6b-822e-68b01e4ab364-c000.json | 10 + ...6-d673-4a89-9c98-fc161d1cc15b-c000.json.gz | Bin 0 -> 323 bytes ...e-c371-4024-ac30-f624ec901b40-c000.json.gz | Bin 0 -> 820 bytes ...3-8d1c-4eca-ae6a-23ab3d52c7fd-c000.json.gz | Bin 0 -> 189 bytes ...1-3033-43f0-b7d7-bb48c8171362-c000.json.gz | Bin 0 -> 20 bytes ...4933-cd50-499e-8244-88a0709369aa-c000.json | 5 + ...6408-77ce-418b-9fc4-2ce60ecca46f-c000.json | 1 + ...2-b249-45dc-b634-b2b28fcb05f8-c000.json.gz | Bin 0 -> 231 bytes ...1-d2b3-404b-8306-696a6584645c-c000.json.gz | Bin 0 -> 1705 bytes ...9-d83f-4761-8c4c-c173b78ad3a3-c000.json.gz | Bin 0 -> 1079 bytes ...0-2ecb-4e75-bb59-310faba9c08a-c000.json.gz | Bin 0 -> 20 bytes ...6-842d-453c-a7ed-ce8b9b8c96cf-c000.json.gz | Bin 0 -> 20 bytes ...8-e680-4f49-848f-dc146d5d880a-c000.json.gz | Bin 0 -> 20 bytes ...d-0d36-46ec-9c7c-f364743f2b43-c000.json.gz | Bin 0 -> 20 bytes ...d-f4c8-47a6-907a-51f6a97ef911-c000.json.gz | Bin 0 -> 20 bytes ...9-47bd-4aa2-950f-6011264dea2b-c000.json.gz | Bin 0 -> 20 bytes ...c-bd25-486d-b9ee-455239caecb9-c000.json.gz | Bin 0 -> 20 bytes ...c-667e-4d85-876a-4d2799896d92-c000.json.gz | Bin 0 -> 1274 bytes ...a-ca9a-4182-8578-6b1b063f70da-c000.json.gz | Bin 0 -> 313 bytes ...f-66a7-4550-9b5a-3aa6e1544414-c000.json.gz | Bin 0 -> 20 bytes ...a-00c5-4f52-ae59-2f4fad6f1aa2-c000.json.gz | Bin 0 -> 20 bytes ...a-00c5-4f52-ae59-2f4fad6f1aa2-c000.json.gz | Bin 0 -> 120 bytes ...a-00c5-4f52-ae59-2f4fad6f1aa2-c000.json.gz | Bin 0 -> 161 bytes ...a-00c5-4f52-ae59-2f4fad6f1aa2-c000.json.gz | Bin 0 -> 163 bytes ...a-00c5-4f52-ae59-2f4fad6f1aa2-c000.json.gz | Bin 0 -> 160 bytes ...e-bc43-4e4a-91d8-2a216edf7ec7-c000.json.gz | Bin 0 -> 20 bytes ...0-8673-4a52-9e3a-cfd029ccd72a-c000.json.gz | Bin 0 -> 20 bytes ...9-9c88-4829-9585-63fbdfcf0de8-c000.json.gz | Bin 0 -> 20 bytes ...9-142f-440f-bd03-5808a6c503f5-c000.json.gz | Bin 0 -> 20 bytes 210 files changed, 2946 insertions(+), 14894 deletions(-) create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Contributor.java create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Datasource.java create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Grant.java create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Licence.java create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Organization.java create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/OrganizationTypes.java create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/PersistentIdentitySystems.java create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Prefixes.java create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Venue.java create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueContribution.java create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueIdentifierType.java create mode 100644 dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueType.java create mode 100644 dump/nullResearchProduct/._SUCCESS.crc create mode 100644 dump/nullResearchProduct/.part-00000-b05caf37-dc8d-4b10-a613-a632f762c6aa-c000.json.gz.crc create mode 100644 dump/nullResearchProduct/.part-00003-b05caf37-dc8d-4b10-a613-a632f762c6aa-c000.json.gz.crc create mode 100644 dump/nullResearchProduct/_SUCCESS create mode 100644 dump/nullResearchProduct/part-00000-b05caf37-dc8d-4b10-a613-a632f762c6aa-c000.json.gz create mode 100644 dump/nullResearchProduct/part-00003-b05caf37-dc8d-4b10-a613-a632f762c6aa-c000.json.gz delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/UtilCommunityAPI.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java delete mode 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dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/country/SparkFindResultsRelatedToCountry.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/AuthorResult.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/Constants.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/DumpCommunities.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkDumpResults.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkMoveOnSigleDir.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkSelectResultsAndDumpRelations.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVAuthor.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVCitation.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVPid.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVRELCommunityResult.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVRelResAut.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVResult.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/organizationonly/SparkDumpOrganizationJob.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/serafeim/SparkSelectResultsAndDumpRelations.java create mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpDatasource.java create mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpGrant.java create mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpOrganization.java create mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpResult.java create mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpVenue.java rename dump/src/main/java/eu/dnetlib/dhp/{ => oa/graph/dump}/skgif/EmitFromResults.java (85%) rename dump/src/main/java/eu/dnetlib/dhp/{ => oa/graph/dump}/skgif/ResultMapper.java (63%) create mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/Utils.java rename dump/src/main/java/eu/dnetlib/dhp/{ => oa/graph/dump}/skgif/beans/EmitPerManifestation.java (95%) rename dump/src/main/java/eu/dnetlib/dhp/{ => oa/graph/dump}/skgif/beans/PartialResearchProduct.java (86%) rename dump/src/main/java/eu/dnetlib/dhp/{ => oa/graph/dump}/skgif/beans/RelationPerProduct.java (95%) rename dump/src/main/java/eu/dnetlib/dhp/{ => oa/graph/dump}/skgif/exception/NoAllowedTypeException.java (91%) rename dump/src/main/java/eu/dnetlib/dhp/{ => oa/graph/dump}/skgif/exception/NoTitleFoundException.java (91%) delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/MasterDuplicate.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/ReadMasterDuplicateFromDB.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkDumpResult.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectSubset.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidContext.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidRelation.java delete mode 100644 dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidRelationContext.java delete mode 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dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/skgif/workingDir_complete_entities/software/manifestation/part-00000-6bb74a70-8673-4a52-9e3a-cfd029ccd72a-c000.json.gz create mode 100644 dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/skgif/workingDir_complete_entities/software/person/part-00000-9d17ff29-9c88-4829-9585-63fbdfcf0de8-c000.json.gz create mode 100644 dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/skgif/workingDir_complete_entities/software/topic/part-00000-0ff5c789-142f-440f-bd03-5808a6c503f5-c000.json.gz diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Affiliation.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Affiliation.java index 8e0654f..8a367d9 100644 --- a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Affiliation.java +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Affiliation.java @@ -12,9 +12,9 @@ import com.fasterxml.jackson.annotation.JsonProperty; public class Affiliation implements Serializable { private String organization; @JsonProperty("start_date") - private String startDate; + private String start_date; @JsonProperty("end_date") - private String endDate; + private String end_date; public String getOrganization() { return organization; @@ -24,19 +24,19 @@ public class Affiliation implements Serializable { this.organization = organization; } - public String getStartDate() { - return startDate; + public String getStart_date() { + return start_date; } - public void setStartDate(String startDate) { - this.startDate = startDate; + public void setStart_date(String start_date) { + this.start_date = start_date; } - public String getEndDate() { - return endDate; + public String getEnd_date() { + return end_date; } - public void setEndDate(String endDate) { - this.endDate = endDate; + public void setEnd_date(String end_date) { + this.end_date = end_date; } } diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Biblio.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Biblio.java index ff8a962..3a7afa1 100644 --- a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Biblio.java +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Biblio.java @@ -12,9 +12,9 @@ import com.fasterxml.jackson.annotation.JsonProperty; public class Biblio implements Serializable { private String issue; @JsonProperty("start_page") - private String startPage; + private String start_page; @JsonProperty("end_page") - private String endPage; + private String end_page; private String volume; private String edition; private String number; @@ -29,20 +29,20 @@ public class Biblio implements Serializable { this.issue = issue; } - public String getStartPage() { - return startPage; + public String getStart_page() { + return start_page; } - public void setStartPage(String startPage) { - this.startPage = startPage; + public void setStart_page(String start_page) { + this.start_page = start_page; } - public String getEndPage() { - return endPage; + public String getEnd_page() { + return end_page; } - public void setEndPage(String endPage) { - this.endPage = endPage; + public void setEnd_page(String end_page) { + this.end_page = end_page; } public String getVolume() { diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Contribution.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Contribution.java index f2ee217..3c23506 100644 --- a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Contribution.java +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Contribution.java @@ -13,7 +13,7 @@ import com.fasterxml.jackson.annotation.JsonProperty; public class Contribution implements Serializable { private String person; @JsonProperty("declared_affiliations") - private List declaredAffiliation; + private List declared_affiliation; private List roles; private Integer rank; @@ -25,12 +25,12 @@ public class Contribution implements Serializable { this.person = person; } - public List getDeclaredAffiliation() { - return declaredAffiliation; + public List getDeclared_affiliation() { + return declared_affiliation; } - public void setDeclaredAffiliation(List declaredAffiliation) { - this.declaredAffiliation = declaredAffiliation; + public void setDeclared_affiliation(List declared_affiliation) { + this.declared_affiliation = declared_affiliation; } public List getRoles() { diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Contributor.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Contributor.java new file mode 100644 index 0000000..ab41a8c --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Contributor.java @@ -0,0 +1,14 @@ +package eu.dnetlib.dhp.skgif.model; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 22/02/24 + */ +public class Contributor implements Serializable { + private String person; //I would not map it because we have only information regarding the person (if any) associated to the leading organization + private String organization ; //contributors.person + + private String role ;//private +} diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Datasource.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Datasource.java new file mode 100644 index 0000000..6a84982 --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Datasource.java @@ -0,0 +1,150 @@ +package eu.dnetlib.dhp.skgif.model; + +import java.io.Serializable; +import java.util.List; + +/** + * @author miriam.baglioni + * @Date 21/02/24 + */ +public class Datasource implements Serializable { + private String local_identifier ;//id + private List identifiers; //.schema pid.qualifier.classid;identifiers.value pid.value + private String name; //officialname.value + private String submission_policy_url;// submissionpolicyurl + private String preservation_policy_url;// preservationpolicyurl + private Boolean version_control;// versioncontrol bool + private List persistent_identity_systems;//. product_type researchentitytype list type to be remapped to the eosc types + //persistent_identity_systems. pid_scheme pidsystems.value when not null. It can be a string with multiple values + private String jurisdiction;// jurisdiction.classname + private String data_source_classification;// eoscdatasourcetype.classname + private List research_product_type;// researchentitytype list type to be remapped to the eosc types + private Boolean thematic ;//thematic bool + private List research_product_license; //.name not mappable listresearch_product_license.url not mappable + private List research_product_access_policy;// "databaseaccesstype if open => open access (https://vocabularies.coar-repositories.org/access_rights/c_abf2/) + //if restricted => restricted access (https://vocabularies.coar-repositories.org/access_rights/c_16ec/) + //if closed => metadata only access (https://vocabularies.coar-repositories.org/access_rights/c_14cb/) " list + private List research_product_metadata_license; //.name not mappable list + //research_product_metadata_license.url not mappable + private Listresearch_product_metadata_access_policy ;//researchproductmetadataccesspolicies list with the same mapping of research_product_access_policy + + public String getLocal_identifier() { + return local_identifier; + } + + public void setLocal_identifier(String local_identifier) { + this.local_identifier = local_identifier; + } + + public List getIdentifiers() { + return identifiers; + } + + public void setIdentifiers(List identifiers) { + this.identifiers = identifiers; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getSubmission_policy_url() { + return submission_policy_url; + } + + public void setSubmission_policy_url(String submission_policy_url) { + this.submission_policy_url = submission_policy_url; + } + + public String getPreservation_policy_url() { + return preservation_policy_url; + } + + public void setPreservation_policy_url(String preservation_policy_url) { + this.preservation_policy_url = preservation_policy_url; + } + + public Boolean getVersion_control() { + return version_control; + } + + public void setVersion_control(Boolean version_control) { + this.version_control = version_control; + } + + public List getPersistent_identity_systems() { + return persistent_identity_systems; + } + + public void setPersistent_identity_systems(List persistent_identity_systems) { + this.persistent_identity_systems = persistent_identity_systems; + } + + public String getJurisdiction() { + return jurisdiction; + } + + public void setJurisdiction(String jurisdiction) { + this.jurisdiction = jurisdiction; + } + + public String getData_source_classification() { + return data_source_classification; + } + + public void setData_source_classification(String data_source_classification) { + this.data_source_classification = data_source_classification; + } + + public List getResearch_product_type() { + return research_product_type; + } + + public void setResearch_product_type(List research_product_type) { + this.research_product_type = research_product_type; + } + + public Boolean getThematic() { + return thematic; + } + + public void setThematic(Boolean thematic) { + this.thematic = thematic; + } + + public List getResearch_product_license() { + return research_product_license; + } + + public void setResearch_product_license(List research_product_license) { + this.research_product_license = research_product_license; + } + + public List getResearch_product_access_policy() { + return research_product_access_policy; + } + + public void setResearch_product_access_policy(List research_product_access_policy) { + this.research_product_access_policy = research_product_access_policy; + } + + public List getResearch_product_metadata_license() { + return research_product_metadata_license; + } + + public void setResearch_product_metadata_license(List research_product_metadata_license) { + this.research_product_metadata_license = research_product_metadata_license; + } + + public List getResearch_product_metadata_access_policy() { + return research_product_metadata_access_policy; + } + + public void setResearch_product_metadata_access_policy(List research_product_metadata_access_policy) { + this.research_product_metadata_access_policy = research_product_metadata_access_policy; + } +} diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Grant.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Grant.java new file mode 100644 index 0000000..780437d --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Grant.java @@ -0,0 +1,153 @@ +package eu.dnetlib.dhp.skgif.model; + +import java.util.List; + +import org.codehaus.jackson.annotate.JsonProperty; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 22/02/24 + */ +public class Grant implements Serializable { + private String local_identifier;// id + private List identifiers;//.schema pid.qualifier.classid identifiers.value pid.value + //identifiers.schema funder acronym to be used the xpath //fundingtree/funder/shortname + //identifiers.value project.code + + private String title;// title.value + @JsonProperty(value="abstract") + private String summary ;//summary.value + private String acronym; //acronym.value + private String funder ;//fundingtree to be used the xpath //funder/name + private String funding_stream;// fundingtree to be used the xpath //funding_level_[n] + private String currency;// currency.value + private Float funded_amount;//' fundedamount.value + private List keywords;// subject.value + private String start_date;// startdate.value + private String end_date;// enddate.value + private String website;// websiteurl.value + private List beneficiaries;// organization.id for the organizations in the relation with semantic class isParticipant produces the list of organization internal identifiers + private List contributors;// + + public String getLocal_identifier() { + return local_identifier; + } + + public void setLocal_identifier(String local_identifier) { + this.local_identifier = local_identifier; + } + + public List getIdentifiers() { + return identifiers; + } + + public void setIdentifiers(List identifiers) { + this.identifiers = identifiers; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public String getSummary() { + return summary; + } + + public void setSummary(String summary) { + this.summary = summary; + } + + public String getAcronym() { + return acronym; + } + + public void setAcronym(String acronym) { + this.acronym = acronym; + } + + public String getFunder() { + return funder; + } + + public void setFunder(String funder) { + this.funder = funder; + } + + public String getFunding_stream() { + return funding_stream; + } + + public void setFunding_stream(String funding_stream) { + this.funding_stream = funding_stream; + } + + public String getCurrency() { + return currency; + } + + public void setCurrency(String currency) { + this.currency = currency; + } + + public Float getFunded_amount() { + return funded_amount; + } + + public void setFunded_amount(Float funded_amount) { + this.funded_amount = funded_amount; + } + + public List getKeywords() { + return keywords; + } + + public void setKeywords(List keywords) { + this.keywords = keywords; + } + + public String getStart_date() { + return start_date; + } + + public void setStart_date(String start_date) { + this.start_date = start_date; + } + + public String getEnd_date() { + return end_date; + } + + public void setEnd_date(String end_date) { + this.end_date = end_date; + } + + public String getWebsite() { + return website; + } + + public void setWebsite(String website) { + this.website = website; + } + + public List getBeneficiaries() { + return beneficiaries; + } + + public void setBeneficiaries(List beneficiaries) { + this.beneficiaries = beneficiaries; + } + + public List getContributors() { + return contributors; + } + + public void setContributors(List contributors) { + this.contributors = contributors; + } +} diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Licence.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Licence.java new file mode 100644 index 0000000..ad73b44 --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Licence.java @@ -0,0 +1,10 @@ +package eu.dnetlib.dhp.skgif.model; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 21/02/24 + */ +public class Licence implements Serializable { +} diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Manifestation.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Manifestation.java index 17af00d..11c470d 100644 --- a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Manifestation.java +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Manifestation.java @@ -2,7 +2,6 @@ package eu.dnetlib.dhp.skgif.model; import java.io.Serializable; -import java.net.URL; import java.util.List; import com.fasterxml.jackson.annotation.JsonProperty; @@ -13,40 +12,40 @@ import com.fasterxml.jackson.annotation.JsonProperty; */ public class Manifestation implements Serializable { @JsonProperty("product_local_type") - private String productLocalType; + private String product_local_type; @JsonProperty("product_local_type_schema") - private String productLocalTypeSchema; + private String product_local_type_schema; private List dates; @JsonProperty("peer_review") - private String peerReview; + private String peer_review; @JsonProperty("metadata_curation") - private String metadataCuration; + private String metadata_curation; private String url; private String pid; @JsonProperty("access_right") - private String accessRight; + private String access_right; private String licence; @JsonProperty("licance_schema") - private String licenceSchema; + private String licence_schema; private Biblio biblio; private String venue; @JsonProperty("hosting_datasource") - private String hostingDatasource; + private String hosting_datasource; - public String getProductLocalType() { - return productLocalType; + public String getProduct_local_type() { + return product_local_type; } - public void setProductLocalType(String productLocalType) { - this.productLocalType = productLocalType; + public void setProduct_local_type(String product_local_type) { + this.product_local_type = product_local_type; } - public String getProductLocalTypeSchema() { - return productLocalTypeSchema; + public String getProduct_local_type_schema() { + return product_local_type_schema; } - public void setProductLocalTypeSchema(String productLocalTypeSchema) { - this.productLocalTypeSchema = productLocalTypeSchema; + public void setProduct_local_type_schema(String product_local_type_schema) { + this.product_local_type_schema = product_local_type_schema; } public List getDates() { @@ -57,20 +56,20 @@ public class Manifestation implements Serializable { this.dates = dates; } - public String getPeerReview() { - return peerReview; + public String getPeer_review() { + return peer_review; } - public void setPeerReview(String peerReview) { - this.peerReview = peerReview; + public void setPeer_review(String peer_review) { + this.peer_review = peer_review; } - public String getMetadataCuration() { - return metadataCuration; + public String getMetadata_curation() { + return metadata_curation; } - public void setMetadataCuration(String metadataCuration) { - this.metadataCuration = metadataCuration; + public void setMetadata_curation(String metadata_curation) { + this.metadata_curation = metadata_curation; } public String getUrl() { @@ -89,12 +88,12 @@ public class Manifestation implements Serializable { this.pid = pid; } - public String getAccessRight() { - return accessRight; + public String getAccess_right() { + return access_right; } - public void setAccessRight(String accessRight) { - this.accessRight = accessRight; + public void setAccess_right(String access_right) { + this.access_right = access_right; } public String getLicence() { @@ -105,12 +104,12 @@ public class Manifestation implements Serializable { this.licence = licence; } - public String getLicenceSchema() { - return licenceSchema; + public String getLicence_schema() { + return licence_schema; } - public void setLicenceSchema(String licenceSchema) { - this.licenceSchema = licenceSchema; + public void setLicence_schema(String licence_schema) { + this.licence_schema = licence_schema; } public Biblio getBiblio() { @@ -129,11 +128,11 @@ public class Manifestation implements Serializable { this.venue = venue; } - public String getHostingDatasource() { - return hostingDatasource; + public String getHosting_datasource() { + return hosting_datasource; } - public void setHostingDatasource(String hostingDatasource) { - this.hostingDatasource = hostingDatasource; + public void setHosting_datasource(String hosting_datasource) { + this.hosting_datasource = hosting_datasource; } } diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Organization.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Organization.java new file mode 100644 index 0000000..f21e36f --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Organization.java @@ -0,0 +1,84 @@ +package eu.dnetlib.dhp.skgif.model; + +import java.io.Serializable; +import java.util.List; + +/** + * @author miriam.baglioni + * @Date 21/02/24 + */ +public class Organization implements Serializable { + private String local_identifier; // id + private List identifiers; // pid.qualifier.classid; pid.value list + private String name ; //legalname.value + + private String short_name; // legalshortname.value + private List other_names;// alternative_names.value list + private String website ;//websiteurl.value + private String country; // country.classid + private String type; // map relevant types from the ec* fields of organisations. If no match, default to "other" + + public String getLocal_identifier() { + return local_identifier; + } + + public void setLocal_identifier(String local_identifier) { + this.local_identifier = local_identifier; + } + + public List getIdentifiers() { + return identifiers; + } + + public void setIdentifiers(List identifiers) { + this.identifiers = identifiers; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getShort_name() { + return short_name; + } + + public void setShort_name(String short_name) { + this.short_name = short_name; + } + + public List getOther_names() { + return other_names; + } + + public void setOther_names(List other_names) { + this.other_names = other_names; + } + + public String getWebsite() { + return website; + } + + public void setWebsite(String website) { + this.website = website; + } + + public String getCountry() { + return country; + } + + public void setCountry(String country) { + this.country = country; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } +} diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/OrganizationTypes.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/OrganizationTypes.java new file mode 100644 index 0000000..e0d1e37 --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/OrganizationTypes.java @@ -0,0 +1,20 @@ +package eu.dnetlib.dhp.skgif.model; + +public enum OrganizationTypes { + ARCHIVE ("archive"), + + COMPANY("company"), + + EDUCATION("education"), +FACILITY("facility"), + GOVERNMENT("government"), + HEALTHCARE("healthcare"), +NONPROFIT("nonprofit"), +FUNDER("funder"), +OTHER("other"); + public final String label; + + private OrganizationTypes(String label) { + this.label = label; + } +} diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/PersistentIdentitySystems.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/PersistentIdentitySystems.java new file mode 100644 index 0000000..db80ed6 --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/PersistentIdentitySystems.java @@ -0,0 +1,10 @@ +package eu.dnetlib.dhp.skgif.model; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 21/02/24 + */ +public class PersistentIdentitySystems implements Serializable { +} diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Persons.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Persons.java index 9d713d2..c91121a 100644 --- a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Persons.java +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Persons.java @@ -12,22 +12,22 @@ import org.codehaus.jackson.annotate.JsonProperty; */ public class Persons implements Serializable { @JsonProperty("local_identifier") - private String localIdentifier; + private String local_identifier; private List identifiers; @JsonProperty("given_name") - private String givenName; + private String given_name; @JsonProperty("family_name") - private String familyName; + private String family_name; private String agent; @JsonProperty("declared_affiliations") - private List declaredAffiliations; + private List declared_affiliations; - public String getLocalIdentifier() { - return localIdentifier; + public String getLocal_identifier() { + return local_identifier; } - public void setLocalIdentifier(String localIdentifier) { - this.localIdentifier = localIdentifier; + public void setLocal_identifier(String local_identifier) { + this.local_identifier = local_identifier; } public List getIdentifiers() { @@ -38,20 +38,20 @@ public class Persons implements Serializable { this.identifiers = identifiers; } - public String getGivenName() { - return givenName; + public String getGiven_name() { + return given_name; } - public void setGivenName(String givenName) { - this.givenName = givenName; + public void setGiven_name(String given_name) { + this.given_name = given_name; } - public String getFamilyName() { - return familyName; + public String getFamily_name() { + return family_name; } - public void setFamilyName(String familyName) { - this.familyName = familyName; + public void setFamily_name(String family_name) { + this.family_name = family_name; } public String getAgent() { @@ -62,11 +62,11 @@ public class Persons implements Serializable { this.agent = agent; } - public List getDeclaredAffiliations() { - return declaredAffiliations; + public List getDeclared_affiliations() { + return declared_affiliations; } - public void setDeclaredAffiliations(List declaredAffiliations) { - this.declaredAffiliations = declaredAffiliations; + public void setDeclared_affiliations(List declared_affiliations) { + this.declared_affiliations = declared_affiliations; } } diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Prefixes.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Prefixes.java new file mode 100644 index 0000000..ab7f159 --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Prefixes.java @@ -0,0 +1,31 @@ +package eu.dnetlib.dhp.skgif.model; + + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 21/02/24 + */ +public enum Prefixes implements Serializable { + RESEARCH_PRODUCT("product_____::"), + + ORGANIZATION("organization::"), + + GRANT("grant_______::"), + + PERSON( + "person______::"), + + TEMPORARY_PERSON("temp_person_::"), + + DATASOURCE("datasource__::"), + TOPIC("topic_______::"), + VENUE("venue_______::"); + + public final String label; + + private Prefixes(String label) { + this.label = label; + } +} \ No newline at end of file diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/RelationType.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/RelationType.java index 8752904..36d79b7 100644 --- a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/RelationType.java +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/RelationType.java @@ -8,8 +8,15 @@ import java.io.Serializable; * @Date 05/09/23 */ public enum RelationType implements Serializable { - OUTCOME("outcome"), AFFILIATION("hasAuthorInstitution"), SUPPLEMENT("IsSupplementedBy"), DOCUMENTS( - "IsDocumentedBy"), PART("IsPartOf"), VERSION("IsNewVersioneOf"); + RESULT_OUTCOME_FUNDING("isProducedBy"), + RESULT_AFFILIATIED_TO_ORGANIZATION("hasAuthorInstitution"), + ORGANIZATION_PARTICIPANT_IN_PROJECT("isParticipant"), + SUPPLEMENT("IsSupplementedBy"), + DOCUMENTS( + "IsDocumentedBy"), + PART("IsPartOf"), + VERSION("IsNewVersionOf"), + CITATION("Cites"); public final String label; diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Relations.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Relations.java index e862758..1e22c69 100644 --- a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Relations.java +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Relations.java @@ -6,38 +6,36 @@ import java.util.List; import com.fasterxml.jackson.annotation.JsonProperty; -import eu.dnetlib.dhp.oa.model.graph.Relation; - /** * @author miriam.baglioni * @Date 01/09/23 */ public class Relations implements Serializable { @JsonProperty("relation_type") - private String relationType; + private String relation_type; @JsonProperty("product_list") - private List productList; + private List product_list; public static Relations newInstance(String relClass, List target) { Relations r = new Relations(); - r.relationType = relClass; - r.productList = target; + r.relation_type = relClass; + r.product_list = target; return r; } - public String getRelationType() { - return relationType; + public String getRelation_type() { + return relation_type; } - public void setRelationType(String relationType) { - this.relationType = relationType; + public void setRelation_type(String relation_type) { + this.relation_type = relation_type; } - public List getProductList() { - return productList; + public List getProduct_list() { + return product_list; } - public void setProductList(List productList) { - this.productList = productList; + public void setProduct_list(List product_list) { + this.product_list = product_list; } } diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/ResearchProduct.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/ResearchProduct.java index 40fa62e..6517667 100644 --- a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/ResearchProduct.java +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/ResearchProduct.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.skgif.model; import java.io.Serializable; import java.util.List; +import java.util.Map; import com.fasterxml.jackson.annotation.JsonProperty; @@ -12,27 +13,27 @@ import com.fasterxml.jackson.annotation.JsonProperty; */ public class ResearchProduct implements Serializable { @JsonProperty("local_identifier") - private String localIdentifier; + private String local_identifier; private List identifiers; - private List titles; - private List abstracts; + private Map> titles; + private Map> abstracts; @JsonProperty("product_type") - private String productType; + private String product_type; private List topics; private List contributions; private List manifestations; @JsonProperty("relevant_organizations") - private List relevantOrganizations; + private List relevant_organizations; private List funding; @JsonProperty("related_products") - private List relatedProducts; + private List related_products; - public String getLocalIdentifier() { - return localIdentifier; + public String getLocal_identifier() { + return local_identifier; } - public void setLocalIdentifier(String localIdentifier) { - this.localIdentifier = localIdentifier; + public void setLocal_identifier(String local_identifier) { + this.local_identifier = local_identifier; } public List getIdentifiers() { @@ -43,28 +44,28 @@ public class ResearchProduct implements Serializable { this.identifiers = identifiers; } - public List getTitles() { + public Map> getTitles() { return titles; } - public void setTitles(List titles) { + public void setTitles(Map> titles) { this.titles = titles; } - public List getAbstracts() { + public Map> getAbstracts() { return abstracts; } - public void setAbstracts(List abstracts) { + public void setAbstracts(Map> abstracts) { this.abstracts = abstracts; } - public String getProductType() { - return productType; + public String getProduct_type() { + return product_type; } - public void setProductType(String productType) { - this.productType = productType; + public void setProduct_type(String product_type) { + this.product_type = product_type; } public List getTopics() { @@ -91,12 +92,12 @@ public class ResearchProduct implements Serializable { this.manifestations = manifestations; } - public List getRelevantOrganizations() { - return relevantOrganizations; + public List getRelevant_organizations() { + return relevant_organizations; } - public void setRelevantOrganizations(List relevantOrganizations) { - this.relevantOrganizations = relevantOrganizations; + public void setRelevant_organizations(List relevant_organizations) { + this.relevant_organizations = relevant_organizations; } public List getFunding() { @@ -107,11 +108,11 @@ public class ResearchProduct implements Serializable { this.funding = funding; } - public List getRelatedProducts() { - return relatedProducts; + public List getRelated_products() { + return related_products; } - public void setRelatedProducts(List relatedProducts) { - this.relatedProducts = relatedProducts; + public void setRelated_products(List related_products) { + this.related_products = related_products; } } diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Venue.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Venue.java new file mode 100644 index 0000000..5b6b120 --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/Venue.java @@ -0,0 +1,102 @@ +package eu.dnetlib.dhp.skgif.model; + +import java.io.Serializable; +import java.util.List; + +/** + * @author miriam.baglioni + * @Date 27/02/24 + */ +public class Venue implements Serializable { + private String local_identifier; + private List identifiers; + private String name; + private String acronym; + private String type; + private String publisher; + private String series; + private Boolean is_currently_full_oa; + + private String creation_date; + private List contributions; + + public String getLocal_identifier() { + return local_identifier; + } + + public void setLocal_identifier(String local_identifier) { + this.local_identifier = local_identifier; + } + + public List getIdentifiers() { + return identifiers; + } + + public void setIdentifiers(List identifiers) { + this.identifiers = identifiers; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getAcronym() { + return acronym; + } + + public void setAcronym(String acronym) { + this.acronym = acronym; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public String getPublisher() { + return publisher; + } + + public void setPublisher(String publisher) { + this.publisher = publisher; + } + + public String getSeries() { + return series; + } + + public void setSeries(String series) { + this.series = series; + } + + public Boolean getIs_currently_full_oa() { + return is_currently_full_oa; + } + + public void setIs_currently_full_oa(Boolean is_currently_full_oa) { + this.is_currently_full_oa = is_currently_full_oa; + } + + public String getCreation_date() { + return creation_date; + } + + public void setCreation_date(String creation_date) { + this.creation_date = creation_date; + } + + public List getContributions() { + return contributions; + } + + public void setContributions(List contributions) { + this.contributions = contributions; + } +} diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueContribution.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueContribution.java new file mode 100644 index 0000000..ee41147 --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueContribution.java @@ -0,0 +1,30 @@ +package eu.dnetlib.dhp.skgif.model; + +import java.io.Serializable; +import java.util.List; + +/** + * @author miriam.baglioni + * @Date 27/02/24 + */ +public class VenueContribution implements Serializable { + private String person; + private List roles; + + public String getPerson() { + + return person; + } + + public void setPerson(String person) { + this.person = person; + } + + public List getRoles() { + return roles; + } + + public void setRoles(List roles) { + this.roles = roles; + } +} diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueIdentifierType.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueIdentifierType.java new file mode 100644 index 0000000..6583147 --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueIdentifierType.java @@ -0,0 +1,22 @@ +package eu.dnetlib.dhp.skgif.model; + +import java.io.Serializable; + +public enum VenueIdentifierType implements Serializable { + + EISSN("eissn"), + ISSN("issn"), + LISSN("lissn"), + ISBN("isbn"), + OPENDOAR( + "opendoar"), + R3DATA("re3data.org"), + FAIRSHARING("fairsharing"); + + + public final String label; + + private VenueIdentifierType(String label) { + this.label = label; + } +} diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueType.java b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueType.java new file mode 100644 index 0000000..65f36d3 --- /dev/null +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/skgif/model/VenueType.java @@ -0,0 +1,21 @@ +package eu.dnetlib.dhp.skgif.model; + +import java.io.Serializable; + +public enum VenueType implements Serializable { + + REPOSITORY("repository"), + JOURNAL("journal"), + CONFERENCE("conference"), + BOOK("book"), + OTHER( + "other"), + UNKNOWN("unknown"); + + + public final String label; + + private VenueType(String label) { + this.label = label; 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- -import static eu.dnetlib.dhp.oa.graph.dump.Constants.*; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.ENTITY_ID_SEPARATOR; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.getEntityId; - -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; - -import org.apache.commons.lang3.StringUtils; - -import eu.dnetlib.dhp.oa.graph.dump.exceptions.CardinalityTooHighException; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; -import eu.dnetlib.dhp.oa.model.*; -import eu.dnetlib.dhp.oa.model.AccessRight; -import eu.dnetlib.dhp.oa.model.Author; -import eu.dnetlib.dhp.oa.model.GeoLocation; -import eu.dnetlib.dhp.oa.model.Instance; -import eu.dnetlib.dhp.oa.model.OpenAccessColor; -import eu.dnetlib.dhp.oa.model.OpenAccessRoute; -import eu.dnetlib.dhp.oa.model.Result; -import eu.dnetlib.dhp.oa.model.Subject; -import eu.dnetlib.dhp.oa.model.community.CfHbKeyValue; -import eu.dnetlib.dhp.oa.model.community.CommunityInstance; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; -import eu.dnetlib.dhp.oa.model.community.Context; -import eu.dnetlib.dhp.oa.model.graph.GraphResult; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; - -public class ResultMapper implements Serializable { - private static final String NULL = "null"; - - public static Result map( - E in, Map communityMap, String dumpType) - throws NoAvailableEntityTypeException, CardinalityTooHighException { - - Result out; - if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - out = new GraphResult(); - } else { - out = new CommunityResult(); - } - - eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; - Optional ort = Optional.ofNullable(input.getResulttype()); - if (ort.isPresent()) { - try { - - addTypeSpecificInformation(out, input, ort.get()); - mapAuthor(out, input); - mapAccessRight(out, input); - mapContributor(out, input); - mapCountry(out, input); - mapCoverage(out, input); - out.setDateofcollection(input.getDateofcollection()); - out.setGreen(input.getIsGreen()); - out.setInDiamondJournal(input.getIsInDiamondJournal()); - out.setPubliclyFunded(input.getPubliclyFunded()); - mapOpenAccessColor(out, input); - mapDescription(out, input); - mapEmbargo(out, input); - mapFormat(out, input); - out.setId(getEntityId(input.getId(), ENTITY_ID_SEPARATOR)); - mapOriginalId(out, input); - mapInstance(dumpType, out, input); - mapLanguage(out, input); - mapLastUpdateTimestamp(out, input); - mapTitle(out, input); - mapPid(out, input); - mapDateOfAcceptance(out, input); - mapPublisher(out, input); - mapSource(out, input); - mapSubject(out, input); - out.setType(input.getResulttype().getClassid()); - mapMeasure(out, input); - if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - mapCollectedfrom((CommunityResult) out, input); - mapContext(communityMap, (CommunityResult) out, input); - } - } catch (ClassCastException cce) { - return null; - } - } - - return out; - - } - - private static void mapOpenAccessColor(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - if (Optional.ofNullable(input.getOpenAccessColor()).isPresent()) - switch (input.getOpenAccessColor()) { - case bronze: - out.setOpenAccessColor(OpenAccessColor.bronze); - break; - case gold: - out.setOpenAccessColor(OpenAccessColor.gold); - break; - case hybrid: - out.setOpenAccessColor(OpenAccessColor.hybrid); - break; - - } - - } - - private static void mapContext(Map communityMap, CommunityResult out, - eu.dnetlib.dhp.schema.oaf.Result input) { - Set communities = communityMap.keySet(); - List contextList = Optional - .ofNullable( - input - .getContext()) - .map( - value -> value - .stream() - .map(c -> { - String communityId = c.getId(); - if (communityId.contains("::")) { - communityId = communityId.substring(0, communityId.indexOf("::")); - } - if (communities.contains(communityId)) { - Context context = new Context(); - context.setCode(communityId); - context.setLabel(communityMap.get(communityId)); - Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); - if (dataInfo.isPresent()) { - List provenance = new ArrayList<>(); - provenance - .addAll( - dataInfo - .get() - .stream() - .map( - di -> Optional - .ofNullable(di.getProvenanceaction()) - .map( - provenanceaction -> Provenance - .newInstance( - provenanceaction.getClassname(), - di.getTrust())) - .orElse(null)) - .filter(Objects::nonNull) - .collect(Collectors.toSet())); - - try { - context.setProvenance(getUniqueProvenance(provenance)); - } catch (NoAvailableEntityTypeException e) { - e.printStackTrace(); - } - } - return context; - } - return null; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList())) - .orElse(new ArrayList<>()); - - if (!contextList.isEmpty()) { - Set hashValue = new HashSet<>(); - List remainigContext = new ArrayList<>(); - contextList.forEach(c -> { - if (!hashValue.contains(c.hashCode())) { - remainigContext.add(c); - hashValue.add(c.hashCode()); - } - }); - out.setContext(remainigContext); - } - } - - private static void mapCollectedfrom(CommunityResult out, eu.dnetlib.dhp.schema.oaf.Result input) { - out - .setCollectedfrom( - input - .getCollectedfrom() - .stream() - .map(cf -> CfHbKeyValue.newInstance(getEntityId(cf.getKey(), ENTITY_ID_SEPARATOR), cf.getValue())) - .collect(Collectors.toList())); - } - - private static void mapMeasure(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - if (Optional.ofNullable(input.getMeasures()).isPresent() && input.getMeasures().size() > 0) { - - out.setIndicators(Utils.getIndicator(input.getMeasures())); - } - } - - private static void mapSubject(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - List subjectList = new ArrayList<>(); - Optional - .ofNullable(input.getSubject()) - .ifPresent( - value -> value - .stream() -// .filter( -// s -> !((s.getQualifier().getClassid().equalsIgnoreCase("fos") && -// Optional.ofNullable(s.getDataInfo()).isPresent() -// && Optional.ofNullable(s.getDataInfo().getProvenanceaction()).isPresent() && -// s.getDataInfo().getProvenanceaction().getClassid().equalsIgnoreCase("subject:fos")) -// || -// (s.getQualifier().getClassid().equalsIgnoreCase("sdg") && -// Optional.ofNullable(s.getDataInfo()).isPresent() -// && Optional.ofNullable(s.getDataInfo().getProvenanceaction()).isPresent() && -// s -// .getDataInfo() -// .getProvenanceaction() -// .getClassid() -// .equalsIgnoreCase("subject:sdg")))) - .filter(s -> !s.getValue().equalsIgnoreCase(NULL)) - .forEach(s -> subjectList.add(getSubject(s)))); - - out.setSubjects(subjectList); - } - - private static void mapSource(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - Optional - .ofNullable(input.getSource()) - .ifPresent( - value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList()))); - } - - private static void mapPublisher(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - Optional> oStr; - oStr = Optional.ofNullable(input.getPublisher()); - if (oStr.isPresent()) { - out.setPublisher(oStr.get().getValue()); - } - } - - private static void mapDateOfAcceptance(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - Optional> oStr; - oStr = Optional.ofNullable(input.getDateofacceptance()); - if (oStr.isPresent()) { - out.setPublicationdate(oStr.get().getValue()); - } - } - - private static void mapPid(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - Optional - .ofNullable(input.getPid()) - .ifPresent( - value -> out - .setPid( - value - .stream() - .map( - p -> ResultPid - .newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - } - - private static void mapTitle(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - Optional> otitle = Optional.ofNullable(input.getTitle()); - if (otitle.isPresent()) { - List iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) - .collect(Collectors.toList()); - if (!iTitle.isEmpty()) { - out.setMaintitle(iTitle.get(0).getValue()); - } - - iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) - .collect(Collectors.toList()); - if (!iTitle.isEmpty()) { - out.setSubtitle(iTitle.get(0).getValue()); - } - - } - } - - private static void mapLastUpdateTimestamp(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); - if (oLong.isPresent()) { - out.setLastupdatetimestamp(oLong.get()); - } - } - - private static void mapLanguage(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - Optional oL = Optional.ofNullable(input.getLanguage()); - if (oL.isPresent()) { - Qualifier language = oL.get(); - out.setLanguage(Language.newInstance(language.getClassid(), language.getClassname())); - } - } - - private static void mapInstance(String dumpType, Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - Optional> oInst = Optional - .ofNullable(input.getInstance()); - - if (oInst.isPresent()) { - if (DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - ((GraphResult) out) - .setInstance( - oInst.get().stream().map(ResultMapper::getGraphInstance).collect(Collectors.toList())); - } else { - ((CommunityResult) out) - .setInstance( - oInst - .get() - .stream() - .map(ResultMapper::getCommunityInstance) - .collect(Collectors.toList())); - } - } - } - - private static void mapOriginalId(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - out.setOriginalId(new ArrayList<>()); - Optional - .ofNullable(input.getOriginalId()) - .ifPresent( - v -> out - .setOriginalId( - input - .getOriginalId() - .stream() - .filter(s -> !s.startsWith("50|")) - .collect(Collectors.toList()))); - } - - private static void mapFormat(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - final List formatList = new ArrayList<>(); - Optional - .ofNullable(input.getFormat()) - .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); - out.setFormat(formatList); - } - - private static void mapEmbargo(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); - if (oStr.isPresent()) { - out.setEmbargoenddate(oStr.get().getValue()); - } - } - - private static void mapDescription(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - final List descriptionList = new ArrayList<>(); - Optional - .ofNullable(input.getDescription()) - .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); - out.setDescription(descriptionList); - } - - private static void mapCoverage(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - final List coverageList = new ArrayList<>(); - Optional - .ofNullable(input.getCoverage()) - .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); - out.setCoverage(coverageList); - } - - private static void mapCountry(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - Optional - .ofNullable(input.getCountry()) - .ifPresent( - value -> out - .setCountry( - value - .stream() - .map( - c -> { - if (c.getClassid().equals((ModelConstants.UNKNOWN))) { - return null; - } - ResultCountry country = new ResultCountry(); - country.setCode(c.getClassid()); - country.setLabel(c.getClassname()); - Optional - .ofNullable(c.getDataInfo()) - .ifPresent( - provenance -> country - .setProvenance( - Provenance - .newInstance( - provenance - .getProvenanceaction() - .getClassname(), - c.getDataInfo().getTrust()))); - return country; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList()))); - } - - private static void mapContributor(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - final List contributorList = new ArrayList<>(); - Optional - .ofNullable(input.getContributor()) - .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); - out.setContributor(contributorList); - } - - private static void mapAccessRight(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - // I do not map Access Right UNKNOWN or OTHER - - Optional oar = Optional.ofNullable(input.getBestaccessright()); - if (oar.isPresent() && Constants.ACCESS_RIGHTS_COAR_MAP.containsKey(oar.get().getClassid())) { - String code = Constants.ACCESS_RIGHTS_COAR_MAP.get(oar.get().getClassid()); - out - .setBestaccessright( - - BestAccessRight - .newInstance( - code, - Constants.COAR_CODE_LABEL_MAP.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - } - } - - private static void mapAuthor(Result out, eu.dnetlib.dhp.schema.oaf.Result input) { - Optional - .ofNullable(input.getAuthor()) - .ifPresent( - ats -> out.setAuthor(ats.stream().map(ResultMapper::getAuthor).collect(Collectors.toList()))); - } - - private static void addTypeSpecificInformation(Result out, eu.dnetlib.dhp.schema.oaf.Result input, - eu.dnetlib.dhp.schema.oaf.Qualifier ort) throws NoAvailableEntityTypeException { - switch (ort.getClassid()) { - case "publication": - Optional journal = Optional - .ofNullable(((Publication) input).getJournal()); - if (journal.isPresent()) { - Journal j = journal.get(); - Container c = new Container(); - c.setConferencedate(j.getConferencedate()); - c.setConferenceplace(j.getConferenceplace()); - c.setEdition(j.getEdition()); - c.setEp(j.getEp()); - c.setIss(j.getIss()); - c.setIssnLinking(j.getIssnLinking()); - c.setIssnOnline(j.getIssnOnline()); - c.setIssnPrinted(j.getIssnPrinted()); - c.setName(j.getName()); - c.setSp(j.getSp()); - c.setVol(j.getVol()); - out.setContainer(c); - out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); - } - break; - case "dataset": - Dataset id = (Dataset) input; - Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); - Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); - - out - .setGeolocation( - Optional - .ofNullable(id.getGeolocation()) - .map( - igl -> igl - .stream() - .filter(Objects::nonNull) - .map(gli -> { - GeoLocation gl = new GeoLocation(); - gl.setBox(gli.getBox()); - gl.setPlace(gli.getPlace()); - gl.setPoint(gli.getPoint()); - return gl; - }) - .collect(Collectors.toList())) - .orElse(null)); - - out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); - break; - case "software": - - Software is = (Software) input; - Optional - .ofNullable(is.getCodeRepositoryUrl()) - .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); - Optional - .ofNullable(is.getDocumentationUrl()) - .ifPresent( - value -> out - .setDocumentationUrl( - value - .stream() - .map(Field::getValue) - .collect(Collectors.toList()))); - - Optional - .ofNullable(is.getProgrammingLanguage()) - .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); - - out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); - break; - case "other": - - OtherResearchProduct ir = (OtherResearchProduct) input; - out - .setContactgroup( - Optional - .ofNullable(ir.getContactgroup()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out - .setContactperson( - Optional - .ofNullable(ir.getContactperson()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - out - .setTool( - Optional - .ofNullable(ir.getTool()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); - - break; - default: - throw new NoAvailableEntityTypeException(); - } - } - - private static Instance getGraphInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { - Instance instance = new Instance(); - - setCommonValue(i, instance); - - return instance; - - } - - private static CommunityInstance getCommunityInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { - CommunityInstance instance = new CommunityInstance(); - - setCommonValue(i, instance); - - if (Optional.ofNullable(i.getCollectedfrom()).isPresent() && - Optional.ofNullable(i.getCollectedfrom().getKey()).isPresent() && - StringUtils.isNotBlank(i.getCollectedfrom().getKey())) - instance - .setCollectedfrom( - CfHbKeyValue - .newInstance( - getEntityId(i.getCollectedfrom().getKey(), ENTITY_ID_SEPARATOR), - i.getCollectedfrom().getValue())); - - if (Optional.ofNullable(i.getHostedby()).isPresent() && - Optional.ofNullable(i.getHostedby().getKey()).isPresent() && - StringUtils.isNotBlank(i.getHostedby().getKey())) - instance - .setHostedby( - CfHbKeyValue - .newInstance( - getEntityId(i.getHostedby().getKey(), ENTITY_ID_SEPARATOR), i.getHostedby().getValue())); - - return instance; - - } - - private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { - Optional opAr = Optional.ofNullable(i.getAccessright()); - - if (opAr.isPresent() && Constants.ACCESS_RIGHTS_COAR_MAP.containsKey(opAr.get().getClassid())) { - String code = Constants.ACCESS_RIGHTS_COAR_MAP.get(opAr.get().getClassid()); - - instance - .setAccessright( - AccessRight - .newInstance( - code, - Constants.COAR_CODE_LABEL_MAP.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - - if (opAr.get().getOpenAccessRoute() != null) { - switch (opAr.get().getOpenAccessRoute()) { - case hybrid: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); - break; - case gold: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold); - break; - case green: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green); - break; - case bronze: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze); - break; - - } - } - - } - - Optional - .ofNullable(i.getPid()) - .ifPresent( - pid -> instance - .setPid( - pid - .stream() - .map(p -> ResultPid.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - Optional - .ofNullable(i.getAlternateIdentifier()) - .ifPresent( - ai -> instance - .setAlternateIdentifier( - ai - .stream() - .map(p -> AlternateIdentifier.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - Optional - .ofNullable(i.getLicense()) - .ifPresent(value -> instance.setLicense(value.getValue())); - Optional - .ofNullable(i.getDateofacceptance()) - .ifPresent(value -> instance.setPublicationdate(value.getValue())); - Optional - .ofNullable(i.getRefereed()) - .ifPresent(value -> instance.setRefereed(value.getClassname())); - Optional - .ofNullable(i.getInstancetype()) - .ifPresent(value -> instance.setType(value.getClassname())); - Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); - Optional> oPca = Optional.ofNullable(i.getProcessingchargeamount()); - Optional> oPcc = Optional.ofNullable(i.getProcessingchargecurrency()); - if (oPca.isPresent() && oPcc.isPresent()) { - Field pca = oPca.get(); - Field pcc = oPcc.get(); - if (!pca.getValue().trim().equals("") && !pcc.getValue().trim().equals("")) { - APC apc = new APC(); - apc.setCurrency(oPcc.get().getValue()); - apc.setAmount(oPca.get().getValue()); - instance.setArticleprocessingcharge(apc); - } - - } - Optional.ofNullable(i.getUrl()).ifPresent(instance::setUrl); - - } - - private static List getUniqueProvenance(List provenance) - throws NoAvailableEntityTypeException { - Provenance iProv = new Provenance(); - - Provenance hProv = new Provenance(); - Provenance lProv = new Provenance(); - - for (Provenance p : provenance) { - switch (p.getProvenance()) { - case Constants.HARVESTED: - hProv = getHighestTrust(hProv, p); - break; - case Constants.INFERRED: - iProv = getHighestTrust(iProv, p); - // To be removed as soon as the new beta run has been done - // this fixex issue of not set trust during bulktagging - if (StringUtils.isEmpty(iProv.getTrust())) { - iProv.setTrust(Constants.DEFAULT_TRUST); - } - break; - case Constants.USER_CLAIM: - lProv = getHighestTrust(lProv, p); - break; - default: - throw new NoAvailableEntityTypeException(); - } - - } - - return Arrays - .asList(iProv, hProv, lProv) - .stream() - .filter(p -> !StringUtils.isEmpty(p.getProvenance())) - .collect(Collectors.toList()); - - } - - private static Provenance getHighestTrust(Provenance hProv, Provenance p) { - if (StringUtils.isNoneEmpty(hProv.getTrust(), p.getTrust())) - return hProv.getTrust().compareTo(p.getTrust()) > 0 ? hProv : p; - - return (StringUtils.isEmpty(p.getTrust()) && !StringUtils.isEmpty(hProv.getTrust())) ? hProv : p; - - } - - private static Subject getSubject(StructuredProperty s) { - Subject subject = new Subject(); - subject.setSubject(SubjectSchemeValue.newInstance(s.getQualifier().getClassid(), s.getValue())); - Optional di = Optional.ofNullable(s.getDataInfo()); - if (di.isPresent()) { - Provenance p = new Provenance(); - p.setProvenance(di.get().getProvenanceaction().getClassname()); - if (!s.getQualifier().getClassid().equalsIgnoreCase("fos") && - !s.getQualifier().getClassid().equalsIgnoreCase("sdg")) - p.setTrust(di.get().getTrust()); - subject.setProvenance(p); - } - - return subject; - } - - private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { - Author a = new Author(); - a.setFullname(oa.getFullname()); - a.setName(oa.getName()); - a.setSurname(oa.getSurname()); - a.setRank(oa.getRank()); - - Optional> oPids = Optional - .ofNullable(oa.getPid()); - if (oPids.isPresent()) { - AuthorPid pid = getOrcid(oPids.get()); - if (pid != null) { - a.setPid(pid); - } - } - - return a; - } - - private static AuthorPid getAuthorPid(StructuredProperty pid) { - Optional di = Optional.ofNullable(pid.getDataInfo()); - if (di.isPresent()) { - return AuthorPid - .newInstance( - AuthorPidSchemeValue - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()), - Provenance - .newInstance( - di.get().getProvenanceaction().getClassname(), - di.get().getTrust())); - } else { - return AuthorPid - .newInstance( - AuthorPidSchemeValue - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()) - - ); - } - } - - private static AuthorPid getOrcid(List p) { - List pidList = p.stream().map(pid -> { - if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) || - (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) { - return pid; - } - return null; - }).filter(Objects::nonNull).collect(Collectors.toList()); - - if (pidList.size() == 1) { - return getAuthorPid(pidList.get(0)); - } - - List orcid = pidList - .stream() - .filter( - ap -> ap - .getQualifier() - .getClassid() - .equals(ModelConstants.ORCID)) - .collect(Collectors.toList()); - if (orcid.size() == 1) { - return getAuthorPid(orcid.get(0)); - } - orcid = pidList - .stream() - .filter( - ap -> ap - .getQualifier() - .getClassid() - .equals(ModelConstants.ORCID_PENDING)) - .collect(Collectors.toList()); - if (orcid.size() == 1) { - return getAuthorPid(orcid.get(0)); - } - - return null; - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java deleted file mode 100644 index 2a7324d..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java +++ /dev/null @@ -1,91 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; -import java.nio.charset.StandardCharsets; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -/** - * This class connects with the community APIs for production. It saves the information about the - * context that will guide the dump of the results. The information saved is a HashMap. The key is the id of a community - * - research infrastructure/initiative , the value is the label of the research community - research - * infrastructure/initiative. - */ - -public class SaveCommunityMap implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SaveCommunityMap.class); - private final transient UtilCommunityAPI queryInformationSystem; - - private final transient BufferedWriter writer; - - public SaveCommunityMap(String hdfsPath, String hdfsNameNode) throws IOException { - final Configuration conf = new Configuration(); - conf.set("fs.defaultFS", hdfsNameNode); - FileSystem fileSystem = FileSystem.get(conf); - Path hdfsWritePath = new Path(hdfsPath); - - if (fileSystem.exists(hdfsWritePath)) { - fileSystem.delete(hdfsWritePath, true); - } - - queryInformationSystem = new UtilCommunityAPI(); - - FSDataOutputStream fos = fileSystem.create(hdfsWritePath); - writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8)); - } - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SaveCommunityMap.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - final String nameNode = parser.get("nameNode"); - log.info("nameNode: {}", nameNode); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final Boolean singleCommunity = Optional - .ofNullable(parser.get("singleDeposition")) - .map(Boolean::valueOf) - .orElse(false); - - final String community_id = Optional.ofNullable(parser.get("communityId")).orElse(null); - - final SaveCommunityMap scm = new SaveCommunityMap(outputPath, nameNode); - - scm.saveCommunityMap(singleCommunity, community_id); - - } - - private void saveCommunityMap(boolean singleCommunity, String communityId) - throws IOException { - final String communityMapString = Utils.OBJECT_MAPPER - .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, communityId)); - log.info("communityMap {} ", communityMapString); - writer - .write( - communityMapString); - writer.close(); - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/UtilCommunityAPI.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/UtilCommunityAPI.java deleted file mode 100644 index 30737e7..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/UtilCommunityAPI.java +++ /dev/null @@ -1,203 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import static eu.dnetlib.dhp.utils.DHPUtils.MAPPER; - -import java.io.IOException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.communityapi.model.*; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.complete.ContextInfo; -import eu.dnetlib.dhp.oa.graph.dump.csv.Constants; -import eu.dnetlib.dhp.utils.DHPUtils; - -public class UtilCommunityAPI { - - private static final Logger log = LoggerFactory.getLogger(UtilCommunityAPI.class); - - public CommunityMap getCommunityMap(boolean singleCommunity, String communityId) - throws IOException { - if (singleCommunity) - return getMap(Arrays.asList(getCommunity(communityId))); - return getMap(getValidCommunities()); - - } - - private CommunityMap getMap(List communities) { - final CommunityMap map = new CommunityMap(); - communities.forEach(c -> map.put(c.getId(), c.getName())); - return map; - } - - public List getCommunityCsv(List comms) { - return comms.stream().map(c -> { - try { - CommunityModel community = getCommunity(c); - StringBuilder builder = new StringBuilder(); - builder.append(DHPUtils.md5(community.getId())); - builder.append(Constants.SEP); - builder.append(community.getName()); - builder.append(Constants.SEP); - builder.append(community.getId()); - builder.append(Constants.SEP); - builder - .append( - community.getDescription()); - return builder.toString(); - } catch (IOException e) { - throw new RuntimeException(e); - } - }).collect(Collectors.toList()); - - } - - private List getValidCommunities() throws IOException { - ObjectMapper mapper = new ObjectMapper(); - return mapper - .readValue(eu.dnetlib.dhp.communityapi.QueryCommunityAPI.communities(), CommunitySummary.class) - .stream() - .filter( - community -> (community.getStatus().equals("all") || community.getStatus().equalsIgnoreCase("public")) - && - (community.getType().equals("ri") || community.getType().equals("community"))) - .collect(Collectors.toList()); - - } - - private CommunityModel getCommunity(String id) throws IOException { - ObjectMapper mapper = new ObjectMapper(); - return mapper - .readValue(eu.dnetlib.dhp.communityapi.QueryCommunityAPI.community(id), CommunityModel.class); - - } - - public List getContextInformation() throws IOException { - - return getValidCommunities() - .stream() - .map(c -> getContext(c)) - .collect(Collectors.toList()); - - } - - public ContextInfo getContext(CommunityModel c) { - - ContextInfo cinfo = new ContextInfo(); - cinfo.setId(c.getId()); - cinfo.setDescription(c.getDescription()); - CommunityModel cm = null; - try { - cm = getCommunity(c.getId()); - } catch (IOException e) { - throw new RuntimeException(e); - } - cinfo.setSubject(new ArrayList<>()); - cinfo.getSubject().addAll(cm.getSubjects()); - cinfo.setZenodocommunity(c.getZenodoCommunity()); - cinfo.setType(c.getType()); - return cinfo; - } - - public List getContextRelation() throws IOException { - return getValidCommunities().stream().map(c -> { - ContextInfo cinfo = new ContextInfo(); - cinfo.setId(c.getId()); - cinfo.setDatasourceList(getDatasourceList(c.getId())); - cinfo.setProjectList(getProjectList(c.getId())); - - return cinfo; - }).collect(Collectors.toList()); - } - - private List getDatasourceList(String id) { - List datasourceList = new ArrayList<>(); - try { - - new ObjectMapper() - .readValue( - eu.dnetlib.dhp.communityapi.QueryCommunityAPI.communityDatasource(id), - DatasourceList.class) - .stream() - .forEach(ds -> { - if (Optional.ofNullable(ds.getOpenaireId()).isPresent()) { - - datasourceList.add(ds.getOpenaireId()); - } - - }); - - } catch (IOException e) { - throw new RuntimeException(e); - } - return datasourceList; - } - - private List getProjectList(String id) { - int page = -1; - int size = 100; - ContentModel cm = null; - ; - ArrayList projectList = new ArrayList<>(); - do { - page++; - try { - cm = new ObjectMapper() - .readValue( - eu.dnetlib.dhp.communityapi.QueryCommunityAPI - .communityProjects( - id, String.valueOf(page), String.valueOf(size)), - ContentModel.class); - if (cm.getContent().size() > 0) { - cm.getContent().forEach(p -> { - if (Optional.ofNullable(p.getOpenaireId()).isPresent()) - projectList.add(p.getOpenaireId()); - - }); - } - } catch (IOException e) { - throw new RuntimeException(e); - } - } while (!cm.getLast()); - - return projectList; - } - - /** - * it returns for each organization the list of associated communities - */ - public CommunityEntityMap getCommunityOrganization() throws IOException { - CommunityEntityMap organizationMap = new CommunityEntityMap(); - getValidCommunities() - .forEach(community -> { - String id = community.getId(); - try { - List associatedOrgs = MAPPER - .readValue( - eu.dnetlib.dhp.communityapi.QueryCommunityAPI.communityPropagationOrganization(id), - OrganizationList.class); - associatedOrgs.forEach(o -> { - if (!organizationMap - .keySet() - .contains(o)) - organizationMap.put(o, new ArrayList<>()); - organizationMap.get(o).add(community.getId()); - }); - } catch (IOException e) { - throw new RuntimeException(e); - } - }); - - return organizationMap; - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java deleted file mode 100644 index c72955c..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java +++ /dev/null @@ -1,200 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import static eu.dnetlib.dhp.oa.graph.dump.Constants.*; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; -import java.util.ArrayList; -import java.util.List; -import java.util.stream.Collectors; - -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -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.SparkSession; -import org.jetbrains.annotations.NotNull; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; - -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.complete.Constants; -import eu.dnetlib.dhp.oa.model.Indicator; -import eu.dnetlib.dhp.oa.model.Score; -import eu.dnetlib.dhp.oa.model.UsageCounts; -import eu.dnetlib.dhp.oa.model.graph.GraphResult; -import eu.dnetlib.dhp.oa.model.graph.Relation; -import eu.dnetlib.dhp.oa.model.graph.ResearchCommunity; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Measure; -import eu.dnetlib.dhp.utils.DHPUtils; -import scala.Tuple2; - -public class Utils { - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final String ENTITY_ID_SEPARATOR = "|"; - - private Utils() { - } - - public static void removeOutputDir(SparkSession spark, String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } - - public static Dataset readPath( - SparkSession spark, String inputPath, Class clazz) { - return spark - .read() - .textFile(inputPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); - } - - public static String getContextId(String id) { - - return String - .format( - "%s::%s", Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5(id)); - } - - public static CommunityMap getCommunityMap(SparkSession spark, String communityMapPath) { - - return new Gson().fromJson(spark.read().textFile(communityMapPath).collectAsList().get(0), CommunityMap.class); - - } - - public static CommunityMap readCommunityMap(FileSystem fileSystem, String communityMapPath) throws IOException { - BufferedReader br = new BufferedReader(new InputStreamReader(fileSystem.open(new Path(communityMapPath)))); - StringBuilder sb = new StringBuilder(); - try { - String line; - while ((line = br.readLine()) != null) { - sb.append(line); - } - } finally { - br.close(); - - } - - return new Gson().fromJson(sb.toString(), CommunityMap.class); - } - - public static String getEntityId(String id, String separator) { - return id.substring(id.indexOf(separator) + 1); - } - - public static Dataset getEntitiesId(SparkSession spark, String inputPath) { - Dataset dumpedIds = Utils - .readPath(spark, inputPath + "/publication", GraphResult.class) - .map((MapFunction) r -> r.getId(), Encoders.STRING()) - .union( - Utils - .readPath(spark, inputPath + "/dataset", GraphResult.class) - .map((MapFunction) r -> r.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/software", GraphResult.class) - .map((MapFunction) r -> r.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/otherresearchproduct", GraphResult.class) - .map((MapFunction) r -> r.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/organization", eu.dnetlib.dhp.oa.model.graph.Organization.class) - .map( - (MapFunction) o -> o.getId(), - Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.oa.model.graph.Project.class) - .map( - (MapFunction) o -> o.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/datasource", eu.dnetlib.dhp.oa.model.graph.Datasource.class) - .map( - (MapFunction) o -> o.getId(), - Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/communities_infrastructures", ResearchCommunity.class) - .map((MapFunction) c -> c.getId(), Encoders.STRING())); - return dumpedIds; - } - - public static Dataset getValidRelations(Dataset relations, - Dataset entitiesIds) { - Dataset> relationSource = relations - .map( - (MapFunction>) r -> new Tuple2<>(r.getSource(), r), - Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class))); - - Dataset> relJoinSource = relationSource - .joinWith(entitiesIds, relationSource.col("_1").equalTo(entitiesIds.col("value"))) - .map( - (MapFunction, String>, Tuple2>) t2 -> new Tuple2<>( - t2._1()._2().getTarget(), t2._1()._2()), - Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class))); - - return relJoinSource - .joinWith(entitiesIds, relJoinSource.col("_1").equalTo(entitiesIds.col("value"))) - .map( - (MapFunction, String>, Relation>) t2 -> t2._1()._2(), - Encoders.bean(Relation.class)); - } - - public static Indicator getIndicator(List measures) { - Indicator i = new Indicator(); - for (eu.dnetlib.dhp.schema.oaf.Measure m : measures) { - switch (m.getId()) { - case USAGE_COUNT_DOWNLOADS: - getUsageCounts(i).setDownloads(m.getUnit().get(0).getValue()); - break; - case USAGE_COUNT_VIEWS: - getUsageCounts(i).setViews(m.getUnit().get(0).getValue()); - break; - default: - getImpactMeasure(i).add(getScore(m.getId(), m.getUnit())); - break; - - } - } - - return i; - } - - @NotNull - private static UsageCounts getUsageCounts(Indicator i) { - if (i.getUsageCounts() == null) { - i.setUsageCounts(new UsageCounts()); - } - return i.getUsageCounts(); - } - - @NotNull - private static List getImpactMeasure(Indicator i) { - if (i.getBipIndicators() == null) { - i.setBipIndicators(new ArrayList<>()); - } - return i.getBipIndicators(); - } - - private static Score getScore(String indicator, List unit) { - Score s = new Score(); - s.setIndicator(indicator); - for (KeyValue u : unit) { - if (u.getKey().equals("score")) { - s.setScore(u.getValue()); - } else { - s.setClazz(u.getValue()); - } - } - return s; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java deleted file mode 100644 index d459063..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java +++ /dev/null @@ -1,8 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import java.io.Serializable; -import java.util.HashMap; - -public class CommunityMap extends HashMap implements Serializable { -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java deleted file mode 100644 index a4f9e2d..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ /dev/null @@ -1,75 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; -import java.util.stream.Collectors; - -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; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; -import eu.dnetlib.dhp.oa.model.community.Context; - -/** - * This class splits the dumped results according to the research community - research initiative/infrastructure they - * are related to. The information about the community is found in the element "context.id" in the result. Since the - * context that can be found in the result can be associated not only to communities, a community Map is provided. It - * will guide the splitting process. Note: the repartition(1) just before writing the results related to a community. - * This is a choice due to uploading constraints (just one file for each community) As soon as a better solution will be - * in place remove the repartition - */ -public class CommunitySplit implements Serializable { - - public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath) { - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - execSplit(spark, inputPath, outputPath, communityMap); - }); - } - - private static void execSplit(SparkSession spark, String inputPath, String outputPath, - CommunityMap communities) { - - Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - - communities - .keySet() - .stream() - .parallel() - .forEach(c -> { - result - .filter( - (FilterFunction) r -> Optional.ofNullable(r.getContext()).isPresent() && - r.getContext().stream().anyMatch(con -> con.getCode().equals(c))) - .map( - (MapFunction) cr -> new ObjectMapper().writeValueAsString(cr), - Encoders.STRING()) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .text(outputPath + "/" + c.replace(" ", "_")); - }); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java deleted file mode 100644 index 599393a..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java +++ /dev/null @@ -1,28 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import java.io.Serializable; -import java.util.List; - -import eu.dnetlib.dhp.oa.model.community.Project; - -public class ResultProject implements Serializable { - private String resultId; - private List projectsList; - - public String getResultId() { - return resultId; - } - - public void setResultId(String resultId) { - this.resultId = resultId; - } - - public List getProjectsList() { - return projectsList; - } - - public void setProjectsList(List projectsList) { - this.projectsList = projectsList; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java deleted file mode 100644 index 97ff9ca..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java +++ /dev/null @@ -1,155 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang.StringUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.CardinalityTooHighException; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Result; - -/** - * Spark action to trigger the dump of results associated to research community - reseach initiative/infrasctructure The - * actual dump if performed via the class DumpProducts that is used also for the entire graph dump - */ -public class SparkDumpCommunityProducts implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkDumpCommunityProducts.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpCommunityProducts.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - String communityMapPath = Optional - .ofNullable(parser.get("communityMapPath")) - .orElse(null); - - String dumpType = Optional - .ofNullable(parser.get("dumpType")) - .orElse(null); - - Class inputClazz = (Class) Class.forName(resultClassName); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - resultDump( - spark, inputPath, outputPath, communityMapPath, inputClazz, dumpType); - }); - - } - - public static void resultDump( - SparkSession spark, - String inputPath, - String outputPath, - String communityMapPath, - Class inputClazz, - String dumpType) { - - CommunityMap communityMap = null; - if (!StringUtils.isEmpty(communityMapPath)) - communityMap = Utils.getCommunityMap(spark, communityMapPath); - - CommunityMap finalCommunityMap = communityMap; - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) value -> execMap(value, finalCommunityMap, dumpType), - Encoders.bean(CommunityResult.class)) - .filter((FilterFunction) value -> value != null) - .map( - (MapFunction) r -> new ObjectMapper().writeValueAsString(r), Encoders.STRING()) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .text(outputPath); - - } - - private static O execMap(I value, - CommunityMap communityMap, String dumpType) throws NoAvailableEntityTypeException, CardinalityTooHighException { - - Optional odInfo = Optional.ofNullable(value.getDataInfo()); - if (Boolean.FALSE.equals(odInfo.isPresent())) { - return null; - } - if (Boolean.TRUE.equals(odInfo.get().getDeletedbyinference()) - || Boolean.TRUE.equals(odInfo.get().getInvisible())) { - return null; - } - if (StringUtils.isEmpty(dumpType)) { - Set communities = communityMap.keySet(); - - Optional> inputContext = Optional - .ofNullable(((eu.dnetlib.dhp.schema.oaf.Result) value).getContext()); - if (!inputContext.isPresent()) { - return null; - } - List toDumpFor = inputContext.get().stream().map(c -> { - if (communities.contains(c.getId())) { - return c.getId(); - } - if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) { - return c.getId().substring(0, c.getId().indexOf("::")); - } - return null; - }).filter(Objects::nonNull).collect(Collectors.toList()); - if (toDumpFor.isEmpty()) { - return null; - } - } - return (O) ResultMapper.map(value, communityMap, Constants.DUMPTYPE.COMMUNITY.getType()); - - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java deleted file mode 100644 index 42fd683..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ /dev/null @@ -1,206 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.ENTITY_ID_SEPARATOR; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.getEntityId; - -import java.io.Serializable; -import java.io.StringReader; -import java.util.*; -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.api.java.function.MapGroupsFunction; -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; -import org.dom4j.DocumentException; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.Provenance; -import eu.dnetlib.dhp.oa.model.community.Funder; -import eu.dnetlib.dhp.oa.model.community.Project; -import eu.dnetlib.dhp.oa.model.community.Validated; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Relation; -import scala.Tuple2; - -/** - * Preparation of the Project information to be added to the dumped results. For each result associated to at least one - * Project, a serialization of an instance af ResultProject class is done. ResultProject contains the resultId, and the - * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to - */ -public class SparkPrepareResultProject implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkPrepareResultProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - Boolean substring = Optional - .ofNullable(parser.get("substring")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - prepareResultProjectList(spark, inputPath, outputPath, substring); - }); - } - - private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath, - Boolean substring) { - Dataset relation = Utils - .readPath(spark, inputPath + "/relation", Relation.class) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - r.getRelClass().equalsIgnoreCase(ModelConstants.IS_PRODUCED_BY)); - - Dataset projects = Utils - .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); - - projects - .joinWith(relation, projects.col("id").equalTo(relation.col("target")), "inner") - .groupByKey( - (MapFunction, String>) value -> value - ._2() - .getSource(), - Encoders.STRING()) - .mapGroups( - (MapGroupsFunction, ResultProject>) (s, - it) -> { - Set projectSet = new HashSet<>(); - Tuple2 first = it.next(); - ResultProject rp = new ResultProject(); - if (substring) - rp.setResultId(getEntityId(s, ENTITY_ID_SEPARATOR)); - else - rp.setResultId(s); - eu.dnetlib.dhp.schema.oaf.Project p = first._1(); - projectSet.add(p.getId()); - Project ps = getProject(p, first._2); - - List projList = new ArrayList<>(); - projList.add(ps); - rp.setProjectsList(projList); - it.forEachRemaining(c -> { - eu.dnetlib.dhp.schema.oaf.Project op = c._1(); - if (!projectSet.contains(op.getId())) { - projList - .add(getProject(op, c._2)); - - projectSet.add(op.getId()); - - } - - }); - return rp; - }, Encoders.bean(ResultProject.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op, Relation relation) { - Project p = Project - .newInstance( - getEntityId(op.getId(), ENTITY_ID_SEPARATOR), - op.getCode().getValue(), - Optional - .ofNullable(op.getAcronym()) - .map(Field::getValue) - .orElse(null), - Optional - .ofNullable(op.getTitle()) - .map(Field::getValue) - .orElse(null), - Optional - .ofNullable(op.getFundingtree()) - .map(value -> { - List tmp = value - .stream() - .map(ft -> getFunder(ft.getValue())) - .collect(Collectors.toList()); - if (!tmp.isEmpty()) { - return tmp.get(0); - } else { - return null; - } - }) - .orElse(null)); - - Optional di = Optional.ofNullable(op.getDataInfo()); - Provenance provenance = new Provenance(); - if (di.isPresent()) { - provenance.setProvenance(di.get().getProvenanceaction().getClassname()); - provenance.setTrust(di.get().getTrust()); - p.setProvenance(provenance); - } - if (Boolean.TRUE.equals(relation.getValidated())) { - p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate())); - } - return p; - - } - - private static Funder getFunder(String fundingtree) { - final Funder f = new Funder(); - final Document doc; - try { - final SAXReader reader = new SAXReader(); - reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); - doc = reader.read(new StringReader(fundingtree)); - f.setShortName(((Node) (doc.selectNodes("//funder/shortname").get(0))).getText()); - f.setName(((Node) (doc.selectNodes("//funder/name").get(0))).getText()); - f.setJurisdiction(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); - for (Object o : doc.selectNodes("//funding_level_0")) { - List node = ((Node) o).selectNodes("./name"); - f.setFundingStream((node.get(0)).getText()); - } - - return f; - } catch (DocumentException | SAXException e) { - throw new IllegalArgumentException(e); - } - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java deleted file mode 100644 index b62bf18..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java +++ /dev/null @@ -1,50 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -/** - * Spark job to trigger the split of results associated to research community - reseach initiative/infrasctructure. The - * actual split is performed by the class CommunitySplit - */ -public class SparkSplitForCommunity implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkSplitForCommunity.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSplitForCommunity.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String communityMapPath = parser.get("communityMapPath"); - - CommunitySplit split = new CommunitySplit(); - split.run(isSparkSessionManaged, inputPath, outputPath, communityMapPath); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java deleted file mode 100644 index 996b4e2..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java +++ /dev/null @@ -1,95 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.ForeachFunction; -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.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; -import scala.Tuple2; - -public class SparkUpdateProjectInfo implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkUpdateProjectInfo.class); - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkUpdateProjectInfo.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String preparedInfoPath = parser.get("preparedInfoPath"); - log.info("preparedInfoPath: {}", preparedInfoPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - extend(spark, inputPath, outputPath, preparedInfoPath); - }); - } - - private static void extend( - SparkSession spark, - String inputPath, - String outputPath, - String preparedInfoPath) { - Dataset result = Utils.readPath(spark, inputPath, CommunityResult.class); - Dataset resultProject = Utils.readPath(spark, preparedInfoPath, ResultProject.class); - - result - .joinWith( - resultProject, result.col("id").equalTo(resultProject.col("resultId")), - "left") - .map((MapFunction, CommunityResult>) value -> { - CommunityResult r = value._1(); - Optional.ofNullable(value._2()).ifPresent(rp -> r.setProjects(rp.getProjectsList())); - return r; - }, Encoders.bean(CommunityResult.class)) - .map( - (MapFunction) cr -> new ObjectMapper().writeValueAsString(cr), - Encoders.STRING()) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .text(outputPath); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java deleted file mode 100644 index 57708a7..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java +++ /dev/null @@ -1,26 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; - -public class Constants implements Serializable { - - public static final String IS_HOSTED_BY = "isHostedBy"; - public static final String HOSTS = "hosts"; - - public static final String IS_FUNDED_BY = "isFundedBy"; - public static final String FUNDS = "funds"; - - public static final String FUNDINGS = "fundings"; - - public static final String RESULT_ENTITY = "result"; - public static final String DATASOURCE_ENTITY = "datasource"; - public static final String CONTEXT_ENTITY = "context"; - public static final String ORGANIZATION_ENTITY = "organization"; - public static final String PROJECT_ENTITY = "project"; - - public static final String CONTEXT_ID = "00"; - public static final String CONTEXT_NS_PREFIX = "context_____"; - public static final String UNKNOWN = "UNKNOWN"; - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java deleted file mode 100644 index 982a69a..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java +++ /dev/null @@ -1,84 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; -import java.util.List; - -/** - * Deserialization of the information in the context needed to create Context Entities, and relations between context - * entities and datasources and projects - */ -public class ContextInfo implements Serializable { - private String id; - private String description; - private String type; - private String zenodocommunity; - private String name; - private List projectList; - private List datasourceList; - private List subject; - - public List getSubject() { - return subject; - } - - public void setSubject(List subject) { - this.subject = subject; - } - - public String getName() { - return name; - } - - public void setName(String name) { - this.name = name; - } - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = id; - } - - public String getDescription() { - return description; - } - - public void setDescription(String description) { - this.description = description; - } - - public String getType() { - return type; - } - - public void setType(String type) { - this.type = type; - } - - public String getZenodocommunity() { - return zenodocommunity; - } - - public void setZenodocommunity(String zenodocommunity) { - this.zenodocommunity = zenodocommunity; - } - - public List getProjectList() { - return projectList; - } - - public void setProjectList(List projectList) { - this.projectList = projectList; - } - - public List getDatasourceList() { - return datasourceList; - } - - public void setDatasourceList(List datasourceList) { - this.datasourceList = datasourceList; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java deleted file mode 100644 index 20bce5d..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java +++ /dev/null @@ -1,106 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; -import java.nio.charset.StandardCharsets; -import java.util.function.Consumer; -import java.util.function.Function; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.io.compress.CompressionCodec; -import org.apache.hadoop.io.compress.CompressionCodecFactory; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.UtilCommunityAPI; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.graph.ResearchInitiative; - -/** - * Writes on HDFS Context entities. It queries the Information System at the lookup url provided as parameter and - * collects the general information for contexes of type community or ri. The general information is the id of the - * context, its label, the subjects associated to the context, its zenodo community, description and type. This - * information is used to create a new Context Entity - */ -public class CreateContextEntities implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(CreateContextEntities.class); - private final transient Configuration conf; - private final transient BufferedWriter writer; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - CreateContextEntities.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - final String hdfsPath = parser.get("hdfsPath"); - log.info("hdfsPath: {}", hdfsPath); - - final String hdfsNameNode = parser.get("nameNode"); - log.info("nameNode: {}", hdfsNameNode); - - final CreateContextEntities cce = new CreateContextEntities(hdfsPath, hdfsNameNode); - - log.info("Processing contexts..."); - cce.execute(Process::getEntity); - - cce.close(); - - } - - private void close() throws IOException { - writer.close(); - } - - public CreateContextEntities(String hdfsPath, String hdfsNameNode) throws IOException { - this.conf = new Configuration(); - this.conf.set("fs.defaultFS", hdfsNameNode); - FileSystem fileSystem = FileSystem.get(this.conf); - Path hdfsWritePath = new Path(hdfsPath); - FSDataOutputStream fsDataOutputStream = null; - if (fileSystem.exists(hdfsWritePath)) { - fsDataOutputStream = fileSystem.append(hdfsWritePath); - } else { - fsDataOutputStream = fileSystem.create(hdfsWritePath); - } - CompressionCodecFactory factory = new CompressionCodecFactory(conf); - CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); - - this.writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), - StandardCharsets.UTF_8)); - - } - - public void execute(final Function producer) - throws IOException { - - UtilCommunityAPI queryInformationSystem = new UtilCommunityAPI(); - - final Consumer consumer = ci -> writeEntity(producer.apply(ci)); - - queryInformationSystem.getContextInformation().forEach(ci -> consumer.accept(ci)); - } - - protected void writeEntity(final R r) { - try { - writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); - writer.newLine(); - } catch (final IOException e) { - throw new IllegalArgumentException(e); - } - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java deleted file mode 100644 index 86106fb..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java +++ /dev/null @@ -1,113 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.*; -import java.nio.charset.StandardCharsets; -import java.util.ArrayList; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.function.Consumer; -import java.util.function.Function; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.UtilCommunityAPI; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; -import eu.dnetlib.dhp.oa.graph.dump.subset.MasterDuplicate; -import eu.dnetlib.dhp.oa.model.graph.*; - -/** - * Writes the set of new Relation between the context and datasources. At the moment the relation between the context - * and the project is not created because of a low coverage in the profiles of openaire ids related to projects - */ -public class CreateContextRelation implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CreateContextRelation.class); - private final transient Configuration conf; - private final transient BufferedWriter writer; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - Objects - .requireNonNull( - CreateContextRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json"))); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String hdfsPath = parser.get("hdfsPath"); - log.info("hdfsPath: {}", hdfsPath); - - final String hdfsNameNode = parser.get("nameNode"); - log.info("hdfsNameNode: {}", hdfsNameNode); - - final CreateContextRelation cce = new CreateContextRelation(hdfsPath, hdfsNameNode); - - log.info("Creating relation for datasources and projects..."); - cce - .execute( - Process::getRelation); - - cce.close(); - - } - - private void close() throws IOException { - writer.close(); - } - - public CreateContextRelation(String hdfsPath, String hdfsNameNode) - throws IOException { - this.conf = new Configuration(); - this.conf.set("fs.defaultFS", hdfsNameNode); - - FileSystem fileSystem = FileSystem.get(this.conf); - Path hdfsWritePath = new Path(hdfsPath); - FSDataOutputStream fsDataOutputStream = null; - if (fileSystem.exists(hdfsWritePath)) { - fsDataOutputStream = fileSystem.append(hdfsWritePath); - } else { - fsDataOutputStream = fileSystem.create(hdfsWritePath); - } - - this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); - - } - - public void execute(final Function> producer) throws IOException { - - final Consumer consumer = ci -> producer.apply(ci).forEach(this::writeEntity); - - UtilCommunityAPI queryCommunityAPI = new UtilCommunityAPI(); - queryCommunityAPI.getContextRelation().forEach(ci -> consumer.accept(ci)); - } - - protected void writeEntity(final Relation r) { - try { - writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); - writer.newLine(); - } catch (final Exception e) { - throw new MyRuntimeException(e); - } - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java deleted file mode 100644 index 794e769..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java +++ /dev/null @@ -1,203 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.ENTITY_ID_SEPARATOR; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.getEntityId; - -import java.io.Serializable; -import java.util.*; - -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FlatMapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; - -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.model.Provenance; -import eu.dnetlib.dhp.oa.model.graph.RelType; -import eu.dnetlib.dhp.oa.model.graph.Relation; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Result; - -/** - * Creates new Relations (as in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation) from the information in the Entity. The - * new Relations are created for the datasource in the collectedfrom and hostedby elements and for the context related - * to communities and research initiative/infrastructures. For collectedfrom elements it creates: datasource -> provides - * -> result and result -> isProvidedBy -> datasource For hostedby elements it creates: datasource -> hosts -> result - * and result -> isHostedBy -> datasource For context elements it creates: context <-> isRelatedTo <-> result. Note for - * context: it gets the first provenance in the dataInfo. If more than one is present the others are not dumped - */ -public class Extractor implements Serializable { - - public void run(Boolean isSparkSessionManaged, - String inputPath, - String outputPath, - Class inputClazz, - String communityMapPath) { - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - extractRelationResult( - spark, inputPath, outputPath, inputClazz, Utils.getCommunityMap(spark, communityMapPath)); - }); - } - - private void extractRelationResult(SparkSession spark, - String inputPath, - String outputPath, - Class inputClazz, - CommunityMap communityMap) { - - Set hashCodes = new HashSet<>(); - - Utils - .readPath(spark, inputPath, inputClazz) - .flatMap((FlatMapFunction) value -> { - List relationList = new ArrayList<>(); - extractRelationsFromInstance(hashCodes, value, relationList); - Set communities = communityMap.keySet(); - Optional - .ofNullable(value.getContext()) - .ifPresent(contexts -> contexts.forEach(context -> { - String id = context.getId(); - if (id.contains(":")) { - id = id.substring(0, id.indexOf(":")); - } - if (communities.contains(id)) { - String contextId = Utils.getContextId(id); - Provenance provenance = Optional - .ofNullable(context.getDataInfo()) - .map( - dinfo -> Optional - .ofNullable(dinfo.get(0).getProvenanceaction()) - .map( - paction -> Provenance - .newInstance( - paction.getClassid(), - dinfo.get(0).getTrust())) - .orElse(null)) - .orElse(null); - Relation r = getRelation( - getEntityId(value.getId(), ENTITY_ID_SEPARATOR), contextId, - Constants.RESULT_ENTITY, - Constants.CONTEXT_ENTITY, - ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP, provenance); - if (!hashCodes.contains(r.hashCode())) { - relationList - .add(r); - hashCodes.add(r.hashCode()); - } - r = getRelation( - contextId, getEntityId(value.getId(), ENTITY_ID_SEPARATOR), - Constants.CONTEXT_ENTITY, - Constants.RESULT_ENTITY, - ModelConstants.IS_RELATED_TO, - ModelConstants.RELATIONSHIP, provenance); - if (!hashCodes.contains(r.hashCode())) { - relationList - .add( - r); - hashCodes.add(r.hashCode()); - } - - } - - })); - - return relationList.iterator(); - }, Encoders.bean(Relation.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .json(outputPath); - - } - - private void extractRelationsFromInstance(Set hashCodes, R value, - List relationList) { - Optional - .ofNullable(value.getInstance()) - .ifPresent(inst -> inst.forEach(instance -> { - Optional - .ofNullable(instance.getCollectedfrom()) - .ifPresent( - cf -> getRelatioPair( - value, relationList, cf, - ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); - Optional - .ofNullable(instance.getHostedby()) - .ifPresent( - hb -> getRelatioPair( - value, relationList, hb, - Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); - })); - } - - private static void getRelatioPair(R value, List relationList, KeyValue cf, - String resultDatasource, String datasourceResult, - Set hashCodes) { - Provenance provenance = Optional - .ofNullable(cf.getDataInfo()) - .map( - dinfo -> Optional - .ofNullable(dinfo.getProvenanceaction()) - .map( - paction -> Provenance - .newInstance( - paction.getClassname(), - dinfo.getTrust())) - .orElse( - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.HARVESTED, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))) - .orElse( - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.HARVESTED, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST)); - Relation r = getRelation( - getEntityId(value.getId(), ENTITY_ID_SEPARATOR), - getEntityId(cf.getKey(), ENTITY_ID_SEPARATOR), Constants.RESULT_ENTITY, Constants.DATASOURCE_ENTITY, - resultDatasource, ModelConstants.PROVISION, - provenance); - if (!hashCodes.contains(r.hashCode())) { - relationList - .add(r); - hashCodes.add(r.hashCode()); - } - - r = getRelation( - getEntityId(cf.getKey(), ENTITY_ID_SEPARATOR), getEntityId(value.getId(), ENTITY_ID_SEPARATOR), - Constants.DATASOURCE_ENTITY, Constants.RESULT_ENTITY, - datasourceResult, ModelConstants.PROVISION, - provenance); - - if (!hashCodes.contains(r.hashCode())) { - relationList - .add(r); - hashCodes.add(r.hashCode()); - } - - } - - private static Relation getRelation(String source, String target, String sourceType, String targetType, - String relName, String relType, Provenance provenance) { - Relation r = new Relation(); - r.setSource(source); - r.setSourceType(sourceType); - r.setTarget(target); - r.setTargetType(targetType); - r.setReltype(RelType.newInstance(relName, relType)); - r.setProvenance(provenance); - return r; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java deleted file mode 100644 index 30088e8..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java +++ /dev/null @@ -1,25 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; - -public class MergedRels implements Serializable { - private String organizationId; - private String representativeId; - - public String getOrganizationId() { - return organizationId; - } - - public void setOrganizationId(String organizationId) { - this.organizationId = organizationId; - } - - public String getRepresentativeId() { - return representativeId; - } - - public void setRepresentativeId(String representativeId) { - this.representativeId = representativeId; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/OrganizationMap.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/OrganizationMap.java deleted file mode 100644 index bf6cdbd..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/OrganizationMap.java +++ /dev/null @@ -1,21 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; - -public class OrganizationMap extends HashMap> { - - public OrganizationMap() { - super(); - } - - public List get(String key) { - - if (super.get(key) == null) { - return new ArrayList<>(); - } - return super.get(key); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java deleted file mode 100644 index 8fd5b3e..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java +++ /dev/null @@ -1,99 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; -import java.util.ArrayList; -import java.util.List; - -import org.apache.commons.lang3.StringUtils; - -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; -import eu.dnetlib.dhp.oa.model.Provenance; -import eu.dnetlib.dhp.oa.model.graph.*; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.common.ModelSupport; - -/** - * It process the ContextInfo information to produce a new Context Entity or a set of Relations between the generic - * context entity and datasource/projects related to the context. - */ -public class Process implements Serializable { - - @SuppressWarnings("unchecked") - public static R getEntity(ContextInfo ci) { - try { - ResearchInitiative ri; - if (ci.getType().equals("community")) { - ri = new ResearchCommunity(); - ((ResearchCommunity) ri).setSubject(ci.getSubject()); - ri.setType(Constants.RESEARCH_COMMUNITY); - } else { - ri = new ResearchInitiative(); - ri.setType(Constants.RESEARCH_INFRASTRUCTURE); - } - ri.setId(Utils.getContextId(ci.getId())); - ri.setAcronym(ci.getId()); - - ri.setDescription(ci.getDescription()); - ri.setName(ci.getName()); - if (StringUtils.isNotEmpty(ci.getZenodocommunity())) { - ri.setZenodo_community(Constants.ZENODO_COMMUNITY_PREFIX + ci.getZenodocommunity()); - } - return (R) ri; - - } catch (final Exception e) { - throw new MyRuntimeException(e); - } - } - - public static List getRelation(ContextInfo ci) { - try { - - List relationList = new ArrayList<>(); - ci - .getDatasourceList() - .forEach(ds -> relationList.addAll(addRelations(ci, ds, ModelSupport.idPrefixEntity.get("10")))); - - ci - .getProjectList() - .forEach(p -> relationList.addAll(addRelations(ci, p, ModelSupport.idPrefixEntity.get("40")))); - - return relationList; - - } catch (final Exception e) { - throw new MyRuntimeException(e); - } - } - - private static List addRelations(ContextInfo ci, String ds, String nodeType) { - List relationList = new ArrayList<>(); - String contextId = Utils.getContextId(ci.getId()); - relationList - .add( - Relation - .newInstance( - contextId, eu.dnetlib.dhp.oa.model.graph.Constants.CONTEXT_ENTITY, - ds, nodeType, - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - Constants.USER_CLAIM, - Constants.DEFAULT_TRUST))); - - relationList - .add( - Relation - .newInstance( - ds, nodeType, - contextId, eu.dnetlib.dhp.oa.model.graph.Constants.CONTEXT_ENTITY, - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - Constants.USER_CLAIM, - Constants.DEFAULT_TRUST))); - return relationList; - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java deleted file mode 100644 index ab37b71..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java +++ /dev/null @@ -1,252 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -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.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.graph.GraphResult; -import eu.dnetlib.dhp.oa.model.graph.Relation; -import it.unimi.dsi.fastutil.objects.Object2BooleanMap; -import scala.Tuple2; - -/** - * Reads all the entities of the same type (Relation / Results) and saves them in the same folder - */ -public class SparkCollectAndSave implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkCollectAndSave.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkCollectAndSave.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final Boolean aggregateResult = Optional - .ofNullable(parser.get("resultAggregation")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath + "/result"); - run(spark, inputPath, outputPath, aggregateResult); - - }); - - } - - private static void run(SparkSession spark, String inputPath, String outputPath, boolean aggregate) { - if (aggregate) { - Utils - .readPath(spark, inputPath + "/result/publication", GraphResult.class) - .union(Utils.readPath(spark, inputPath + "/result/dataset", GraphResult.class)) - .union(Utils.readPath(spark, inputPath + "/result/otherresearchproduct", GraphResult.class)) - .union(Utils.readPath(spark, inputPath + "/result/software", GraphResult.class)) - .map( - (MapFunction) r -> new ObjectMapper().writeValueAsString(r), Encoders.STRING()) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .text(outputPath + "/result"); - } else { - write( - Utils - .readPath(spark, inputPath + "/result/publication", GraphResult.class), - outputPath + "/publication"); - write( - Utils - .readPath(spark, inputPath + "/result/dataset", GraphResult.class), - outputPath + "/dataset"); - write( - Utils - .readPath(spark, inputPath + "/result/otherresearchproduct", GraphResult.class), - outputPath + "/otherresearchproduct"); - write( - Utils - .readPath(spark, inputPath + "/result/software", GraphResult.class), - outputPath + "/software"); - - } - - // Dataset dumpedIds = Utils.getEntitiesId(spark, outputPath); - -// Dataset relations = Utils -// .readPath(spark, inputPath + "/relation/publication", Relation.class) -// .union(Utils.readPath(spark, inputPath + "/relation/dataset", Relation.class)) -// .union(Utils.readPath(spark, inputPath + "/relation/orp", Relation.class)) -// .union(Utils.readPath(spark, inputPath + "/relation/software", Relation.class)) -// .union(Utils.readPath(spark, inputPath + "/relation/contextOrg", Relation.class)) -// .union(Utils.readPath(spark, inputPath + "/relation/context", Relation.class)) -// .union(Utils.readPath(spark, inputPath + "/relation/relation", Relation.class)); - -// Utils.getValidRelations(relations, Utils.getEntitiesId(spark, outputPath)) - Utils - .readPath(spark, inputPath + "/relation/publication", Relation.class) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/relation"); - Utils - .readPath(spark, inputPath + "/relation/dataset", Relation.class) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(outputPath + "/relation"); - Utils - .readPath(spark, inputPath + "/relation/orp", Relation.class) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(outputPath + "/relation"); - - Utils - .readPath(spark, inputPath + "/relation/software", Relation.class) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(outputPath + "/relation"); - Utils - .readPath(spark, inputPath + "/relation/contextOrg", Relation.class) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(outputPath + "/relation"); - Utils - .readPath(spark, inputPath + "/relation/context", Relation.class) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(outputPath + "/relation"); - Utils - .readPath(spark, inputPath + "/relation/relation", Relation.class) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(outputPath + "/relation"); -// relSource( -// inputPath, dumpedIds, Utils -// .readPath(spark, inputPath + "/relation/publication", Relation.class), -// inputPath + "/relSource/publication"); -// relSource( -// inputPath, dumpedIds, Utils -// .readPath(spark, inputPath + "/relation/dataset", Relation.class), -// inputPath + "/relSource/dataset"); -// relSource( -// inputPath, dumpedIds, Utils -// .readPath(spark, inputPath + "/relation/orp", Relation.class), -// inputPath + "/relSource/orp"); -// relSource( -// inputPath, dumpedIds, Utils -// .readPath(spark, inputPath + "/relation/software", Relation.class), -// inputPath + "/relSource/software"); -// relSource( -// inputPath, dumpedIds, Utils -// .readPath(spark, inputPath + "/relation/contextOrg", Relation.class), -// inputPath + "/relSource/contextOrg"); -// relSource( -// inputPath, dumpedIds, Utils -// .readPath(spark, inputPath + "/relation/context", Relation.class), -// inputPath + "/relSource/context"); -// relSource( -// inputPath, dumpedIds, Utils -// .readPath(spark, inputPath + "/relation/relation", Relation.class), -// inputPath + "/relSource/relation"); - -// relTarget( -// outputPath, dumpedIds, Utils.readPath(spark, inputPath + "/relSource/publication", Relation.class), -// SaveMode.Overwrite); -// relTarget( -// outputPath, dumpedIds, Utils.readPath(spark, inputPath + "/relSource/dataset", Relation.class), -// SaveMode.Append); -// relTarget( -// outputPath, dumpedIds, Utils.readPath(spark, inputPath + "/relSource/orp", Relation.class), -// SaveMode.Append); -// relTarget( -// outputPath, dumpedIds, Utils.readPath(spark, inputPath + "/relSource/software", Relation.class), -// SaveMode.Append); -// relTarget( -// outputPath, dumpedIds, Utils.readPath(spark, inputPath + "/relSource/contextOrg", Relation.class), -// SaveMode.Append); -// relTarget( -// outputPath, dumpedIds, Utils.readPath(spark, inputPath + "/relSource/context", Relation.class), -// SaveMode.Append); -// relTarget( -// outputPath, dumpedIds, Utils.readPath(spark, inputPath + "/relSource/relation", Relation.class), -// SaveMode.Append); - - } - - private static void relTarget(String outputPath, Dataset dumpedIds, Dataset relJoinSource, - SaveMode saveMode) { - relJoinSource - .joinWith(dumpedIds, relJoinSource.col("target").equalTo(dumpedIds.col("value"))) - .map( - (MapFunction, Relation>) t2 -> t2._1(), - Encoders.bean(Relation.class)) - .write() - .mode(saveMode) - .option("compression", "gzip") - .json(outputPath + "/relation"); - } - - private static void relSource(String inputPath, Dataset dumpedIds, Dataset relations, - String outputPath) { - - relations - .joinWith(dumpedIds, relations.col("source").equalTo(dumpedIds.col("value"))) - .map( - (MapFunction, Relation>) t2 -> t2._1(), - Encoders.bean(Relation.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static void write(Dataset dataSet, String outputPath) { - dataSet - .map((MapFunction) r -> new ObjectMapper().writeValueAsString(r), Encoders.STRING()) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .text(outputPath); - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java deleted file mode 100644 index 218a123..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java +++ /dev/null @@ -1,639 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.ENTITY_ID_SEPARATOR; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.getEntityId; - -import java.io.Serializable; -import java.io.StringReader; -import java.util.*; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang.StringUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.ForeachFunction; -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; -import org.dom4j.DocumentException; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; -import com.jayway.jsonpath.DocumentContext; -import com.jayway.jsonpath.JsonPath; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.CardinalityTooHighException; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; -import eu.dnetlib.dhp.oa.model.Container; -import eu.dnetlib.dhp.oa.model.Result; -import eu.dnetlib.dhp.oa.model.graph.*; -import eu.dnetlib.dhp.oa.model.graph.Datasource; -import eu.dnetlib.dhp.oa.model.graph.Organization; -import eu.dnetlib.dhp.oa.model.graph.Project; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.*; - -/** - * Spark Job that fires the dump for the entites - */ -public class SparkDumpEntitiesJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkDumpEntitiesJob.class); - public static final String COMPRESSION = "compression"; - public static final String GZIP = "gzip"; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpEntitiesJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - Optional communityMap = Optional.ofNullable(parser.get("communityMapPath")); - String communityMapPath = null; - if (communityMap.isPresent()) - communityMapPath = communityMap.get(); - - Class inputClazz = (Class) Class.forName(resultClassName); - - run(isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz); - - } - - private static void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath, - Class inputClazz) { - SparkConf conf = new SparkConf(); - - switch (ModelSupport.idPrefixMap.get(inputClazz)) { - case "50": - String finalCommunityMapPath = communityMapPath; - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - resultDump( - spark, inputPath, outputPath, finalCommunityMapPath, inputClazz); - }); - - break; - case "40": - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - projectMap(spark, inputPath, outputPath, inputClazz); - - }); - break; - case "20": - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - organizationMap(spark, inputPath, outputPath, inputClazz); - - }); - break; - case "10": - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - datasourceMap(spark, inputPath, outputPath, inputClazz); - - }); - break; - } - } - - public static void resultDump( - SparkSession spark, - String inputPath, - String outputPath, - String communityMapPath, - Class inputClazz) { - - CommunityMap communityMap = null; - if (!StringUtils.isEmpty(communityMapPath)) - communityMap = Utils.getCommunityMap(spark, communityMapPath); - - CommunityMap finalCommunityMap = communityMap; - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) value -> execMap(value, finalCommunityMap), - Encoders.bean(GraphResult.class)) - .filter((FilterFunction) value -> value != null) - .map((MapFunction) r -> new ObjectMapper().writeValueAsString(r), Encoders.STRING()) - .write() - .mode(SaveMode.Overwrite) - .option(COMPRESSION, GZIP) - .text(outputPath); - - } - - private static O execMap(I value, - CommunityMap communityMap) throws NoAvailableEntityTypeException, CardinalityTooHighException { - - Optional odInfo = Optional.ofNullable(value.getDataInfo()); - if (Boolean.FALSE.equals(odInfo.isPresent())) { - return null; - } - if (Boolean.TRUE.equals(odInfo.get().getDeletedbyinference()) - || Boolean.TRUE.equals(odInfo.get().getInvisible())) { - return null; - } - - return (O) ResultMapper.map(value, communityMap, Constants.DUMPTYPE.COMPLETE.getType()); - - } - - private static void datasourceMap(SparkSession spark, String inputPath, String outputPath, - Class inputClazz) { - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) d -> mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) d), - Encoders.bean(Datasource.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option(COMPRESSION, GZIP) - .json(outputPath); - } - - private static void projectMap(SparkSession spark, String inputPath, String outputPath, - Class inputClazz) { - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) p -> mapProject((eu.dnetlib.dhp.schema.oaf.Project) p), - Encoders.bean(Project.class)) - .filter((FilterFunction) p -> p != null) - .write() - .mode(SaveMode.Overwrite) - .option(COMPRESSION, GZIP) - .json(outputPath); - } - - private static Datasource mapDatasource(eu.dnetlib.dhp.schema.oaf.Datasource d) { - if (Boolean.TRUE.equals(d.getDataInfo().getDeletedbyinference())) - return null; - Datasource datasource = new Datasource(); - - datasource.setId(getEntityId(d.getId(), ENTITY_ID_SEPARATOR)); - - Optional - .ofNullable(d.getOriginalId()) - .ifPresent( - oId -> datasource.setOriginalId(oId.stream().filter(Objects::nonNull).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getPid()) - .ifPresent( - pids -> datasource - .setPid( - pids - .stream() - .map(p -> DatasourcePid.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - Optional - .ofNullable(d.getDatasourcetype()) - .ifPresent( - dsType -> datasource - .setDatasourcetype(DatasourceSchemeValue.newInstance(dsType.getClassid(), dsType.getClassname()))); - - Optional - .ofNullable(d.getOpenairecompatibility()) - .ifPresent(v -> datasource.setOpenairecompatibility(v.getClassname())); - - Optional - .ofNullable(d.getOfficialname()) - .ifPresent(oname -> datasource.setOfficialname(oname.getValue())); - - Optional - .ofNullable(d.getEnglishname()) - .ifPresent(ename -> datasource.setEnglishname(ename.getValue())); - - Optional - .ofNullable(d.getWebsiteurl()) - .ifPresent(wsite -> datasource.setWebsiteurl(wsite.getValue())); - - Optional - .ofNullable(d.getLogourl()) - .ifPresent(lurl -> datasource.setLogourl(lurl.getValue())); - - Optional - .ofNullable(d.getDateofvalidation()) - .ifPresent(dval -> datasource.setDateofvalidation(dval.getValue())); - - Optional - .ofNullable(d.getDescription()) - .ifPresent(dex -> datasource.setDescription(dex.getValue())); - - Optional - .ofNullable(d.getSubjects()) - .ifPresent( - sbjs -> datasource.setSubjects(sbjs.stream().map(sbj -> sbj.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getOdpolicies()) - .ifPresent(odp -> datasource.setPolicies(Arrays.asList(odp.getValue()))); - - Optional - .ofNullable(d.getOdlanguages()) - .ifPresent( - langs -> datasource - .setLanguages(langs.stream().map(lang -> lang.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getOdcontenttypes()) - .ifPresent( - ctypes -> datasource - .setContenttypes(ctypes.stream().map(ctype -> ctype.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getReleasestartdate()) - .ifPresent(rd -> datasource.setReleasestartdate(rd.getValue())); - - Optional - .ofNullable(d.getReleaseenddate()) - .ifPresent(ed -> datasource.setReleaseenddate(ed.getValue())); - - Optional - .ofNullable(d.getMissionstatementurl()) - .ifPresent(ms -> datasource.setMissionstatementurl(ms.getValue())); - - Optional - .ofNullable(d.getDatabaseaccesstype()) - .ifPresent(ar -> datasource.setAccessrights(ar.getValue())); - - Optional - .ofNullable(d.getDatauploadtype()) - .ifPresent(dut -> datasource.setUploadrights(dut.getValue())); - - Optional - .ofNullable(d.getDatabaseaccessrestriction()) - .ifPresent(dar -> datasource.setDatabaseaccessrestriction(dar.getValue())); - - Optional - .ofNullable(d.getDatauploadrestriction()) - .ifPresent(dur -> datasource.setDatauploadrestriction(dur.getValue())); - - Optional - .ofNullable(d.getVersioning()) - .ifPresent(v -> datasource.setVersioning(v.getValue())); - - Optional - .ofNullable(d.getCitationguidelineurl()) - .ifPresent(cu -> datasource.setCitationguidelineurl(cu.getValue())); - - Optional - .ofNullable(d.getPidsystems()) - .ifPresent(ps -> datasource.setPidsystems(ps.getValue())); - - Optional - .ofNullable(d.getCertificates()) - .ifPresent(c -> datasource.setCertificates(c.getValue())); - - Optional - .ofNullable(d.getPolicies()) - .ifPresent(ps -> datasource.setPolicies(ps.stream().map(p -> p.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getJournal()) - .ifPresent(j -> datasource.setJournal(getContainer(j))); - -// Optional -// .ofNullable(d.getMeasures()) -// .ifPresent(m -> datasource.setIndicators(Utils.getIndicator(d.getMeasures()))); - - return datasource; - - } - - private static Container getContainer(Journal j) { - Container c = new Container(); - - Optional - .ofNullable(j.getName()) - .ifPresent(n -> c.setName(n)); - - Optional - .ofNullable(j.getIssnPrinted()) - .ifPresent(issnp -> c.setIssnPrinted(issnp)); - - Optional - .ofNullable(j.getIssnOnline()) - .ifPresent(issno -> c.setIssnOnline(issno)); - - Optional - .ofNullable(j.getIssnLinking()) - .ifPresent(isnl -> c.setIssnLinking(isnl)); - - Optional - .ofNullable(j.getEp()) - .ifPresent(ep -> c.setEp(ep)); - - Optional - .ofNullable(j.getIss()) - .ifPresent(iss -> c.setIss(iss)); - - Optional - .ofNullable(j.getSp()) - .ifPresent(sp -> c.setSp(sp)); - - Optional - .ofNullable(j.getVol()) - .ifPresent(vol -> c.setVol(vol)); - - Optional - .ofNullable(j.getEdition()) - .ifPresent(edition -> c.setEdition(edition)); - - Optional - .ofNullable(j.getConferencedate()) - .ifPresent(cdate -> c.setConferencedate(cdate)); - - Optional - .ofNullable(j.getConferenceplace()) - .ifPresent(cplace -> c.setConferenceplace(cplace)); - - return c; - } - - private static Project mapProject(eu.dnetlib.dhp.schema.oaf.Project p) throws DocumentException { - if (Boolean.TRUE.equals(p.getDataInfo().getDeletedbyinference())) - return null; - - Project project = new Project(); - - Optional - .ofNullable(p.getId()) - .ifPresent(id -> project.setId(getEntityId(id, ENTITY_ID_SEPARATOR))); - - Optional - .ofNullable(p.getWebsiteurl()) - .ifPresent(w -> project.setWebsiteurl(w.getValue())); - - Optional - .ofNullable(p.getCode()) - .ifPresent(code -> project.setCode(code.getValue())); - - Optional - .ofNullable(p.getAcronym()) - .ifPresent(acronynim -> project.setAcronym(acronynim.getValue())); - - Optional - .ofNullable(p.getTitle()) - .ifPresent(title -> project.setTitle(title.getValue())); - - Optional - .ofNullable(p.getStartdate()) - .ifPresent(sdate -> project.setStartdate(sdate.getValue())); - - Optional - .ofNullable(p.getEnddate()) - .ifPresent(edate -> project.setEnddate(edate.getValue())); - - Optional - .ofNullable(p.getCallidentifier()) - .ifPresent(cide -> project.setCallidentifier(cide.getValue())); - - Optional - .ofNullable(p.getKeywords()) - .ifPresent(key -> project.setKeywords(key.getValue())); - - Optional> omandate = Optional.ofNullable(p.getOamandatepublications()); - Optional> oecsc39 = Optional.ofNullable(p.getEcsc39()); - boolean mandate = false; - if (omandate.isPresent()) { - if (omandate.get().getValue().equals("true")) { - mandate = true; - } - } - if (oecsc39.isPresent()) { - if (oecsc39.get().getValue().equals("true")) { - mandate = true; - } - } - - project.setOpenaccessmandateforpublications(mandate); - project.setOpenaccessmandatefordataset(false); - - Optional - .ofNullable(p.getEcarticle29_3()) - .ifPresent(oamandate -> project.setOpenaccessmandatefordataset(oamandate.getValue().equals("true"))); - - project - .setSubject( - Optional - .ofNullable(p.getSubjects()) - .map(subjs -> subjs.stream().map(s -> s.getValue()).collect(Collectors.toList())) - .orElse(new ArrayList<>())); - - Optional - .ofNullable(p.getSummary()) - .ifPresent(summary -> project.setSummary(summary.getValue())); - - Optional ofundedamount = Optional.ofNullable(p.getFundedamount()); - Optional> ocurrency = Optional.ofNullable(p.getCurrency()); - Optional ototalcost = Optional.ofNullable(p.getTotalcost()); - - if (ocurrency.isPresent()) { - if (ofundedamount.isPresent()) { - if (ototalcost.isPresent()) { - project - .setGranted( - Granted.newInstance(ocurrency.get().getValue(), ototalcost.get(), ofundedamount.get())); - } else { - project.setGranted(Granted.newInstance(ocurrency.get().getValue(), ofundedamount.get())); - } - } - } - - project - .setH2020programme( - Optional - .ofNullable(p.getH2020classification()) - .map( - classification -> classification - .stream() - .map( - c -> Programme - .newInstance( - c.getH2020Programme().getCode(), c.getH2020Programme().getDescription())) - .collect(Collectors.toList())) - .orElse(new ArrayList<>())); - - Optional>> ofundTree = Optional - .ofNullable(p.getFundingtree()); - List funList = new ArrayList<>(); - if (ofundTree.isPresent()) { - for (Field fundingtree : ofundTree.get()) { - funList.add(getFunder(fundingtree.getValue())); - } - } - project.setFunding(funList); - -// if (Optional.ofNullable(p.getMeasures()).isPresent()) { -// project.setIndicators(Utils.getIndicator(p.getMeasures())); -// } - return project; - } - - public static Funder getFunder(String fundingtree) throws DocumentException { - Funder f = new Funder(); - final Document doc; - - doc = new SAXReader().read(new StringReader(fundingtree)); - f.setShortName(((org.dom4j.Node) (doc.selectNodes("//funder/shortname").get(0))).getText()); - f.setName(((org.dom4j.Node) (doc.selectNodes("//funder/name").get(0))).getText()); - f.setJurisdiction(((org.dom4j.Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); - - String id = ""; - - StringBuilder bld = new StringBuilder(); - - int level = 0; - List nodes = doc.selectNodes("//funding_level_" + level); - while (!nodes.isEmpty()) { - for (org.dom4j.Node n : nodes) { - - List node = n.selectNodes("./id"); - id = ((org.dom4j.Node) node.get(0)).getText(); - id = id.substring(id.indexOf("::") + 2); - - node = n.selectNodes("./description"); - bld.append(((Node) node.get(0)).getText() + " - "); - - } - level += 1; - nodes = doc.selectNodes("//funding_level_" + level); - } - String description = bld.toString(); - if (!id.equals("")) { - Fundings fundings = new Fundings(); - fundings.setId(id); - fundings.setDescription(description.substring(0, description.length() - 3).trim()); - f.setFunding_stream(fundings); - } - - return f; - - } - - private static void organizationMap(SparkSession spark, String inputPath, String outputPath, - Class inputClazz) { - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), - Encoders.bean(Organization.class)) - .filter((FilterFunction) o -> o != null) - .write() - .mode(SaveMode.Overwrite) - .option(COMPRESSION, GZIP) - .json(outputPath); - } - - private static eu.dnetlib.dhp.oa.model.graph.Organization mapOrganization( - eu.dnetlib.dhp.schema.oaf.Organization org) { - if (Boolean.TRUE.equals(org.getDataInfo().getDeletedbyinference())) - return null; - if (!Optional.ofNullable(org.getLegalname()).isPresent() - && !Optional.ofNullable(org.getLegalshortname()).isPresent()) - return null; - - Organization organization = new Organization(); - - Optional - .ofNullable(org.getLegalshortname()) - .ifPresent(value -> organization.setLegalshortname(value.getValue())); - - Optional - .ofNullable(org.getLegalname()) - .ifPresent(value -> organization.setLegalname(value.getValue())); - - Optional - .ofNullable(org.getWebsiteurl()) - .ifPresent(value -> organization.setWebsiteurl(value.getValue())); - - Optional - .ofNullable(org.getAlternativeNames()) - .ifPresent( - value -> organization - .setAlternativenames( - value - .stream() - .map(v -> v.getValue()) - .collect(Collectors.toList()))); - - Optional - .ofNullable(org.getCountry()) - .ifPresent( - value -> { - if (!value.getClassid().equals(eu.dnetlib.dhp.oa.graph.dump.complete.Constants.UNKNOWN)) { - organization - .setCountry( - eu.dnetlib.dhp.oa.model.Country.newInstance(value.getClassid(), value.getClassname())); - } - - }); - - Optional - .ofNullable(org.getId()) - .ifPresent(value -> organization.setId(getEntityId(value, ENTITY_ID_SEPARATOR))); - - Optional - .ofNullable(org.getPid()) - .ifPresent( - value -> organization - .setPid( - value - .stream() - .map(p -> OrganizationPid.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - return organization; - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java deleted file mode 100644 index 0abf994..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java +++ /dev/null @@ -1,132 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.ENTITY_ID_SEPARATOR; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.getEntityId; - -import java.io.Serializable; -import java.util.Collections; -import java.util.HashSet; -import java.util.Optional; -import java.util.Set; - -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; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.Provenance; -import eu.dnetlib.dhp.oa.model.graph.RelType; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Relation; - -/** - * Dumps eu.dnetlib.dhp.schema.oaf.Relation in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation - */ -public class SparkDumpRelationJob implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkDumpRelationJob.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpRelationJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - Optional rs = Optional.ofNullable(parser.get("removeSet")); - final Set removeSet = new HashSet<>(); - if (rs.isPresent()) { - Collections.addAll(removeSet, rs.get().split(";")); - } - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - dumpRelation(spark, inputPath, outputPath, removeSet); - - }); - - } - - private static void dumpRelation(SparkSession spark, String inputPath, String outputPath, Set removeSet) { - Dataset relations = Utils.readPath(spark, inputPath, Relation.class); - relations - .filter( - (FilterFunction) r -> !removeSet.contains(r.getRelClass()) - && !r.getSubRelType().equalsIgnoreCase("resultService")) - .map((MapFunction) relation -> { - eu.dnetlib.dhp.oa.model.graph.Relation relNew = new eu.dnetlib.dhp.oa.model.graph.Relation(); - relNew - .setSource(getEntityId(relation.getSource(), ENTITY_ID_SEPARATOR)); - relNew.setSourceType(ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2))); - - relNew - .setTarget(getEntityId(relation.getTarget(), ENTITY_ID_SEPARATOR)); - relNew.setTargetType(ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2))); - - relNew - .setReltype( - RelType - .newInstance( - relation.getRelClass(), - relation.getSubRelType())); - - Optional odInfo = Optional.ofNullable(relation.getDataInfo()); - if (odInfo.isPresent()) { - DataInfo dInfo = odInfo.get(); - if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() && - Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { - relNew - .setProvenance( - Provenance - .newInstance( - dInfo.getProvenanceaction().getClassname(), - dInfo.getTrust())); - } - } - if (Boolean.TRUE.equals(relation.getValidated())) { - relNew.setValidated(relation.getValidated()); - relNew.setValidationDate(relation.getValidationDate()); - } - - return relNew; - - }, Encoders.bean(eu.dnetlib.dhp.oa.model.graph.Relation.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .json(outputPath); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkExtractRelationFromEntities.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkExtractRelationFromEntities.java deleted file mode 100644 index 7f42b4a..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkExtractRelationFromEntities.java +++ /dev/null @@ -1,54 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.Result; - -/** - * Spark job that fires the extraction of relations from entities - */ -public class SparkExtractRelationFromEntities implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkExtractRelationFromEntities.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkExtractRelationFromEntities.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final String communityMapPath = parser.get("communityMapPath"); - - Class inputClazz = (Class) Class.forName(resultClassName); - - Extractor extractor = new Extractor(); - extractor.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMapPath); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java deleted file mode 100644 index aa9b7a0..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java +++ /dev/null @@ -1,188 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.ENTITY_ID_SEPARATOR; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.getEntityId; -import static eu.dnetlib.dhp.schema.common.ModelSupport.idPrefixMap; - -import java.io.Serializable; -import java.util.ArrayList; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.function.Consumer; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.*; -import org.jetbrains.annotations.NotNull; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.google.gson.Gson; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.communityapi.model.CommunityEntityMap; -import eu.dnetlib.dhp.oa.graph.dump.UtilCommunityAPI; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.model.Provenance; -import eu.dnetlib.dhp.oa.model.graph.RelType; -import eu.dnetlib.dhp.schema.common.EntityType; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.Relation; - -/** - * Create new Relations between Context Entities and Organizations whose products are associated to the context. It - * produces relation such as: organization <-> isRelatedTo <-> context - */ -public class SparkOrganizationRelation implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkOrganizationRelation.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkOrganizationRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - UtilCommunityAPI queryCommunityAPI = new UtilCommunityAPI(); - final CommunityEntityMap organizationMap = queryCommunityAPI.getCommunityOrganization(); - - final String serializedOrganizationMap = new Gson().toJson(organizationMap); - log.info("organization map : {}", serializedOrganizationMap); - - final String communityMapPath = parser.get("communityMapPath"); - log.info("communityMapPath: {}", communityMapPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - extractRelation(spark, inputPath, organizationMap, outputPath, communityMapPath); - - }); - - } - - private static void extractRelation(SparkSession spark, String inputPath, CommunityEntityMap organizationMap, - String outputPath, String communityMapPath) { - - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - - Dataset relationDataset = Utils.readPath(spark, inputPath, Relation.class); - - relationDataset.createOrReplaceTempView("relation"); - - List relList = new ArrayList<>(); - - Dataset mergedRelsDataset = spark - .sql( - "SELECT target organizationId, source representativeId " + - "FROM relation " + - "WHERE datainfo.deletedbyinference = false " + - "AND relclass = 'merges' " + - "AND substr(source, 1, 2) = '20'") - .as(Encoders.bean(MergedRels.class)); - - mergedRelsDataset.map((MapFunction) mergedRels -> { - if (organizationMap.containsKey(getEntityId(mergedRels.getOrganizationId(), ENTITY_ID_SEPARATOR))) { - return mergedRels; - } - return null; - }, Encoders.bean(MergedRels.class)) - .filter(Objects::nonNull) - .collectAsList() - .forEach(getMergedRelsConsumer(organizationMap, relList, communityMap)); - - organizationMap - .keySet() - .forEach( - oId -> organizationMap - .get(oId) - .forEach(community -> { - if (communityMap.containsKey(community)) { - addRelations(relList, community, oId); - } - })); - - spark - .createDataset(relList, Encoders.bean(eu.dnetlib.dhp.oa.model.graph.Relation.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - @NotNull - private static Consumer getMergedRelsConsumer(CommunityEntityMap organizationMap, - List relList, CommunityMap communityMap) { - return mergedRels -> { - String oId = getEntityId(mergedRels.getOrganizationId(), ENTITY_ID_SEPARATOR); - organizationMap - .get(oId) - .forEach(community -> { - if (communityMap.containsKey(community)) { - addRelations( - relList, community, getEntityId(mergedRels.getRepresentativeId(), ENTITY_ID_SEPARATOR)); - } - - }); - organizationMap.remove(oId); - }; - } - - private static void addRelations(List relList, String community, - String organization) { - - String id = Utils.getContextId(community); - log.info("create relation for organization: {}", organization); - relList - .add( - eu.dnetlib.dhp.oa.model.graph.Relation - .newInstance( - id, Constants.CONTEXT_ENTITY, - organization, - ModelSupport.idPrefixEntity.get(idPrefixMap.get(Organization.class)), - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.USER_CLAIM, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))); - - relList - .add( - eu.dnetlib.dhp.oa.model.graph.Relation - .newInstance( - organization, ModelSupport.idPrefixEntity.get(idPrefixMap.get(Organization.class)), - id, Constants.CONTEXT_ENTITY, - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.USER_CLAIM, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))); - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java deleted file mode 100644 index 12c2c00..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java +++ /dev/null @@ -1,101 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.sql.*; -import org.apache.spark.sql.types.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.oaf.*; - -/** - * It selects the valid relations among those present in the graph. One relation is valid if it is not deletedbyinference - * and if both the source and the target node are present in the graph and are not deleted by inference nor invisible. - * To check this I made a view of the ids of all the entities in the graph, and select the relations for which a join exists - * with this view for both the source and the target - */ - -public class SparkSelectValidRelationsJob implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSelectValidRelationsJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - selectValidRelation2(spark, inputPath, outputPath); - - }); - - } - - private static void selectValidRelation2(SparkSession spark, String inputPath, String outputPath) { - final StructType structureSchema = new StructType() - .fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>"); - - org.apache.spark.sql.Dataset df = spark.createDataFrame(new ArrayList(), structureSchema); - List entities = Arrays - .asList( - "publication", "dataset", "otherresearchproduct", "software", "organization", "project", "datasource"); - for (String e : entities) - df = df - .union( - spark - .read() - .schema(structureSchema) - .json(inputPath + "/" + e) - .filter("dataInfo.deletedbyinference != true and dataInfo.invisible != true")); - - org.apache.spark.sql.Dataset relations = spark - .read() - .schema(Encoders.bean(Relation.class).schema()) - .json(inputPath + "/relation") - .filter("dataInfo.deletedbyinference == false"); - - relations - .join(df, relations.col("source").equalTo(df.col("id")), "leftsemi") - .join(df, relations.col("target").equalTo(df.col("id")), "leftsemi") - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/country/SparkFindResultWithCountry.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/country/SparkFindResultWithCountry.java deleted file mode 100644 index 6088099..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/country/SparkFindResultWithCountry.java +++ /dev/null @@ -1,136 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.country; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; - -import javax.rmi.CORBA.Util; - -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; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; -import com.jayway.jsonpath.DocumentContext; -import com.jayway.jsonpath.JsonPath; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.subset.MasterDuplicate; -import eu.dnetlib.dhp.oa.graph.dump.subset.SparkDumpResult; -import eu.dnetlib.dhp.oa.graph.dump.subset.criteria.VerbResolver; -import eu.dnetlib.dhp.oa.graph.dump.subset.criteria.VerbResolverFactory; -import eu.dnetlib.dhp.oa.graph.dump.subset.selectionconstraints.Param; -import eu.dnetlib.dhp.oa.graph.dump.subset.selectionconstraints.SelectionConstraints; -import eu.dnetlib.dhp.oa.model.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 27/04/23 - * Selects the results having in the country the given country - */ -public class SparkFindResultWithCountry implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkFindResultWithCountry.class); - - public static final String COMPRESSION = "compression"; - public static final String GZIP = "gzip"; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkFindResultWithCountry.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/result_country_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultType = parser.get("resultType"); - log.info("resultType: {}", resultType); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final String preparedInfoPath = parser.get("resultWithCountry"); - - Class inputClazz = (Class) Class - .forName(resultClassName); - - run( - isSparkSessionManaged, inputPath, outputPath, inputClazz, - resultType, preparedInfoPath); - - } - - private static void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, - - Class inputClazz, String resultType, String preparedInfoPath) { - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath + "/original/" + resultType); - - resultDump( - spark, inputPath, outputPath, inputClazz, resultType, preparedInfoPath); - }); - - } - - public static void resultDump( - SparkSession spark, - String inputPath, - String outputPath, - Class inputClazz, - - String resultType, - - String preparedInfoPath) { - - Dataset resultsWithCountry = spark.read().textFile(preparedInfoPath).distinct(); - - Dataset result = Utils - .readPath(spark, inputPath, inputClazz) - .filter( - (FilterFunction) r -> !r.getDataInfo().getInvisible() && !r.getDataInfo().getDeletedbyinference()); - - resultsWithCountry - .joinWith(result, resultsWithCountry.col("value").equalTo(result.col("id"))) - .map((MapFunction, I>) t2 -> t2._2(), Encoders.bean(inputClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/original/" + resultType); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/country/SparkFindResultsRelatedToCountry.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/country/SparkFindResultsRelatedToCountry.java deleted file mode 100644 index 0f4908c..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/country/SparkFindResultsRelatedToCountry.java +++ /dev/null @@ -1,173 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.country; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.io.StringReader; -import java.util.*; - -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; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 27/04/23 - * Finds the results id which are in relation with another entity having the given country - * or that have that country in the country list - */ -public class SparkFindResultsRelatedToCountry implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkFindResultsRelatedToCountry.class); - - public static final String COMPRESSION = "compression"; - public static final String GZIP = "gzip"; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkFindResultsRelatedToCountry.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/result_related_country_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String country = parser.get("country"); - - run( - isSparkSessionManaged, inputPath, outputPath, country); - - } - - private static void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, - String country) { - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - findRelatedEntities( - spark, inputPath, outputPath, country); - }); - - } - - public static void findRelatedEntities( - SparkSession spark, - String inputPath, - String outputPath, - String country) { - - Dataset projectsInCountry = Utils - .readPath(spark, inputPath + "/project", Project.class) - .filter((FilterFunction) p -> isCountryInFunderJurisdiction(p.getFundingtree(), country)); - - Dataset relsProjectResults = Utils - .readPath(spark, inputPath + "/relation", Relation.class) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - r.getRelClass().equals(ModelConstants.PRODUCES)); - - projectsInCountry - .joinWith(relsProjectResults, projectsInCountry.col("id").equalTo(relsProjectResults.col("source"))) - .map((MapFunction, String>) t2 -> t2._2().getTarget(), Encoders.STRING()) - .write() - .option(COMPRESSION, GZIP) - .mode(SaveMode.Overwrite) - .text(outputPath); - - Dataset organizationsInCountry = Utils - .readPath(spark, inputPath + "/organization", Organization.class) - .filter( - (FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() - && o.getCountry().getClassid().equals(country)); - - Dataset relsOrganizationResults = Utils - .readPath(spark, inputPath + "/relation", Relation.class) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - r.getRelClass().equals(ModelConstants.IS_AUTHOR_INSTITUTION_OF)); - - organizationsInCountry - .joinWith( - relsOrganizationResults, - organizationsInCountry.col("id").equalTo(relsOrganizationResults.col("source"))) - .map((MapFunction, String>) t2 -> t2._2().getTarget(), Encoders.STRING()) - .write() - .option(COMPRESSION, GZIP) - .mode(SaveMode.Append) - .text(outputPath); - - selectResultWithCountry(spark, inputPath, outputPath, country, "publication", Publication.class); - selectResultWithCountry( - spark, inputPath, outputPath, country, "dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); - selectResultWithCountry(spark, inputPath, outputPath, country, "software", Software.class); - selectResultWithCountry( - spark, inputPath, outputPath, country, "otherresearchproduct", OtherResearchProduct.class); - - } - - private static void selectResultWithCountry(SparkSession spark, String inputPath, - String outputPath, String country, String type, Class inputClazz) { - Utils - .readPath(spark, inputPath + "/" + type, inputClazz) - .filter( - (FilterFunction) p -> !p.getDataInfo().getDeletedbyinference() && !p.getDataInfo().getInvisible() && - p.getCountry() != null && - p.getCountry().stream().anyMatch(c -> c.getClassid().equals(country))) - .map((MapFunction) p -> p.getId(), Encoders.STRING()) - .write() - .option(COMPRESSION, GZIP) - .mode(SaveMode.Append) - .text(outputPath); - } - - private static boolean isCountryInFunderJurisdiction(List> fundingtrees, String country) { - try { - final SAXReader reader = new SAXReader(); - reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); - for (Field fundingtree : fundingtrees) { - final Document doc = reader.read(new StringReader(fundingtree.getValue())); - if (((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText().equals(country)) { - return true; - } - } - return false; - } catch (DocumentException | SAXException e) { - throw new IllegalArgumentException(e); - } - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/AuthorResult.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/AuthorResult.java deleted file mode 100644 index 1628fdd..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/AuthorResult.java +++ /dev/null @@ -1,102 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv; - -import java.io.Serializable; - -import eu.dnetlib.dhp.utils.DHPUtils; - -/** - * @author miriam.baglioni - * @Date 05/05/23 - */ -public class AuthorResult implements Serializable { - private String authorId; - private String firstName; - private String lastName; - private String fullName; - private String orcid; - private String resultId; - private String rank; - private Boolean fromOrcid; - - public Boolean getFromOrcid() { - return fromOrcid; - } - - public void setFromOrcid(Boolean fromOrcid) { - this.fromOrcid = fromOrcid; - } - - public String getFullName() { - return fullName; - } - - public void setFullName(String fullName) { - this.fullName = fullName; - } - - public String getAuthorId() { - return authorId; - } - - public void setAuthorId(String authorId) { - this.authorId = authorId; - } - - public String getResultId() { - return resultId; - } - - public void setResultId(String resultId) { - this.resultId = resultId; - } - - public String getRank() { - return rank; - } - - public void setRank(String rank) { - this.rank = rank; - } - - public String getId() { - return authorId; - } - - public void setId(String id) { - this.authorId = id; - } - - public String getFirstName() { - return firstName; - } - - public void setFirstName(String firstName) { - this.firstName = firstName; - } - - public String getLastName() { - return lastName; - } - - public void setLastName(String lastName) { - this.lastName = lastName; - } - - public String getOrcid() { - return orcid; - } - - public void setOrcid(String orcid) { - this.orcid = orcid; - } - - public void autosetId() { - if (orcid != null) { - authorId = DHPUtils.md5(orcid); - } else { - authorId = DHPUtils.md5(resultId + rank); - } - - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/Constants.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/Constants.java deleted file mode 100644 index bca06fd..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/Constants.java +++ /dev/null @@ -1,20 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv; - -import java.io.Serializable; - -import org.apache.commons.lang.StringUtils; - -/** - * @author miriam.baglioni - * @Date 10/05/23 - */ -public class Constants implements Serializable { - public final static String SEP = "\t"; - - public static final String addQuotes(String id) { -// if (StringUtils.isNotEmpty(id)) -// return "\"" + id + "\""; - return id; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/DumpCommunities.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/DumpCommunities.java deleted file mode 100644 index 2231dac..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/DumpCommunities.java +++ /dev/null @@ -1,96 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static org.apache.commons.lang3.StringUtils.split; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; -import java.nio.charset.StandardCharsets; -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.UtilCommunityAPI; - -/** - * @author miriam.baglioni - * @Date 09/05/23 - */ -//STEP 1 -public class DumpCommunities implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(DumpCommunities.class); - private final BufferedWriter writer; - private final static String HEADER = "id" + Constants.SEP + "name" + Constants.SEP + "acronym" + Constants.SEP - + " description \n"; - private final transient UtilCommunityAPI queryCommunityAPI; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - DumpCommunities.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_dump_csv_ste1.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String nameNode = parser.get("nameNode"); - log.info("nameNode: {}", nameNode); - - final List communities = Arrays.asList(split(parser.get("communities"), ";")); - - final DumpCommunities dc = new DumpCommunities(outputPath, nameNode); - - dc.writeCommunity(communities); - - } - - private void writeCommunity(List communities) - throws IOException { - writer.write(HEADER); - writer.flush(); - - for (String community : queryCommunityAPI - .getCommunityCsv(communities)) { - writer - .write( - community); - writer.write("\n"); - - } - writer.close(); - } - - public DumpCommunities(String hdfsPath, String hdfsNameNode) throws Exception { - final Configuration conf = new Configuration(); - queryCommunityAPI = new UtilCommunityAPI(); - - conf.set("fs.defaultFS", hdfsNameNode); - FileSystem fileSystem = FileSystem.get(conf); - Path hdfsWritePath = new Path(hdfsPath); - - if (fileSystem.exists(hdfsWritePath)) { - fileSystem.delete(hdfsWritePath, true); - } - FSDataOutputStream fos = fileSystem.create(hdfsWritePath); - - writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8)); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkDumpResults.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkDumpResults.java deleted file mode 100644 index 625c85c..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkDumpResults.java +++ /dev/null @@ -1,362 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static org.apache.commons.lang3.StringUtils.remove; -import static org.apache.commons.lang3.StringUtils.split; - -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collector; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang.StringUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.*; -import org.apache.spark.sql.*; -import org.apache.spark.sql.Dataset; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVAuthor; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVPid; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVRelResAut; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVResult; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.utils.DHPUtils; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 04/05/23 - */ -//STEP 3 -public class SparkDumpResults implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkDumpResults.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_dump_csv_ste3.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String resultType = parser.get("resultType"); - log.info("resultType: {}", resultType); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final String workingPath = parser.get("workingPath"); - - Class inputClazz = (Class) Class.forName(resultClassName); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - // Utils.removeOutputDir(spark, outputPath); - run(spark, inputPath, inputClazz, resultType, workingPath); - - }); - - } - - private static void run(SparkSession spark, String inputPath, - Class inputClazz, String resultType, String workingPath) { - - Dataset resultIds = spark.read().textFile(workingPath + "/resultIds"); - // resultIds.foreach((ForeachFunction) r -> System.out.println(r)); - Dataset results = Utils - .readPath(spark, inputPath + "/" + resultType, inputClazz) - .filter( - (FilterFunction) p -> !p.getDataInfo().getDeletedbyinference() && !p.getDataInfo().getInvisible()); - - resultIds - .joinWith(results, resultIds.col("value").equalTo(results.col("id"))) - .map((MapFunction, R>) t2 -> t2._2(), Encoders.bean(inputClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingPath + "/" + resultType + "/temp/result"); - - // map results - results = Utils.readPath(spark, workingPath + "/" + resultType + "/temp/result", inputClazz); - results - .map( - (MapFunction) r -> mapResultInfo(r), - Encoders.bean(CSVResult.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(workingPath + "/" + resultType + "/result"); - - // map relations between pid and result - results - .flatMap((FlatMapFunction) r -> { - List pids = new ArrayList<>(); - if (Optional.ofNullable(r.getPid()).isPresent() && r.getPid().size() > 0) { - pids.addAll(mapPid(r.getPid(), r.getId())); - } - return pids.iterator(); - }, Encoders.bean(CSVPid.class)) - .filter(Objects::nonNull) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(workingPath + "/" + resultType + "/result_pid"); - - // map authors from the result - // per ogni autore nel result - // se l'autore ha un orcid il suo id dipende dall'orcid (tipo md5(orcid)) - // se non ha orcid il suo id si costruisce come result_id + authorrank ( se non ha il rank si sua - // la sua posizione nell'insieme degli autori) sempre con md5 - results - .flatMap((FlatMapFunction) r -> { - int count = 0; - List arl = new ArrayList<>(); - Set authorIds = new HashSet(); - if (Optional.ofNullable(r.getAuthor()).isPresent()) { - for (Author a : r.getAuthor()) { - count += 1; - AuthorResult ar = new AuthorResult(); - ar.setResultId(r.getId()); - if (Optional.ofNullable(a.getRank()).isPresent()) { - if (a.getRank() > 0) { - ar.setRank(String.valueOf(a.getRank())); - } else { - ar.setRank(String.valueOf(count)); - } - } - ar.setFirstName(removeBreaks(a.getName())); - ar.setLastName(removeBreaks(a.getSurname())); - ar.setFullName(removeBreaks(a.getFullname())); - Tuple2 orcid = getOrcid(a.getPid()); - if (Optional.ofNullable(orcid).isPresent()) { - ar.setOrcid(orcid._1()); - ar.setFromOrcid(orcid._2()); - } - - ar.autosetId(); - - if (!authorIds.contains(ar.getAuthorId())) { - arl.add(ar); - authorIds.add(ar.getAuthorId()); - } - - } - } - - return arl.iterator(); - }, Encoders.bean(AuthorResult.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingPath + "/" + resultType + "/temp/authorresult"); - - Dataset authorResult = Utils - .readPath(spark, workingPath + "/" + resultType + "/temp/authorresult", AuthorResult.class); - // map the relation between author and result - authorResult - .map( - (MapFunction) ar -> { - CSVRelResAut ret = new CSVRelResAut(); - ret.setResult_id(ar.getResultId()); - ret.setAuthor_id(ar.getAuthorId()); - return ret; - }, - Encoders.bean(CSVRelResAut.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(workingPath + "/" + resultType + "/result_author"); - - // ma the authors in the working dir. I do not want to have them repeated. If I have an orcid as id, I choose - // the one from orcid if any - authorResult - .groupByKey((MapFunction) ar -> ar.getAuthorId(), Encoders.STRING()) - .mapGroups( - (MapGroupsFunction) (k, it) -> { - AuthorResult first = it.next(); - if (!Optional.ofNullable(first.getFromOrcid()).isPresent() || first.getFromOrcid()) - return getAuthorDump(first); - while (it.hasNext()) { - AuthorResult ar = it.next(); - if (ar.getFromOrcid()) - return getAuthorDump(ar); - } - return getAuthorDump(first); - }, - Encoders.bean(CSVAuthor.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(workingPath + "/" + resultType + "/author"); - - } - - private static List mapPid(List pid, String resultId) { - return pid - .stream() - .map(p -> p.getQualifier().getClassid().toLowerCase() + "@" + p.getValue().toLowerCase()) - .distinct() - .map(p -> { - CSVPid ret = new CSVPid(); - ret.setId(DHPUtils.md5(p + "@" + resultId)); - ret.setResult_id(resultId); - ret.setPid(split(p, "@")[1]); - ret.setType(split(p, "@")[0]); - - return ret; - }) - .collect(Collectors.toList()); - - } - - private static CSVAuthor getAuthorDump(AuthorResult ar) { - CSVAuthor ret = new CSVAuthor(); - ret.setFirstname(ar.getFirstName()); - - ret.setId(ar.getAuthorId()); - ret.setLastname(ar.getLastName()); - - ret.setFullname(ar.getFullName()); - - if (ar.getOrcid() != null) { - ret.setOrcid(ar.getOrcid()); - ret.setFromOrcid(ar.getFromOrcid()); - } else { - ret.setOrcid(""); - } - - return ret; - } - - private static Tuple2 getOrcid(List pid) { - if (!Optional.ofNullable(pid).isPresent()) - return null; - if (pid.size() == 0) - return null; - for (StructuredProperty p : pid) { - if (p.getQualifier().getClassid().equals(ModelConstants.ORCID)) { - return new Tuple2<>(p.getValue(), Boolean.TRUE); - } - } - for (StructuredProperty p : pid) { - if (p.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING)) { - return new Tuple2<>(p.getValue(), Boolean.FALSE); - } - } - return null; - } - - private static String getFieldValue(Field input) { - if (input != null && - StringUtils.isNotEmpty(input.getValue())) { - return removeBreaks(input.getValue()); - } else { - return ""; - } - } - - private static CSVResult mapResultInfo(R r) { - CSVResult ret = new CSVResult(); - ret.setId(removeBreaks(r.getId())); - ret.setType(removeBreaks(r.getResulttype().getClassid())); - ret.setTitle(getTitle(r.getTitle())); - ret.setDescription(getAbstract(r.getDescription())); - ret.setAccessright(removeBreaks(r.getBestaccessright().getClassid())); - ret.setPublication_date(removeBreaks(getFieldValue(r.getDateofacceptance()))); - ret.setPublisher(removeBreaks(getFieldValue(r.getPublisher()))); - - if (Optional.ofNullable(r.getSubject()).isPresent()) - ret.setKeywords(String.join(", ", r.getSubject().stream().map(s -> { - if (StringUtils.isNotEmpty(s.getValue())) - return removeBreaks(s.getValue().toLowerCase()); - else - return null; - }).filter(Objects::nonNull).distinct().collect(Collectors.toList()))); - else - ret.setKeywords(""); - - if (Optional.ofNullable(r.getCountry()).isPresent()) - ret - .setCountry( - String.join(", ", r.getCountry().stream().map(Country::getClassid).collect(Collectors.toList()))); - else - ret.setCountry(""); - - if (Optional.ofNullable(r.getLanguage()).isPresent() && StringUtils.isNotEmpty(r.getLanguage().getClassid())) { - ret.setLanguage(r.getLanguage().getClassid()); - } else { - ret.setLanguage(""); - } - - return ret; - } - - private static String getAbstract(List> description) { - if (description == null) - return ""; - for (Field abs : description) { - if (StringUtils.isNotEmpty(abs.getValue())) { - return removeBreaks(abs.getValue()); - } - } - return ""; - } - - private static String getTitle(List titles) { - String firstTitle = null; - for (StructuredProperty title : titles) { - if (StringUtils.isEmpty(firstTitle)) { - if (StringUtils.isNotEmpty(title.getValue())) - firstTitle = removeBreaks(title.getValue()); - } - if (title.getQualifier().getClassid().equals(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) { - if (StringUtils.isNotEmpty(title.getValue())) - return removeBreaks(title.getValue()); - } - } - if (firstTitle != null) { - return removeBreaks(firstTitle); - } - return ""; - } - - private static String removeBreaks(String input) { - if (StringUtils.isNotEmpty(input)) - return input - .replace("\n", " ") - .replace("\t", " ") - .replace("\r", " ") - // .replace("\\", " ") - .replace("\"", " "); - - return input; - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkMoveOnSigleDir.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkMoveOnSigleDir.java deleted file mode 100644 index 5a41ae8..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkMoveOnSigleDir.java +++ /dev/null @@ -1,133 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -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.Row; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVAuthor; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVPid; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVRelResAut; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVResult; -import eu.dnetlib.dhp.schema.oaf.*; - -/** - * @author miriam.baglioni - * @Date 10/05/23 - */ -//STEP 4 -public class SparkMoveOnSigleDir implements Serializable { - - // All the products saved in different directories are put under the same one. - // For the authors also a step of reconciliation mast be done, since the same author id can be saved in more than - // one directory - - private static final Logger log = LoggerFactory.getLogger(SparkMoveOnSigleDir.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkMoveOnSigleDir.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_dump_csv_ste4.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - // Utils.removeOutputDir(spark, outputPath); - run(spark, outputPath, workingPath); - - }); - - } - - private static void run(SparkSession spark, String outputPath, - String workingPath) { - - Utils - .readPath(spark, workingPath + "/publication/result", CSVResult.class) - .union(Utils.readPath(spark, workingPath + "/dataset/result", CSVResult.class)) - .union(Utils.readPath(spark, workingPath + "/software/result", CSVResult.class)) - .union(Utils.readPath(spark, workingPath + "/otherresearchproduct/result", CSVResult.class)) - .write() - .mode(SaveMode.Overwrite) - .option("header", "true") - .option("delimiter", Constants.SEP) - .option("compression", "gzip") - .csv(outputPath + "/result"); - - Utils - .readPath(spark, workingPath + "/publication/result_pid", CSVPid.class) - .union(Utils.readPath(spark, workingPath + "/dataset/result_pid", CSVPid.class)) - .union(Utils.readPath(spark, workingPath + "/software/result_pid", CSVPid.class)) - .union(Utils.readPath(spark, workingPath + "/otherresearchproduct/result_pid", CSVPid.class)) - .write() - .mode(SaveMode.Overwrite) - .option("header", "true") - .option("delimiter", Constants.SEP) - .option("compression", "gzip") - .csv(outputPath + "/result_pid"); - - Utils - .readPath(spark, workingPath + "/publication/result_author", CSVRelResAut.class) - .union(Utils.readPath(spark, workingPath + "/dataset/result_author", CSVRelResAut.class)) - .union(Utils.readPath(spark, workingPath + "/software/result_author", CSVRelResAut.class)) - .union(Utils.readPath(spark, workingPath + "/otherresearchproduct/result_author", CSVRelResAut.class)) - .write() - .mode(SaveMode.Overwrite) - .option("header", "true") - .option("delimiter", Constants.SEP) - .option("compression", "gzip") - .csv(outputPath + "/result_author"); - - Utils - .readPath(spark, workingPath + "/publication/author", CSVAuthor.class) - .union(Utils.readPath(spark, workingPath + "/dataset/author", CSVAuthor.class)) - .union(Utils.readPath(spark, workingPath + "/software/author", CSVAuthor.class)) - .union(Utils.readPath(spark, workingPath + "/otherresearchproduct/author", CSVAuthor.class)) - .groupByKey((MapFunction) r -> r.getId(), Encoders.STRING()) - .mapGroups( - (MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(CSVAuthor.class)) - .write() - .mode(SaveMode.Overwrite) - .option("header", "true") - .option("delimiter", Constants.SEP) - .option("compression", "gzip") - .csv(outputPath + "/author"); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkSelectResultsAndDumpRelations.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkSelectResultsAndDumpRelations.java deleted file mode 100644 index 30772fa..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkSelectResultsAndDumpRelations.java +++ /dev/null @@ -1,227 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; -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.FlatMapFunction; -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.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVCitation; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVRELCommunityResult; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.utils.DHPUtils; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 04/05/23 - */ -//STEP 2 -public class SparkSelectResultsAndDumpRelations implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkSelectResultsAndDumpRelations.class); - private static String RESULT_COMMUNITY_TABLE = "/result_community"; - private static String COMMUNITY_RESULT_IDS = "/communityResultIds"; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSelectResultsAndDumpRelations.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_dump_csv_ste2.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String workingPath = parser.get("workingPath"); - - List communityList = null; - Optional communities = Optional.ofNullable(parser.get("communities")); - if (communities.isPresent()) { - communityList = Arrays.asList(communities.get().split(";")); - } - - SparkConf conf = new SparkConf(); - - List finalCommunityList = communityList; - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - // Utils.removeOutputDir(spark, outputPath); - run(spark, inputPath, outputPath, workingPath, finalCommunityList); - - }); - - } - - private static void run(SparkSession spark, String inputPath, String outputPath, - String workingPath, - List communityList) { - - // select the result ids related to the set of communities considered - writeCommunityRelatedIds( - spark, inputPath + "/publication", Publication.class, communityList, workingPath + COMMUNITY_RESULT_IDS); - writeCommunityRelatedIds( - spark, inputPath + "/dataset", Dataset.class, communityList, workingPath + COMMUNITY_RESULT_IDS); - writeCommunityRelatedIds( - spark, inputPath + "/software", Software.class, communityList, workingPath + COMMUNITY_RESULT_IDS); - writeCommunityRelatedIds( - spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class, communityList, - workingPath + COMMUNITY_RESULT_IDS); - - // write the relations result communities - writeCommunityResultRelations( - spark, inputPath + "/publication", Publication.class, communityList, outputPath + RESULT_COMMUNITY_TABLE); - writeCommunityResultRelations( - spark, inputPath + "/dataset", Dataset.class, communityList, outputPath + RESULT_COMMUNITY_TABLE); - writeCommunityResultRelations( - spark, inputPath + "/software", Software.class, communityList, outputPath + RESULT_COMMUNITY_TABLE); - writeCommunityResultRelations( - spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class, communityList, - outputPath + RESULT_COMMUNITY_TABLE); - - // select the relations with semantics cites - org.apache.spark.sql.Dataset relations = Utils - .readPath(spark, inputPath + "/relation", Relation.class) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - r.getRelClass().equals(ModelConstants.CITES)); - - // select the results target of the selected relations having as source one of the results related to the - // communities - org.apache.spark.sql.Dataset resultIds = spark - .read() - .textFile(workingPath + COMMUNITY_RESULT_IDS) - .distinct(); - - resultIds - .joinWith(relations, resultIds.col("value").equalTo(relations.col("source")), "left") - .flatMap((FlatMapFunction, String>) t2 -> { - if (Optional.ofNullable(t2._2()).isPresent()) { - return Arrays.asList(t2._1(), t2._2().getTarget()).iterator(); - } else { - return Arrays.asList(t2._1()).iterator(); - } - }, Encoders.STRING()) - .distinct() - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - - .text(workingPath + "/resultIds"); - - resultIds - .joinWith(relations, resultIds.col("value").equalTo(relations.col("source"))) - .map( - (MapFunction, CSVCitation>) t2 -> mapToCitation(t2._2()), - Encoders.bean(CSVCitation.class)) - .write() - .option("compression", "gzip") - .option("header", "true") - .option("delimiter", Constants.SEP) - .mode(SaveMode.Overwrite) - .csv(outputPath + "/relation"); - - } - - private static CSVCitation mapToCitation(Relation relation) { - CSVCitation ret = new CSVCitation(); - ret.setId(DHPUtils.md5(relation.getSource() + relation.getRelClass().toLowerCase() + relation.getTarget())); - ret.setResult_id_cites(relation.getSource()); - ret.setResult_id_cited(relation.getTarget()); - return ret; - } - - private static void writeCommunityResultRelations(SparkSession spark, String inputPath, - Class clazz, List communityList, String outputPath) { - Utils - .readPath(spark, inputPath, clazz) - .filter( - (FilterFunction) p -> !p.getDataInfo().getDeletedbyinference() && - !p.getDataInfo().getInvisible()) - .flatMap((FlatMapFunction) p -> { - Set inserted = new HashSet<>(); - List ret = new ArrayList<>(); - - for (String context : p - .getContext() - .stream() - .map(Context::getId) - .distinct() - .collect(Collectors.toList())) { - String cId = context.contains("::") - ? context.substring(0, context.indexOf("::")) - : context; - if (communityList.contains(cId) && !inserted.contains(cId)) { - CSVRELCommunityResult crc = new CSVRELCommunityResult(); - crc.setResult_id(p.getId()); - crc.setCommunity_id(DHPUtils.md5(cId)); - ret.add(crc); - inserted.add(cId); - } - } - return ret.iterator(); - }, Encoders.bean(CSVRELCommunityResult.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .option("header", "true") - .option("delimiter", Constants.SEP) - .csv(outputPath); - } - - private static void writeCommunityRelatedIds(SparkSession spark, String inputPath, - Class clazz, List communityList, String outputPath) { - Utils - .readPath(spark, inputPath, clazz) - .filter( - (FilterFunction) p -> !p.getDataInfo().getDeletedbyinference() && - !p.getDataInfo().getInvisible() && - isRelatedToCommunities(p, communityList)) - .map((MapFunction) Result::getId, Encoders.STRING()) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .text(outputPath); - - } - - private static boolean isRelatedToCommunities(R p, List communityList) { - return p - .getContext() - .stream() - .anyMatch( - c -> communityList.contains(c.getId()) || - (c.getId().contains("::") - && communityList.contains(c.getId().substring(0, c.getId().indexOf("::"))))); - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVAuthor.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVAuthor.java deleted file mode 100644 index c27190a..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVAuthor.java +++ /dev/null @@ -1,68 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv.model; - -import java.io.Serializable; - -import eu.dnetlib.dhp.oa.graph.dump.csv.Constants; - -/** - * @author miriam.baglioni - * @Date 11/05/23 - */ -public class CSVAuthor implements Serializable { - private String id; - private String firstname; - private String lastname; - private String fullname; - private String orcid; - private Boolean fromOrcid; - - public Boolean getFromOrcid() { - return fromOrcid; - } - - public void setFromOrcid(Boolean fromOrcid) { - this.fromOrcid = fromOrcid; - } - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = Constants.addQuotes(id); - } - - public String getFirstname() { - return firstname; - } - - public void setFirstname(String firstname) { - this.firstname = Constants.addQuotes(firstname); - } - - public String getLastname() { - return lastname; - } - - public void setLastname(String lastname) { - this.lastname = Constants.addQuotes(lastname); - } - - public String getFullname() { - return fullname; - } - - public void setFullname(String fullname) { - this.fullname = Constants.addQuotes(fullname); - } - - public String getOrcid() { - return orcid; - } - - public void setOrcid(String orcid) { - this.orcid = Constants.addQuotes(orcid); - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVCitation.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVCitation.java deleted file mode 100644 index e027b6d..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVCitation.java +++ /dev/null @@ -1,40 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv.model; - -import java.io.Serializable; - -import eu.dnetlib.dhp.oa.graph.dump.csv.Constants; - -/** - * @author miriam.baglioni - * @Date 11/05/23 - */ -public class CSVCitation implements Serializable { - private String id; - private String result_id_cites; - private String result_id_cited; - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = Constants.addQuotes(id); - } - - public String getResult_id_cites() { - return result_id_cites; - } - - public void setResult_id_cites(String result_id_cites) { - this.result_id_cites = Constants.addQuotes(result_id_cites); - } - - public String getResult_id_cited() { - return result_id_cited; - } - - public void setResult_id_cited(String result_id_cited) { - this.result_id_cited = Constants.addQuotes(result_id_cited); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVPid.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVPid.java deleted file mode 100644 index a255fe1..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVPid.java +++ /dev/null @@ -1,50 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv.model; - -import java.io.Serializable; - -import eu.dnetlib.dhp.oa.graph.dump.csv.Constants; - -/** - * @author miriam.baglioni - * @Date 11/05/23 - */ -public class CSVPid implements Serializable { - - private String id; - private String result_id; - private String pid; - private String type; - - public String getResult_id() { - return result_id; - } - - public void setResult_id(String result_id) { - this.result_id = Constants.addQuotes(result_id); - } - - public String getPid() { - return pid; - } - - public void setPid(String pid) { - this.pid = Constants.addQuotes(pid); - } - - public String getType() { - return type; - } - - public void setType(String type) { - this.type = Constants.addQuotes(type); - } - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = Constants.addQuotes(id); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVRELCommunityResult.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVRELCommunityResult.java deleted file mode 100644 index c35a9ee..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVRELCommunityResult.java +++ /dev/null @@ -1,31 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv.model; - -import java.io.Serializable; - -import eu.dnetlib.dhp.oa.graph.dump.csv.Constants; - -/** - * @author miriam.baglioni - * @Date 11/05/23 - */ -public class CSVRELCommunityResult implements Serializable { - private String result_id; - private String community_id; - - public String getResult_id() { - return result_id; - } - - public void setResult_id(String result_id) { - this.result_id = Constants.addQuotes(result_id); - } - - public String getCommunity_id() { - return community_id; - } - - public void setCommunity_id(String community_id) { - this.community_id = Constants.addQuotes(community_id); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVRelResAut.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVRelResAut.java deleted file mode 100644 index 47ec628..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVRelResAut.java +++ /dev/null @@ -1,31 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv.model; - -import java.io.Serializable; - -import eu.dnetlib.dhp.oa.graph.dump.csv.Constants; - -/** - * @author miriam.baglioni - * @Date 11/05/23 - */ -public class CSVRelResAut implements Serializable { - private String result_id; - private String author_id; - - public String getResult_id() { - return result_id; - } - - public void setResult_id(String result_id) { - this.result_id = Constants.addQuotes(result_id); - } - - public String getAuthor_id() { - return author_id; - } - - public void setAuthor_id(String author_id) { - this.author_id = Constants.addQuotes(author_id); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVResult.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVResult.java deleted file mode 100644 index 27dd7dd..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVResult.java +++ /dev/null @@ -1,113 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv.model; - -import java.io.Serializable; - -import org.apache.commons.lang.StringUtils; - -import com.fasterxml.jackson.annotation.JsonGetter; -import com.fasterxml.jackson.annotation.JsonProperty; -import com.fasterxml.jackson.annotation.JsonSetter; - -import eu.dnetlib.dhp.oa.graph.dump.csv.Constants; -import eu.dnetlib.dhp.schema.oaf.Country; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import sun.swing.StringUIClientPropertyKey; - -/** - * @author miriam.baglioni - * @Date 11/05/23 - */ -public class CSVResult implements Serializable { - private String id; - private String type; - private String title; - private String description; - private String accessright; - private String publication_date; - private String publisher; - private String keywords; - private String country; - private String language; - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = Constants.addQuotes(id); - } - - public String getType() { - return type; - } - - public void setType(String type) { - this.type = Constants.addQuotes(type); - } - - public String getTitle() { - return title; - } - - public void setTitle(String title) { - this.title = Constants.addQuotes(title); - } - - public String getDescription() { - return description; - } - - public void setDescription(String description) { - this.description = Constants.addQuotes(description); - } - - public String getAccessright() { - return accessright; - } - - public void setAccessright(String accessright) { - this.accessright = Constants.addQuotes(accessright); - } - - public String getPublication_date() { - return publication_date; - } - - public void setPublication_date(String publication_date) { - this.publication_date = Constants.addQuotes(publication_date); - } - - public String getPublisher() { - return publisher; - } - - public void setPublisher(String publisher) { - this.publisher = Constants.addQuotes(publisher); - } - - public String getKeywords() { - return keywords; - } - - public void setKeywords(String keywords) { - this.keywords = Constants.addQuotes(keywords); - } - - public String getCountry() { - return country; - } - - public void setCountry(String country) { - this.country = Constants.addQuotes(country); - } - - public String getLanguage() { - return language; - } - - public void setLanguage(String language) { - this.language = Constants.addQuotes(language); - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/CardinalityTooHighException.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/CardinalityTooHighException.java index 0a4f25b..c4cf084 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/CardinalityTooHighException.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/CardinalityTooHighException.java @@ -1,4 +1,3 @@ - package eu.dnetlib.dhp.oa.graph.dump.exceptions; public class CardinalityTooHighException extends Exception { diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java deleted file mode 100644 index e325c43..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.exceptions; - -public class MyRuntimeException extends RuntimeException { - - public MyRuntimeException() { - super(); - } - - public MyRuntimeException( - final String message, - final Throwable cause, - final boolean enableSuppression, - final boolean writableStackTrace) { - super(message, cause, enableSuppression, writableStackTrace); - } - - public MyRuntimeException(final String message, final Throwable cause) { - super(message, cause); - } - - public MyRuntimeException(final String message) { - super(message); - } - - public MyRuntimeException(final Throwable cause) { - super(cause); - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java index f3fbf74..3d614eb 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java @@ -1,4 +1,3 @@ - package eu.dnetlib.dhp.oa.graph.dump.exceptions; public class NoAvailableEntityTypeException extends Exception { diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java deleted file mode 100644 index ad11516..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ /dev/null @@ -1,129 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresults; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -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.FlatMapFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.*; -import org.jetbrains.annotations.NotNull; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.amazonaws.transform.SimpleTypeUnmarshallers; -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; -import eu.dnetlib.dhp.oa.model.community.Funder; -import eu.dnetlib.dhp.oa.model.community.Project; -import io.netty.util.internal.StringUtil; - -/** - * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC - * for the EC it specifies also the fundingStream (FP7 or H2020) - */ -public class SparkDumpFunderResults implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); - private static final ObjectMapper MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpFunderResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath); - }); - } - - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { - Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - log.info("Number of result {}", result.count()); - - Dataset tmp = result - .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { - return getFunderName(p); - }).collect(Collectors.toList()).iterator(), Encoders.STRING()) - .distinct(); - List funderList = tmp.collectAsList(); - funderList.stream().parallel().forEach(funder -> { - result - .filter( - (FilterFunction) r -> Optional.ofNullable(r.getProjects()).isPresent() && - r.getProjects().stream().anyMatch(p -> getFunderName(p).equals(funder))) - .map((MapFunction) r -> MAPPER.writeValueAsString(r), Encoders.STRING()) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .text(outputPath + "/" + funder); - - }); - } - - @NotNull - private static String getFunderName(Project p) { - Optional ofunder = Optional.ofNullable(p.getFunder()); - if (ofunder.isPresent()) { - String fName = ofunder.get().getShortName(); - if (StringUtil.isNullOrEmpty(fName)) - return ofunder.get().getName(); - if (fName.equalsIgnoreCase("ec")) { - fName += "_" + ofunder.get().getFundingStream(); - } - return fName; - } else { - String fName = p.getId().substring(0, p.getId().indexOf("_")).toUpperCase(); - if (fName.equalsIgnoreCase("ec")) { - if (p.getId().contains("he")) { - fName += "_HE"; - } else if (p.getId().contains("h2020")) { - fName += "_H2020"; - } else { - fName += "_FP7"; - } - } else if (fName.equalsIgnoreCase("conicytf")) { - fName = "CONICYT"; - } else if (fName.equalsIgnoreCase("dfgf")) { - fName = "DFG"; - } else if (fName.equalsIgnoreCase("tubitakf")) { - fName = "TUBITAK"; - } else if (fName.equalsIgnoreCase("euenvagency")) { - fName = "EEA"; - } - return fName; - } - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java deleted file mode 100644 index 57e7f9f..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ /dev/null @@ -1,120 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresults; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Objects; -import java.util.Optional; - -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; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; -import eu.dnetlib.dhp.schema.oaf.Result; -import scala.Tuple2; - -/** - * Selects the results linked to projects. Only for these results the dump will be performed. - * The code to perform the dump and to expend the dumped results with the information related to projects - * is the one used for the dump of the community products - */ -public class SparkResultLinkedToProject implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkResultLinkedToProject.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkResultLinkedToProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final String resultProjectsPath = parser.get("graphPath"); - log.info("graphPath: {}", resultProjectsPath); - - String communityMapPath = parser.get("communityMapPath"); - - @SuppressWarnings("unchecked") - Class inputClazz = (Class) Class.forName(resultClassName); - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects( - communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); - }); - } - - private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, - Class inputClazz, - String inputPath, String outputPath, String resultProjectsPath) { - - Dataset results = Utils - .readPath(spark, inputPath, inputClazz) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - !r.getDataInfo().getInvisible()); - Dataset resultProjectDataset = Utils - .readPath(spark, resultProjectsPath, ResultProject.class); - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - results - .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) - .map((MapFunction, CommunityResult>) t2 -> { - CommunityResult cr = (CommunityResult) ResultMapper - .map( - t2._1(), - communityMap, Constants.DUMPTYPE.FUNDER.getType()); - if (cr != null) { - cr.setProjects(t2._2().getProjectsList()); - } - return cr; - }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .map( - (MapFunction) cr -> new ObjectMapper().writeValueAsString(cr), - Encoders.STRING()) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .text(outputPath); - - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/organizationonly/SparkDumpOrganizationJob.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/organizationonly/SparkDumpOrganizationJob.java deleted file mode 100644 index c218600..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/organizationonly/SparkDumpOrganizationJob.java +++ /dev/null @@ -1,270 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.organizationonly; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.ENTITY_ID_SEPARATOR; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.getEntityId; - -import java.io.Serializable; -import java.io.StringReader; -import java.util.*; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang.StringUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.CardinalityTooHighException; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; -import eu.dnetlib.dhp.oa.model.Container; -import eu.dnetlib.dhp.oa.model.Provenance; -import eu.dnetlib.dhp.oa.model.Result; -import eu.dnetlib.dhp.oa.model.graph.*; -import eu.dnetlib.dhp.oa.model.graph.Datasource; -import eu.dnetlib.dhp.oa.model.graph.Organization; -import eu.dnetlib.dhp.oa.model.graph.Project; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.Relation; -import scala.Tuple2; - -/** - * Spark Job that fires the dump for the entites - */ -public class SparkDumpOrganizationJob implements Serializable { - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.organizationonly.SparkDumpOrganizationJob.class); - public static final String COMPRESSION = "compression"; - public static final String GZIP = "gzip"; - - public static void main(String[] args) throws Exception { - - Boolean isSparkSessionManaged = Boolean.TRUE; - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = "/tmp/prod_provision/graph/20_graph_blacklisted/"; - log.info("inputPath: {}", inputPath); - - final String outputPath = "/tmp/miriam/organizationsOnly/"; - log.info("outputPath: {}", outputPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - // Utils.removeOutputDir(spark, outputPath); - organizationMap(spark, inputPath, outputPath); - // relationMap2(spark, inputPath, outputPath); - }); - - } - - private static void relationMap2(SparkSession spark, String inputPath, String outputPath) { - Utils - .readPath(spark, inputPath + "relation", Relation.class) - .filter((FilterFunction) r -> r.getRelType().equalsIgnoreCase("organizationOrganization")) - .map((MapFunction) relation -> { - eu.dnetlib.dhp.oa.model.graph.Relation relNew = new eu.dnetlib.dhp.oa.model.graph.Relation(); - relNew - .setSource(getEntityId(relation.getSource(), ENTITY_ID_SEPARATOR)); - relNew.setSourceType(ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2))); - - relNew - .setTarget(getEntityId(relation.getTarget(), ENTITY_ID_SEPARATOR)); - relNew.setTargetType(ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2))); - - relNew - .setReltype( - RelType - .newInstance( - relation.getRelClass(), - relation.getSubRelType())); - - Optional odInfo = Optional.ofNullable(relation.getDataInfo()); - if (odInfo.isPresent()) { - DataInfo dInfo = odInfo.get(); - if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() && - Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { - relNew - .setProvenance( - Provenance - .newInstance( - dInfo.getProvenanceaction().getClassname(), - dInfo.getTrust())); - } - } - if (Boolean.TRUE.equals(relation.getValidated())) { - relNew.setValidated(relation.getValidated()); - relNew.setValidationDate(relation.getValidationDate()); - } - - return relNew; - }, Encoders.bean(eu.dnetlib.dhp.oa.model.graph.Relation.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "relation"); - } - - private static void relationMap(SparkSession spark, String inputPath, String outputPath) { - Dataset organization = Utils - .readPath(spark, inputPath + "organization", eu.dnetlib.dhp.schema.oaf.Organization.class); - Dataset rels = Utils.readPath(spark, inputPath + "relation", Relation.class); - organization - .joinWith(rels, organization.col("id").equalTo(rels.col("source")), "left") - .map( - (MapFunction, Relation>) t2 -> t2._2(), - Encoders.bean(Relation.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json("/tmp/orgSource"); - - rels = Utils.readPath(spark, "/tmp/orgSource", Relation.class); - - organization - .joinWith(rels, organization.col("id").equalTo(rels.col("target")), "left") - .map( - (MapFunction, Relation>) t2 -> t2._2(), - Encoders.bean(Relation.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json("/tmp/orgSourceTarget"); - - Utils - .readPath(spark, "/tmp/orgSourceTarget", Relation.class) - .map((MapFunction) relation -> { - eu.dnetlib.dhp.oa.model.graph.Relation relNew = new eu.dnetlib.dhp.oa.model.graph.Relation(); - relNew - .setSource(getEntityId(relation.getSource(), ENTITY_ID_SEPARATOR)); - relNew.setSourceType(ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2))); - - relNew - .setTarget(getEntityId(relation.getTarget(), ENTITY_ID_SEPARATOR)); - relNew.setTargetType(ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2))); - - relNew - .setReltype( - RelType - .newInstance( - relation.getRelClass(), - relation.getSubRelType())); - - Optional odInfo = Optional.ofNullable(relation.getDataInfo()); - if (odInfo.isPresent()) { - DataInfo dInfo = odInfo.get(); - if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() && - Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { - relNew - .setProvenance( - Provenance - .newInstance( - dInfo.getProvenanceaction().getClassname(), - dInfo.getTrust())); - } - } - if (Boolean.TRUE.equals(relation.getValidated())) { - relNew.setValidated(relation.getValidated()); - relNew.setValidationDate(relation.getValidationDate()); - } - - return relNew; - }, Encoders.bean(eu.dnetlib.dhp.oa.model.graph.Relation.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "relation"); - } - - private static void organizationMap(SparkSession spark, String inputPath, String outputPath) { - Utils - .readPath(spark, inputPath + "organization", eu.dnetlib.dhp.schema.oaf.Organization.class) - .map( - (MapFunction) o -> mapOrganization(o), - Encoders.bean(Organization.class)) - .filter((FilterFunction) o -> o != null) - .write() - .mode(SaveMode.Overwrite) - .option(COMPRESSION, GZIP) - .json(outputPath + "/organization"); - } - - private static eu.dnetlib.dhp.oa.model.graph.Organization mapOrganization( - eu.dnetlib.dhp.schema.oaf.Organization org) { - - Organization organization = new Organization(); - - Optional - .ofNullable(org.getLegalshortname()) - .ifPresent(value -> organization.setLegalshortname(value.getValue())); - - Optional - .ofNullable(org.getLegalname()) - .ifPresent(value -> organization.setLegalname(value.getValue())); - - Optional - .ofNullable(org.getWebsiteurl()) - .ifPresent(value -> organization.setWebsiteurl(value.getValue())); - - Optional - .ofNullable(org.getAlternativeNames()) - .ifPresent( - value -> organization - .setAlternativenames( - value - .stream() - .map(v -> v.getValue()) - .collect(Collectors.toList()))); - - Optional - .ofNullable(org.getCountry()) - .ifPresent( - value -> { - if (!value.getClassid().equals(eu.dnetlib.dhp.oa.graph.dump.complete.Constants.UNKNOWN)) { - organization - .setCountry( - eu.dnetlib.dhp.oa.model.Country.newInstance(value.getClassid(), value.getClassname())); - } - - }); - - Optional - .ofNullable(org.getId()) - .ifPresent(value -> organization.setId(getEntityId(value, ENTITY_ID_SEPARATOR))); - - Optional - .ofNullable(org.getPid()) - .ifPresent( - value -> organization - .setPid( - value - .stream() - .map(p -> OrganizationPid.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - return organization; - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java deleted file mode 100644 index b95312f..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java +++ /dev/null @@ -1,87 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.projectssubset; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Objects; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -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.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.graph.Project; -import scala.Tuple2; - -public class ProjectsSubsetSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - ProjectsSubsetSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - final String projectListPath = parser.get("projectListPath"); - log.info("projectListPath: {}", projectListPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - getNewProjectList(spark, inputPath, outputPath, projectListPath); - }); - } - - private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, - String projectListPath) { - Dataset projectList = spark.read().textFile(projectListPath); - Dataset projects; - projects = Utils - .readPath(spark, inputPath, Project.class) - .map((MapFunction) p -> { - p.setId("40|" + p.getId()); - return p; - }, Encoders.bean(Project.class)); - projects - .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") - .map((MapFunction, Project>) t2 -> { - if (Optional.ofNullable(t2._2()).isPresent()) - return null; - return t2._1(); - }, Encoders.bean(Project.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - Utils - .readPath(spark, outputPath, Project.class) - .map((MapFunction) p -> p.getId(), Encoders.STRING()) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .text(projectListPath); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/serafeim/SparkSelectResultsAndDumpRelations.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/serafeim/SparkSelectResultsAndDumpRelations.java deleted file mode 100644 index 1f31c3c..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/serafeim/SparkSelectResultsAndDumpRelations.java +++ /dev/null @@ -1,241 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.serafeim; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; -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.FlatMapFunction; -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.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.csv.Constants; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 04/05/23 - */ -//STEP 2 -public class SparkSelectResultsAndDumpRelations implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkSelectResultsAndDumpRelations.class); - private static String RESULT_COMMUNITY_TABLE = "/result_community"; - private static String COMMUNITY_RESULT_IDS = "/communityResultIds"; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSelectResultsAndDumpRelations.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_dump_csv_ste2.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String workingPath = parser.get("workingPath"); - - List communityList = null; - Optional communities = Optional.ofNullable(parser.get("communities")); - if (communities.isPresent()) { - communityList = Arrays.asList(communities.get().split(";")); - } - - SparkConf conf = new SparkConf(); - - List finalCommunityList = communityList; - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - run(spark, inputPath, outputPath, workingPath, finalCommunityList); - - }); - - } - - private static void run(SparkSession spark, String inputPath, String outputPath, - String workingPath, - List communityList) { - - // select the result ids related to the set of communities considered - writeCommunityRelatedIds( - spark, inputPath, Publication.class, communityList, workingPath, "publication"); - writeCommunityRelatedIds( - spark, inputPath, Dataset.class, communityList, workingPath, "dataset"); - writeCommunityRelatedIds( - spark, inputPath, Software.class, communityList, workingPath, "software"); - writeCommunityRelatedIds( - spark, inputPath, OtherResearchProduct.class, communityList, - workingPath, "otherresearchproduct"); - - // select the relations with semantics cites - org.apache.spark.sql.Dataset relations = Utils - .readPath(spark, inputPath + "/relation", Relation.class) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - r.getRelClass().equals(ModelConstants.CITES)); - - // select the relations having as source one of the results related to the - // communities - org.apache.spark.sql.Dataset communityResultIds = spark - .read() - .textFile(workingPath + COMMUNITY_RESULT_IDS) - .distinct(); - - Utils - .readPath(spark, inputPath + "/publication", Publication.class) - .filter( - (FilterFunction) p -> !p.getDataInfo().getDeletedbyinference() - && !p.getDataInfo().getInvisible()) - .map((MapFunction) p -> p.getId(), Encoders.STRING()) - .union( - Utils - .readPath(spark, inputPath + "/dataset", Dataset.class) - .filter( - (FilterFunction) p -> !p.getDataInfo().getDeletedbyinference() - && !p.getDataInfo().getInvisible()) - .map((MapFunction) p -> p.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/software", Software.class) - .filter( - (FilterFunction) p -> !p.getDataInfo().getDeletedbyinference() - && !p.getDataInfo().getInvisible()) - .map((MapFunction) p -> p.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) - .filter( - (FilterFunction) p -> !p.getDataInfo().getDeletedbyinference() - && !p.getDataInfo().getInvisible()) - .map((MapFunction) p -> p.getId(), Encoders.STRING())) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .text(workingPath + "/resultIds"); - - org.apache.spark.sql.Dataset resultIds = spark.read().textFile(workingPath + "/resultIds"); - - org.apache.spark.sql.Dataset oksource = communityResultIds - .joinWith(relations, communityResultIds.col("value").equalTo(relations.col("source"))) - .map( - (MapFunction, Relation>) t2 -> t2._2(), - Encoders.bean(Relation.class)); - oksource - .joinWith(resultIds, oksource.col("target").equalTo(resultIds.col("value"))) - .map((MapFunction, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath + "/relation"); - - writeNodes( - spark, inputPath + "/publication", Publication.class, outputPath + "/publication", - outputPath + "/relation", workingPath); - writeNodes( - spark, inputPath + "/dataset", Dataset.class, outputPath + "/dataset", outputPath + "/relation", - workingPath); - writeNodes( - spark, inputPath + "/software", Software.class, outputPath + "/software", outputPath + "/relation", - workingPath); - writeNodes( - spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class, - outputPath + "/otherresearchproduct", outputPath + "/relation", workingPath); - - } - - private static void writeNodes(SparkSession spark, String inputPath, Class clazz, - String outputPath, String relationPath, String workingPath) { - org.apache.spark.sql.Dataset citingRelations = Utils.readPath(spark, relationPath, Relation.class); - org.apache.spark.sql.Dataset result = Utils - .readPath(spark, inputPath, clazz) - .filter( - (FilterFunction) p -> !p.getDataInfo().getDeletedbyinference() && - !p.getDataInfo().getInvisible()); - - // take the distinct result id for source and target of the relations - citingRelations - .flatMap( - (FlatMapFunction) r -> Arrays - .asList(r.getSource(), r.getTarget()) - .iterator(), - Encoders.STRING()) - .distinct() - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .text(workingPath + "/relationIds"); - - org.apache.spark.sql.Dataset relationIds = spark.read().textFile(workingPath + "/relationIds"); - - relationIds - .joinWith(result, relationIds.col("value").equalTo(result.col("id"))) - .map((MapFunction, R>) t2 -> t2._2(), Encoders.bean(clazz)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - } - - private static void writeCommunityRelatedIds(SparkSession spark, String inputPath, - Class clazz, List communityList, String outputPath, String resultType) { - org.apache.spark.sql.Dataset results = Utils - .readPath(spark, inputPath + "/" + resultType, clazz) - .filter( - (FilterFunction) p -> !p.getDataInfo().getDeletedbyinference() && - !p.getDataInfo().getInvisible() && - isRelatedToCommunities(p, communityList)); - results - .map((MapFunction) Result::getId, Encoders.STRING()) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .text(outputPath + COMMUNITY_RESULT_IDS); - -// results -// // .repartition(10000) -// .write() -// .option("compression", "gzip") -// .mode(SaveMode.Append) -// .json(outputPath + "/" + resultType); - - } - - private static boolean isRelatedToCommunities(R p, List communityList) { - return p - .getContext() - .stream() - .anyMatch( - c -> communityList.contains(c.getId()) || - (c.getId().contains("::") - && communityList.contains(c.getId().substring(0, c.getId().indexOf("::"))))); - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpDatasource.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpDatasource.java new file mode 100644 index 0000000..f2e2578 --- /dev/null +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpDatasource.java @@ -0,0 +1,147 @@ +package eu.dnetlib.dhp.oa.graph.dump.skgif; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.skgif.model.Identifier; +import eu.dnetlib.dhp.skgif.model.Prefixes; +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; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +/** + * @author miriam.baglioni + * @Date 21/02/24 + */ +public class DumpDatasource implements Serializable { + private static final Logger log = LoggerFactory.getLogger(DumpDatasource.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + DumpDatasource.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/dump_datasource_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath + "Datasources"); + + mapDatasource(spark, inputPath, outputPath); + }); + } + + private static void mapDatasource(SparkSession spark, String inputPath, String outputPath) { + Utils.readPath(spark, inputPath + "datasource", Datasource.class) + .filter((FilterFunction) d -> !d.getDataInfo().getInvisible() && ! d.getDataInfo().getDeletedbyinference()) + .map((MapFunction) d -> { + eu.dnetlib.dhp.skgif.model.Datasource datasource = new eu.dnetlib.dhp.skgif.model.Datasource(); + datasource.setLocal_identifier(Utils.getIdentifier(Prefixes.DATASOURCE, d.getId())); + datasource.setIdentifiers(d.getPid() + .stream() + .map(p -> Identifier.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList())); + + datasource.setName(d.getOfficialname().getValue()); + datasource.setSubmission_policy_url(d.getSubmissionpolicyurl()); + datasource.setJurisdiction(Optional.ofNullable(d.getJurisdiction()) + .map(v -> v.getClassid()). + orElse(new String())); + datasource.setPreservation_policy_url(d.getPreservationpolicyurl()); + datasource.setVersion_control(d.getVersioncontrol()); + + datasource.setData_source_classification(Optional.ofNullable(d.getEoscdatasourcetype()) + .map(v -> v.getClassname()). + orElse(new String())); + datasource.setResearch_product_type(getEoscProductType(d.getResearchentitytypes())); + datasource.setThematic(d.getThematic()); + datasource.setResearch_product_access_policy(Optional.ofNullable(d.getDatabaseaccesstype()) + .map(v -> getResearchProductAccessPolicy(d.getDatabaseaccesstype().getValue())) + .orElse(new ArrayList<>())); + datasource.setResearch_product_metadata_access_policy(Optional.ofNullable(d.getResearchproductmetadataaccesspolicies()) + .map(v->getResearchProductAccessPolicy(d.getResearchproductmetadataaccesspolicies())) + .orElse(new ArrayList<>())); + return datasource; + }, Encoders.bean(eu.dnetlib.dhp.skgif.model.Datasource.class) ) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(outputPath + "Datasource"); + } + + private static List getResearchProductAccessPolicy(List value) { + + return value.stream().map(v -> getResearchProductAccessPolicy(v)).filter(Objects::nonNull) + .map(v -> v.get(0)).distinct().collect(Collectors.toList()); + } + private static List getResearchProductAccessPolicy(String value) { + // "databaseaccesstype if open => open access (https://vocabularies.coar-repositories.org/access_rights/c_abf2/) + //if restricted => restricted access (https://vocabularies.coar-repositories.org/access_rights/c_16ec/) + //if closed => metadata only access (https://vocabularies.coar-repositories.org/access_rights/c_14cb/) " + switch(value){ + case "open"://(https://vocabularies.coar-repositories.org/access_rights/c_abf2/) + return Arrays.asList("open access"); + case "restricted"://(https://vocabularies.coar-repositories.org/access_rights/c_16ec/) + return Arrays.asList("restricted access"); + case "closed"://(https://vocabularies.coar-repositories.org/access_rights/c_14cb/) + return Arrays.asList("metadata only access"); + default: + return null; + } + } + + private static List getEoscProductType(List researchentitytypes) { + + List eoscProductType = new ArrayList<>(); + if(researchentitytypes != null) { + + if (researchentitytypes.contains("Software")) + eoscProductType.add("Research Software"); + if (researchentitytypes.contains("Research Publications") || researchentitytypes.contains("Literature")) + eoscProductType.add("Research Literature"); + if (researchentitytypes.contains("Research Data")) + eoscProductType.add("Research Data"); + if (researchentitytypes.contains("Organization") || + researchentitytypes.contains("Organizations") || + researchentitytypes.contains("Services") || + researchentitytypes.contains("Projects")) + eoscProductType.add("Other research product"); + } + return eoscProductType; + } +} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpGrant.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpGrant.java new file mode 100644 index 0000000..b63b68f --- /dev/null +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpGrant.java @@ -0,0 +1,162 @@ +package eu.dnetlib.dhp.oa.graph.dump.skgif; + + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.skgif.model.Grant; +import eu.dnetlib.dhp.skgif.model.Identifier; +import eu.dnetlib.dhp.skgif.model.Prefixes; +import eu.dnetlib.dhp.skgif.model.RelationType; +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.api.java.function.MapGroupsFunction; +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; +import org.dom4j.DocumentException; +import org.dom4j.io.SAXReader; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import scala.Tuple2; + + +import java.io.Serializable; +import java.io.StringReader; +import java.util.ArrayList; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +/** + * @author miriam.baglioni + * @Date 22/02/24 + */ +public class DumpGrant implements Serializable { + private static final Logger log = LoggerFactory.getLogger(DumpGrant.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + DumpGrant.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/dump_grant_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath + "Grant"); + + mapGrants(spark, inputPath, outputPath); + }); + } + + private static void mapGrants(SparkSession spark, String inputPath, String outputPath) { + Dataset projects = Utils.readPath(spark, inputPath + "project", Project.class) + .filter((FilterFunction) p -> !p.getDataInfo().getDeletedbyinference() && + !p.getDataInfo().getInvisible()); + Dataset relations = Utils.readPath(spark, inputPath + "relation", Relation.class) + .filter((FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible() && + r.getRelClass().equalsIgnoreCase(RelationType.ORGANIZATION_PARTICIPANT_IN_PROJECT.label)); + projects.joinWith(relations, projects.col("id").equalTo(relations.col("target")), "left") + .groupByKey((MapFunction, String>) t2 -> t2._1().getId(), Encoders.STRING() ) + .mapGroups((MapGroupsFunction, Grant>) (k,v) ->{ + Grant g = new Grant(); + Tuple2 first = v.next(); + g.setLocal_identifier(Utils.getIdentifier(Prefixes.GRANT, k)); + g.setIdentifiers(getProjectIdentifier(first._1())); + g.setTitle(first._1().getTitle().getValue()); + g.setSummary(Optional.ofNullable(first._1().getSummary()) + .map(value->value.getValue()).orElse(new String())); + g.setAcronym(Optional.ofNullable(first._1().getAcronym()) + .map(value->value.getValue()).orElse(new String())); + g.setFunder(getFunderName(first._1().getFundingtree().get(0).getValue())); + // * private String funding_stream;// fundingtree to be used the xpath //funding_level_[n] + g.setFunding_stream(getFundingStream(first._1().getFundingtree().get(0).getValue())); + g.setCurrency(Optional.ofNullable(first._1().getCurrency()) + .map(value -> value.getValue()).orElse(new String())); + g.setFunded_amount(Optional.ofNullable(first._1().getFundedamount()) + .orElse(null)); + g.setKeywords(first._1().getSubjects() + .stream().map(s -> s.getValue()).collect(Collectors.toList())); + g.setStart_date(Optional.ofNullable(first._1().getStartdate()) + .map(value -> value.getValue()).orElse(new String())); + g.setEnd_date(Optional.ofNullable(first._1().getEnddate()) + .map(value -> value.getValue()).orElse(new String())); + g.setWebsite(Optional.ofNullable(first._1().getWebsiteurl()) + .map(value -> value.getValue()).orElse(new String())); + if(Optional.ofNullable(first._2()).isPresent()) { + List relevantOrganizatios = new ArrayList<>(); + relevantOrganizatios.add(Utils.getIdentifier(Prefixes.ORGANIZATION, first._2().getSource())); + v.forEachRemaining(t2 -> relevantOrganizatios.add(Utils.getIdentifier(Prefixes.ORGANIZATION, t2._2().getSource()))); + g.setBeneficiaries(relevantOrganizatios); + } + return g; + } , Encoders.bean(Grant.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(outputPath + "Grant"); + } + + private static String getFundingStream(String fundingtree) throws DocumentException { + final Document doc; + + doc = new SAXReader().read(new StringReader(fundingtree)); + if(Optional.ofNullable(doc.selectNodes("//funding_level_0")).isPresent() && + doc.selectNodes("//funding_level_0").size() > 0) + return ((org.dom4j.Node) (doc.selectNodes("//funding_level_0").get(0))).getText(); + return new String(); + + } + + private static String getFunderName(String fundingtree) throws DocumentException { + final Document doc; + + doc = new SAXReader().read(new StringReader(fundingtree)); + // f.setShortName(((org.dom4j.Node) (doc.selectNodes("//funder/shortname").get(0))).getText()); + return ((org.dom4j.Node) (doc.selectNodes("//funder/name").get(0))).getText(); + //f.setJurisdiction(((org.dom4j.Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); + + } + + private static List getProjectIdentifier(Project project) { + if (project.getPid().size() > 0 ) + return project.getPid().stream().map(p -> Identifier.newInstance(p.getQualifier().getClassid(), p.getValue())).collect(Collectors.toList()); + return new ArrayList<>(); + // private List identifiers;//.schema pid.qualifier.classid identifiers.value pid.value + //identifiers.schema funder acronym to be used the xpath //fundingtree/funder/shortname + //identifiers.value project.code + + + } +} \ No newline at end of file diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpOrganization.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpOrganization.java new file mode 100644 index 0000000..b302f91 --- /dev/null +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpOrganization.java @@ -0,0 +1,110 @@ +package eu.dnetlib.dhp.oa.graph.dump.skgif; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.skgif.model.Identifier; +import eu.dnetlib.dhp.skgif.model.OrganizationTypes; +import eu.dnetlib.dhp.skgif.model.Prefixes; +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; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.Serializable; +import java.util.Optional; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +/** + * @author miriam.baglioni + * @Date 21/02/24 + */ +public class DumpOrganization implements Serializable { + private static final Logger log = LoggerFactory.getLogger(DumpOrganization.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + DumpOrganization.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/dump_organization_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath + "Organization"); + + mapOrganization(spark, inputPath, outputPath); + }); + } + + private static void mapOrganization(SparkSession spark, String inputPath, String outputPath) { + Dataset organizations = Utils.readPath(spark, inputPath + "organization", Organization.class); + organizations.filter((FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() && !o.getDataInfo().getInvisible()) + .map((MapFunction) o -> { + eu.dnetlib.dhp.skgif.model.Organization organization = new eu.dnetlib.dhp.skgif.model.Organization(); + organization.setLocal_identifier(Utils.getIdentifier(Prefixes.ORGANIZATION, o.getId())); + organization.setCountry(Optional.ofNullable(o.getCountry().getClassid()) + .orElse(new String())); + organization.setName(Optional.ofNullable(o.getLegalname().getValue()) + .orElse(new String())); + organization.setShort_name(Optional.ofNullable(o.getLegalshortname()) + .map(v-> v.getValue()) + .orElse(new String())); + organization.setIdentifiers(o.getPid() + .stream() + .map(p -> Identifier.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList())); + organization.setOther_names(o.getAlternativeNames().stream() + .map(a -> a.getValue()) + .collect(Collectors.toList())); + organization.setType(getOrganizationType(o)); + return organization; + } + , Encoders.bean(eu.dnetlib.dhp.skgif.model.Organization.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(outputPath + "Organization"); + } + + private static String getOrganizationType(Organization o) { + if(Optional.ofNullable(o.getEcenterprise()).isPresent() && o.getEcenterprise().getValue().equalsIgnoreCase("true")) + return OrganizationTypes.COMPANY.label; + if(Optional.ofNullable(o.getEchighereducation()).isPresent() && o.getEchighereducation().getValue().equalsIgnoreCase("true")) + return OrganizationTypes.EDUCATION.label; + if(Optional.ofNullable(o.getEcresearchorganization()).isPresent() && o.getEcresearchorganization().getValue().equalsIgnoreCase("true")) + return OrganizationTypes.EDUCATION.label; + if(Optional.ofNullable(o.getEcnonprofit()).isPresent() && o.getEcnonprofit().getValue().equalsIgnoreCase("true")) + return OrganizationTypes.NONPROFIT.label; + + return OrganizationTypes.OTHER.label; + + } +} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpResult.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpResult.java new file mode 100644 index 0000000..3f8f4c4 --- /dev/null +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpResult.java @@ -0,0 +1,394 @@ + +package eu.dnetlib.dhp.oa.graph.dump.skgif; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.*; + +import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.EmitPerManifestation; +import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.PartialResearchProduct; +import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.RelationPerProduct; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.oaf.Datasource; +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.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.*; +import org.apache.spark.sql.Dataset; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.skgif.model.*; +import eu.dnetlib.dhp.skgif.model.AccessRight; +import eu.dnetlib.dhp.utils.DHPUtils; +import scala.Tuple2; + +/** + * @author miriam.baglioni + * @Date 06/02/24 + */ +public class DumpResult implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(DumpResult.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + DumpResult.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/dump_result_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, workingDir + "aggrelation"); + + mapResult(spark, inputPath, workingDir, outputPath); + }); + } + +//per ogni result emetto id + journal se esiste + istanza + hosted by dell'istanza + public static void mapResult(SparkSession spark, String inputPath, + String workingDir, String outputPath) { + + // selection of the relevant relations from result type to other entity. Only teh semantic relevant ones are + // considered + selectRelations(spark, inputPath, workingDir); + + // merge of relations and manifestation for the same result + getRelationAndManifestation(spark, workingDir, inputPath); + + // dump of the result and enrichment with relevant information for relations and manifestations + dumpResult(spark, inputPath, workingDir, outputPath); + + } + + private static void getRelationAndManifestation(SparkSession spark, String workingDir, String inputPath) { + Dataset aggRelations = Utils + .readPath(spark, workingDir + "aggrelation", RelationPerProduct.class); + aggRelations.count(); + ModelSupport.entityTypes + .keySet() + .stream() + .filter(ModelSupport::isResult) + .forEach(e -> { + Utils.removeOutputDir(spark, workingDir + e.name() + "/partialresearchproduct"); + + Dataset datasource = Utils + .readPath(spark, inputPath + "/datasource", Datasource.class) + .filter( + (FilterFunction) d -> Optional.ofNullable(d.getEosctype()).isPresent() && + d.getEoscdatasourcetype().getClassid().equalsIgnoreCase("Journal archive")); + + Dataset man = Utils + .readPath(spark, workingDir + e.name() + "/manifestation", EmitPerManifestation.class); + + Dataset partialResearchProduct = man.joinWith(datasource, man.col("instance.hostedby.key").equalTo(datasource.col("id")), "left") + .groupByKey((MapFunction, String>) t2 -> t2._1().getResultId(), Encoders.STRING()) + .mapGroups((MapGroupsFunction, PartialResearchProduct>) (k, v) -> { + PartialResearchProduct prp = new PartialResearchProduct(); + prp.setResultId(k); + List manifestationList = new ArrayList<>(); + while (v.hasNext()) + manifestationList.add(getManifestation(v.next())); + prp.setManifestations(manifestationList); + return prp; + }, Encoders.bean(PartialResearchProduct.class)); + partialResearchProduct + .joinWith(aggRelations, partialResearchProduct.col("resultId").equalTo(aggRelations.col("resultId")), "left") + .map((MapFunction, PartialResearchProduct>) t2 -> { + PartialResearchProduct prp = t2._1(); + if(Optional.ofNullable(t2._2()).isPresent()){ + prp.setRelated_products(t2._2().getRelatedProduct()); + prp.setRelevant_organizations(t2._2().getOrganizations()); + prp.setFunding(t2._2().getFunding()); + } + return prp; + }, Encoders.bean(PartialResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir + e.name() + "/partialresearchproduct"); + + }); + } + + private static Manifestation getManifestation(Tuple2 t2) { + + // se il lato sinistro c'e' allora ho la biblio e la venue + // se non c'e' allora ho solo gli altri valori + EmitPerManifestation epm = t2._1(); + Manifestation manifestation = new Manifestation(); + manifestation.setProduct_local_type(epm.getInstance().getInstancetype().getClassname()); + manifestation.setProduct_local_type_schema(epm.getInstance().getInstancetype().getSchemename()); + if(Optional.ofNullable(epm.getInstance().getDateofacceptance()).isPresent()) + manifestation + .setDates( + Arrays + .asList( + Dates.newInstance(epm.getInstance().getDateofacceptance().getValue(), "publishing"))); + if (Optional.ofNullable(epm.getInstance().getRefereed()).isPresent()) + switch (epm.getInstance().getRefereed().getClassid()) { + case "0000": + manifestation.setPeer_review(PeerReview.UNAVAILABLE.label); + break; + case "0001": + manifestation.setPeer_review(PeerReview.PEER_REVIEWED.label); + break; + case "0002": + manifestation.setPeer_review(PeerReview.NON_PEER_REVIEWED.label); + break; + } + + manifestation.setMetadata_curation("unavailable"); + if (Optional.ofNullable(epm.getInstance().getAccessright()).isPresent()) + switch (epm.getInstance().getAccessright().getClassid()) { + case "OPEN": + case "OPEN DATA": + case "OPEN SOURCE": + manifestation.setAccess_right(AccessRight.OPEN.label); + break; + case "CLOSED": + manifestation.setAccess_right(AccessRight.CLOSED.label); + break; + case "RESTRICTED": + manifestation.setAccess_right(AccessRight.RESTRICTED.label); + break; + case "EMBARGO": + case "12MONTHS": + case "6MONTHS": + manifestation.setAccess_right(AccessRight.EMBARGO.label); + break; + default: + manifestation.setAccess_right(AccessRight.UNAVAILABLE.label); + + } + manifestation.setLicence(Optional.ofNullable(epm.getInstance().getLicense()) + .map(value -> value.getValue()) + .orElse(null)); + manifestation.setUrl(Optional.ofNullable(epm.getInstance().getUrl()) + .map(value -> value.get(0)) + .orElse(null)); + + if (Optional.ofNullable(epm.getInstance().getPid()).isPresent()) { + manifestation.setPid(epm.getInstance().getPid().get(0).getValue()); + } + if (Optional.ofNullable(t2._2()).isPresent()) { + manifestation.setBiblio(getBiblio(epm)); + if (Optional.ofNullable(t2._2().getJournal().getIssnPrinted()).isPresent()) + manifestation.setVenue(Utils.getIdentifier(Prefixes.VENUE, t2._1().getJournal().getIssnPrinted())); + else if(Optional.ofNullable(t2._2().getJournal().getIssnOnline()).isPresent()) + manifestation.setVenue(Utils.getIdentifier(Prefixes.VENUE, t2._1().getJournal().getIssnOnline())); + } + manifestation + .setHosting_datasource(Utils.getIdentifier(Prefixes.DATASOURCE,epm.getInstance().getHostedby().getKey())); + + return manifestation; + } + +// private static List getManifestationList(Dataset emitformanifestation, +// Dataset datasource) { +// return emitformanifestation +// .joinWith( +// datasource, emitformanifestation +// .col("hostedBy") +// .equalTo(datasource.col("id")), +// "left") +// .map((MapFunction, Manifestation>) t2 -> { +// // se il lato sinistro c'e' allora ho la biblio e la venue +// // se non c'e' allora ho solo gli altri valori +// EmitPerManifestation epm = t2._1(); +// Manifestation manifestation = new Manifestation(); +// manifestation.setProduct_local_type_schema(epm.getInstance().getInstancetype().getClassname()); +// manifestation.setProduct_local_type_schema(epm.getInstance().getInstancetype().getSchemename()); +// manifestation +// .setDates( +// Arrays +// .asList( +// Dates.newInstance(epm.getInstance().getDateofacceptance().getValue(), "publishing"))); +// if (Optional.ofNullable(epm.getInstance().getRefereed()).isPresent()) +// switch (epm.getInstance().getRefereed().getClassid()) { +// case "0000": +// manifestation.setPeer_review(PeerReview.UNAVAILABLE.label); +// break; +// case "0001": +// manifestation.setPeer_review(PeerReview.PEER_REVIEWED.label); +// break; +// case "0002": +// manifestation.setPeer_review(PeerReview.NON_PEER_REVIEWED.label); +// break; +// } +// +// manifestation.setMetadata_curation("unavailable"); +// if (Optional.ofNullable(epm.getInstance().getAccessright()).isPresent()) +// switch (epm.getInstance().getAccessright().getClassid()) { +// case "OPEN": +// case "OPEN DATA": +// case "OPEN SOURCE": +// manifestation.setAccess_right(AccessRight.OPEN.label); +// break; +// case "CLOSED": +// manifestation.setAccess_right(AccessRight.CLOSED.label); +// break; +// case "RESTRICTED": +// manifestation.setAccess_right(AccessRight.RESTRICTED.label); +// break; +// case "EMBARGO": +// case "12MONTHS": +// case "6MONTHS": +// manifestation.setAccess_right(AccessRight.EMBARGO.label); +// break; +// default: +// manifestation.setAccess_right(AccessRight.UNAVAILABLE.label); +// +// } +// manifestation.setLicence(epm.getInstance().getLicense().getValue()); +// manifestation.setUrl(epm.getInstance().getUrl().get(0)); +// if (Optional.ofNullable(epm.getInstance().getPid()).isPresent()) { +// manifestation.setPid(epm.getInstance().getPid().get(0).getValue()); +// } +// if (Optional.ofNullable(t2._2()).isPresent()) +// manifestation.setBiblio(getBiblio(epm)); +// manifestation.setVenue("venue_______::" + DHPUtils.md5(epm.getInstance().getHostedby().getKey())); +// manifestation +// .setHosting_datasource("datasource__::" + DHPUtils.md5(epm.getInstance().getHostedby().getKey())); +// return manifestation; +// }, Encoders.bean(Manifestation.class)) +// .collectAsList(); +// } + + private static Biblio getBiblio(EmitPerManifestation epm) { + Biblio biblio = new Biblio(); + biblio.setEdition(epm.getJournal().getEdition()); + biblio.setIssue(epm.getJournal().getIss()); + biblio.setPublisher(epm.getPublisher()); + biblio.setVolume(epm.getJournal().getVol()); + biblio.setEnd_page(epm.getJournal().getEp()); + biblio.setStart_page(epm.getJournal().getSp()); + return biblio; + } + + private static void dumpResult(SparkSession spark, String inputPath, String workingDir, + String outputPath) { + ModelSupport.entityTypes + .keySet() + .parallelStream() + .filter(ModelSupport::isResult) + .forEach(e -> { + Class resultClazz = ModelSupport.entityTypes.get(e); + Utils.removeOutputDir(spark, workingDir + e.name() + "/researchproduct"); + Dataset results = Utils.readPath(spark, inputPath + e.name(), resultClazz); + Dataset prr = Utils + .readPath(spark, workingDir + e.name() + "/partialresearchproduct", PartialResearchProduct.class); + + results + .joinWith(prr, results.col("id").equalTo(prr.col("resultId")), "left") + .map((MapFunction, ResearchProduct>) t2 -> { + ResearchProduct rp = ResultMapper.map(t2._1()); + if(Optional.ofNullable(t2._2()).isPresent()) { + if(Optional.ofNullable(t2._2().getRelated_products()).isPresent()) + rp.setRelated_products(t2._2().getRelated_products()); + if(Optional.ofNullable(t2._2().getFunding()).isPresent()) + rp.setFunding(t2._2().getFunding()); + if(Optional.ofNullable(t2._2().getRelevant_organizations()).isPresent()) + rp.setRelevant_organizations(t2._2().getRelevant_organizations()); + if(Optional.ofNullable(t2._2().getManifestations()).isPresent()) + rp.setManifestations(t2._2().getManifestations()); + } + return rp; + }, Encoders.bean(ResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir + e.name() + "/researchproduct"); + + }); + Dataset researchProducts = spark.emptyDataset(Encoders.bean(ResearchProduct.class)); + for(EntityType e : ModelSupport.entityTypes.keySet()) { + if(ModelSupport.isResult(e)) + researchProducts = researchProducts.union(Utils.readPath(spark,workingDir + e.name() + "/researchproduct", ResearchProduct.class)); + } + researchProducts + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(outputPath + "ResearchProduct"); + + } + + private static void selectRelations(SparkSession spark, String inputPath, String workingDir) { + Dataset relation = Utils.readPath(spark, + inputPath + "relation", Relation.class) + .filter((FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible()) + .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase(RelationType.RESULT_AFFILIATIED_TO_ORGANIZATION.label) || + r.getRelClass().equalsIgnoreCase(RelationType.RESULT_OUTCOME_FUNDING.label) || + r.getRelClass().equalsIgnoreCase(RelationType.SUPPLEMENT.label) || + r.getRelClass().equalsIgnoreCase(RelationType.DOCUMENTS.label)|| + r.getRelClass().equalsIgnoreCase(RelationType.PART.label) || + r.getRelClass().equalsIgnoreCase(RelationType.VERSION.label) || + r.getRelClass().equalsIgnoreCase(RelationType.CITATION.label)); + + relation + .groupByKey((MapFunction) r -> r.getSource(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, v) -> { + RelationPerProduct rpp = new RelationPerProduct(); + rpp.setResultId(k); + Map> remainignRelations = new HashMap<>(); + while (v.hasNext()) { + Relation rel = v.next(); + String target = rel.getTarget(); + String relClass = rel.getRelClass(); + switch (rel.getRelClass().toLowerCase()) { + case "hasauthorinstitution": + rpp.getOrganizations().add(Utils.getIdentifier(Prefixes.ORGANIZATION, target)); + break; + case "isproducedby": + rpp.getFunding().add(Utils.getIdentifier(Prefixes.GRANT ,target)); + break; + default: + if (!remainignRelations.keySet().contains(relClass)) + remainignRelations.put(relClass, new ArrayList<>()); + remainignRelations.get(relClass).add(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, target)); + } + } + for (String key : remainignRelations.keySet()) + rpp.getRelatedProduct().add(Relations.newInstance(key, remainignRelations.get(key))); + return rpp; + }, Encoders.bean(RelationPerProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir + "/aggrelation"); + } + +} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpVenue.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpVenue.java new file mode 100644 index 0000000..648b0a1 --- /dev/null +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpVenue.java @@ -0,0 +1,156 @@ +package eu.dnetlib.dhp.oa.graph.dump.skgif; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.skgif.model.*; +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.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +/** + * @author miriam.baglioni + * @Date 21/02/24 + */ +public class DumpVenue implements Serializable { + private static final Logger log = LoggerFactory.getLogger(DumpVenue.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + DumpVenue.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/dump_datasource_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath + "Venue"); + + mapDatasource(spark, inputPath, outputPath, workingDir); + }); + } + + private static void mapDatasource(SparkSession spark, String inputPath, String outputPath, String workingDir) { + Utils.readPath(spark, inputPath + "datasource", Datasource.class) + .filter((FilterFunction) d -> !d.getDataInfo().getInvisible() && ! d.getDataInfo().getDeletedbyinference() + && d.getEoscdatasourcetype().getClassid().equalsIgnoreCase("Journal archive")) + .map((MapFunction) d -> { + Venue venue = new Venue(); + if(Optional.ofNullable(d.getJournal().getIssnPrinted()).isPresent()) + venue.setLocal_identifier(Utils.getIdentifier(Prefixes.VENUE, d.getJournal().getIssnPrinted())); + else if(Optional.ofNullable(d.getJournal().getIssnOnline()).isPresent()) + venue.setLocal_identifier(Utils.getIdentifier(Prefixes.VENUE, d.getJournal().getIssnOnline())); + venue.setIdentifiers(getVenueIdentifier(d.getJournal())); + venue.setName(d.getOfficialname().getValue()); + venue.setType(VenueType.JOURNAL.label); + //todo add map for publisher. Get from results? + venue.setPublisher("find it from result"); + venue.setAcronym(null); + venue.setSeries(null); + venue.setIs_currently_full_oa(null); + venue.setCreation_date(null); + venue.setContributions(null); + return venue; + }, Encoders.bean(Venue.class) ) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingDir + "Venues"); + + Utils.readPath(spark, workingDir + "Venues", Venue.class) + .groupByKey((MapFunction)v -> v.getLocal_identifier() , Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k,v) -> v.next(), Encoders.bean(Venue.class) ) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(outputPath + "Venues"); + } + + private static List getVenueIdentifier(Journal journal) { + List identifiers = new ArrayList<>(); + if (Optional.ofNullable((journal.getIssnOnline())).isPresent()) + identifiers.add(Identifier.newInstance(VenueIdentifierType.EISSN.label, journal.getIssnOnline())); + if(Optional.ofNullable(journal.getIssnPrinted()).isPresent()) + identifiers.add(Identifier.newInstance(VenueIdentifierType.ISSN.label, journal.getIssnPrinted())); + if (Optional.ofNullable(journal.getIssnLinking()).isPresent()) + identifiers.add(Identifier.newInstance(VenueIdentifierType.LISSN.label, journal.getIssnLinking())); + return identifiers; + } + + private static List getResearchProductAccessPolicy(List value) { + + return value.stream().map(v -> getResearchProductAccessPolicy(v)).filter(Objects::nonNull) + .map(v -> v.get(0)).distinct().collect(Collectors.toList()); + } + private static List getResearchProductAccessPolicy(String value) { + // "databaseaccesstype if open => open access (https://vocabularies.coar-repositories.org/access_rights/c_abf2/) + //if restricted => restricted access (https://vocabularies.coar-repositories.org/access_rights/c_16ec/) + //if closed => metadata only access (https://vocabularies.coar-repositories.org/access_rights/c_14cb/) " + switch(value){ + case "open"://(https://vocabularies.coar-repositories.org/access_rights/c_abf2/) + return Arrays.asList("open access"); + case "restricted"://(https://vocabularies.coar-repositories.org/access_rights/c_16ec/) + return Arrays.asList("restricted access"); + case "closed"://(https://vocabularies.coar-repositories.org/access_rights/c_14cb/) + return Arrays.asList("metadata only access"); + default: + return null; + } + } + + private static List getEoscProductType(List researchentitytypes) { + + List eoscProductType = new ArrayList<>(); + if(researchentitytypes != null) { + + if (researchentitytypes.contains("Software")) + eoscProductType.add("Research Software"); + if (researchentitytypes.contains("Research Publications") || researchentitytypes.contains("Literature")) + eoscProductType.add("Research Literature"); + if (researchentitytypes.contains("Research Data")) + eoscProductType.add("Research Data"); + if (researchentitytypes.contains("Organization") || + researchentitytypes.contains("Organizations") || + researchentitytypes.contains("Services") || + researchentitytypes.contains("Projects")) + eoscProductType.add("Other research product"); + } + return eoscProductType; + } +} diff --git a/dump/src/main/java/eu/dnetlib/dhp/skgif/EmitFromResults.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/EmitFromResults.java similarity index 85% rename from dump/src/main/java/eu/dnetlib/dhp/skgif/EmitFromResults.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/EmitFromResults.java index 5c456ad..1cf1c1a 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/skgif/EmitFromResults.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/EmitFromResults.java @@ -1,13 +1,14 @@ -package eu.dnetlib.dhp.skgif; +package eu.dnetlib.dhp.oa.graph.dump.skgif; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.skgif.Utils.getOrcid; import java.io.Serializable; import java.util.*; import java.util.stream.Collectors; +import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.EmitPerManifestation; +import eu.dnetlib.dhp.schema.oaf.Datasource; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -18,21 +19,16 @@ 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.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.oa.graph.dump.Utils; + import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.skgif.beans.EmitPerManifestation; import eu.dnetlib.dhp.skgif.model.*; -import eu.dnetlib.dhp.skgif.model.AccessRight; import eu.dnetlib.dhp.utils.DHPUtils; -import scala.Array; import scala.Tuple2; /** @@ -46,7 +42,7 @@ public class EmitFromResults implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( - PrepareResultRelation.class + EmitFromResults.class .getResourceAsStream( "/eu/dnetlib/dhp/oa/graph/dump/emit_biblio_parameters.json")); @@ -100,17 +96,17 @@ public class EmitFromResults implements Serializable { (FlatMapFunction) r -> r .getSubject() .stream() - .filter(s -> !s.getQualifier().getClassid().equalsIgnoreCase("keyword")) + .filter(s -> s.getQualifier().getClassid().equalsIgnoreCase("fos") || s.getQualifier().getClassid().equalsIgnoreCase("sdg")) .map(s -> { Topic t = new Topic(); t .setLocal_identifier( - "topic_______::" + DHPUtils.md5(s.getQualifier().getSchemeid() + s.getValue())); + Utils.getIdentifier(Prefixes.TOPIC ,s.getQualifier().getClassid() + s.getValue())); t .setIdentifiers( Arrays .asList( - Identifier.newInstance(s.getQualifier().getSchemeid(), s.getValue()))); + Identifier.newInstance(s.getQualifier().getClassid(), s.getValue()))); t.setName(s.getValue()); return t; }) @@ -149,18 +145,18 @@ public class EmitFromResults implements Serializable { .flatMap((FlatMapFunction) r -> { List authors = new ArrayList<>(); - if (Optional.ofNullable(r.getAuthor()).isPresent()) { + if (Optional.ofNullable(r.getAuthor()).isPresent() && r.getAuthor().size() > 0) { int count = 0; for (Author a : r.getAuthor()) { count += 1; Persons p = new Persons(); - p.setFamilyName(a.getSurname()); - p.setGivenName(a.getName()); + p.setFamily_name(a.getSurname()); + p.setGiven_name(a.getName()); String identifier = new String(); if (Optional.ofNullable(a.getPid()).isPresent()) { - Tuple2 orcid = getOrcid(a.getPid()); + Tuple2 orcid = eu.dnetlib.dhp.oa.graph.dump.skgif.Utils.getOrcid(a.getPid()); if (orcid != null) { - identifier = "person______::" + DHPUtils.md5(orcid._1() + orcid._2()); + identifier = Utils.getIdentifier(Prefixes.PERSON, orcid._1() + orcid._2()); if (orcid._2()) p .setIdentifiers( @@ -168,17 +164,18 @@ public class EmitFromResults implements Serializable { else p .setIdentifiers( - Arrays.asList(Identifier.newInstance("orcid_pending", orcid._1()))); + Arrays.asList(Identifier.newInstance("inferred_orcid", orcid._1()))); } else { if (Optional.ofNullable(a.getRank()).isPresent()) { - identifier = "tmp_person__::" + DHPUtils.md5(r.getId() + a.getRank()); + identifier = Utils.getIdentifier(Prefixes.TEMPORARY_PERSON,r.getId() + a.getRank()); } else { - identifier = "tmp_person__::" + DHPUtils.md5(r.getId() + count); + identifier = Utils.getIdentifier(Prefixes.TEMPORARY_PERSON,r.getId() + count); } } } - p.setLocalIdentifier(identifier); + p.setLocal_identifier(identifier); + authors.add(p); } } @@ -199,7 +196,7 @@ public class EmitFromResults implements Serializable { .union(Utils.readPath(spark, workingDir + entityType.name() + "/person", Persons.class)); } persons - .groupByKey((MapFunction) p -> p.getLocalIdentifier(), Encoders.STRING()) + .groupByKey((MapFunction) p -> p.getLocal_identifier(), Encoders.STRING()) .mapGroups((MapGroupsFunction) (k, v) -> v.next(), Encoders.bean(Persons.class)) .write() .mode(SaveMode.Overwrite) diff --git a/dump/src/main/java/eu/dnetlib/dhp/skgif/ResultMapper.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/ResultMapper.java similarity index 63% rename from dump/src/main/java/eu/dnetlib/dhp/skgif/ResultMapper.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/ResultMapper.java index dad6108..3d358f2 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/skgif/ResultMapper.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/ResultMapper.java @@ -1,30 +1,17 @@ -package eu.dnetlib.dhp.skgif; - -import static eu.dnetlib.dhp.oa.graph.dump.ResultMapper.*; +package eu.dnetlib.dhp.oa.graph.dump.skgif; import java.io.Serializable; -import java.net.MalformedURLException; -import java.net.URL; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Optional; +import java.util.*; import java.util.stream.Collectors; -import javax.management.RuntimeErrorException; -import eu.dnetlib.dhp.oa.graph.dump.csv.AuthorResult; -import eu.dnetlib.dhp.oa.model.ResultPid; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.skgif.exception.NoAllowedTypeException; -import eu.dnetlib.dhp.skgif.exception.NoTitleFoundException; +import eu.dnetlib.dhp.oa.graph.dump.skgif.exception.NoAllowedTypeException; +import eu.dnetlib.dhp.oa.graph.dump.skgif.exception.NoTitleFoundException; import eu.dnetlib.dhp.skgif.model.*; -import eu.dnetlib.dhp.skgif.model.AccessRight; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; -import scala.reflect.internal.Trees; /** * @author miriam.baglioni @@ -41,7 +28,7 @@ public class ResultMapper implements Serializable { Optional ort = Optional.ofNullable(input.getResulttype()); if (ort.isPresent()) { try { - out.setLocalIdentifier("product___::" + DHPUtils.md5(input.getId())); + out.setLocal_identifier(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, input.getId())); mapPid(out, input); mapTitle(out, input); mapAbstract(out, input); @@ -50,7 +37,7 @@ public class ResultMapper implements Serializable { mapContribution(out, input); //The manifestation will be included extending the result as well as the relations to funder, organization and other results - + return out; } catch (ClassCastException cce) { return null; } @@ -63,23 +50,28 @@ public class ResultMapper implements Serializable { private static void mapContribution(ResearchProduct out, E input) { if (Optional.ofNullable(input.getAuthor()).isPresent()) { int count = 0; + List contributionList = new ArrayList<>(); for (Author a : input.getAuthor()) { count += 1; Contribution contribution = new Contribution(); - if (Optional.ofNullable(a.getPid()).isPresent()) { Tuple2 orcid = Utils.getOrcid(a.getPid()); if (orcid != null) { - contribution.setPerson("person______::" + DHPUtils.md5(orcid._1() + orcid._2())); + contribution.setPerson(Utils.getIdentifier(Prefixes.PERSON, orcid._1() + orcid._2())); } else { if (Optional.ofNullable(a.getRank()).isPresent()) { - contribution.setPerson("person______::" + DHPUtils.md5(input.getId() + a.getRank())); + contribution.setPerson(Utils.getIdentifier(Prefixes.TEMPORARY_PERSON,input.getId() + a.getRank())); } else { - contribution.setPerson("tmp_person__::" + DHPUtils.md5(input.getId() + count)); + contribution.setPerson(Utils.getIdentifier(Prefixes.TEMPORARY_PERSON,input.getId() + count)); } } - } + if(Optional.ofNullable(a.getRank()).isPresent()){ + contribution.setRank(a.getRank()); + } + + contributionList.add(contribution); } + out.setContributions(contributionList); } } @@ -91,37 +83,38 @@ public class ResultMapper implements Serializable { input .getSubject() .stream() - .filter(s -> !s.getQualifier().getClassid().equalsIgnoreCase("keyword")) + .filter(s -> s.getQualifier().getClassid().equalsIgnoreCase("fos") || + s.getQualifier().getClassid().equalsIgnoreCase("sdg")) .map(s -> { ResultTopic topic = new ResultTopic(); - topic.setTopic(getIdentifier(s)); - Provenance provenance = new Provenance(); - provenance.setTrust(Double.valueOf(s.getDataInfo().getTrust())); - provenance.setType(s.getDataInfo().getInferenceprovenance()); - topic.setProvenance(provenance); + topic.setTopic(Utils.getIdentifier(Prefixes.TOPIC, s.getQualifier().getClassid() + s.getValue())); + if(Optional.ofNullable(s.getDataInfo()).isPresent()){ + Provenance provenance = new Provenance(); + provenance.setTrust(Double.valueOf(s.getDataInfo().getTrust())); + provenance.setType(s.getDataInfo().getInferenceprovenance()); + topic.setProvenance(provenance); + } + return topic; }) .collect(Collectors.toList())); } } - private static String getIdentifier(StructuredProperty s) { - return "topic_______::" + DHPUtils.md5(s.getQualifier().getClassid() + s.getValue()); - } private static void mapType(ResearchProduct out, E input) throws NoAllowedTypeException { switch (input.getResulttype().getClassid()) { case "publication": - out.setProductType(ResearchTypes.LITERATURE.label); + out.setProduct_type(ResearchTypes.LITERATURE.label); break; case "dataset": - out.setProductType(ResearchTypes.RESEARCH_DATA.label); + out.setProduct_type(ResearchTypes.RESEARCH_DATA.label); break; case "software": - out.setProductType(ResearchTypes.RESEARCH_SOFTWARE.label); + out.setProduct_type(ResearchTypes.RESEARCH_SOFTWARE.label); break; case "other": - out.setProductType(ResearchTypes.OTHER.label); + out.setProduct_type(ResearchTypes.OTHER.label); break; default: throw new ClassCastException("Result type not present or not allowed"); @@ -140,7 +133,7 @@ public class ResultMapper implements Serializable { p -> { Identifier identifier = new Identifier(); identifier.setValue(p.getValue()); - identifier.setScheme(p.getQualifier().getSchemeid()); + identifier.setScheme(p.getQualifier().getClassid()); return identifier; }) .collect(Collectors.toList()))); @@ -155,7 +148,7 @@ public class ResultMapper implements Serializable { .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) .collect(Collectors.toList()); if (!iTitle.isEmpty()) { - out.setTitles(Arrays.asList(iTitle.get(0).getValue())); + out.setTitles(Collections.singletonMap("none",Arrays.asList(iTitle.get(0).getValue()))); return; } @@ -165,7 +158,7 @@ public class ResultMapper implements Serializable { .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) .collect(Collectors.toList()); if (!iTitle.isEmpty()) { - out.setTitles(Arrays.asList(iTitle.get(0).getValue())); + out.setTitles(Collections.singletonMap("none",Arrays.asList(iTitle.get(0).getValue()))); } } @@ -176,6 +169,6 @@ public class ResultMapper implements Serializable { Optional .ofNullable(input.getDescription()) .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); - out.setAbstracts(descriptionList); + out.setAbstracts(Collections.singletonMap("none",descriptionList)); } } diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/Utils.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/Utils.java new file mode 100644 index 0000000..8990760 --- /dev/null +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/Utils.java @@ -0,0 +1,64 @@ + +package eu.dnetlib.dhp.oa.graph.dump.skgif; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.skgif.model.Prefixes; +import eu.dnetlib.dhp.utils.DHPUtils; +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.SparkSession; +import scala.Tuple2; + +/** + * @author miriam.baglioni + * @Date 16/02/24 + */ +public class Utils implements Serializable { + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private Utils() { + } + + public static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + public static Tuple2 getOrcid(List pid) { + if (!Optional.ofNullable(pid).isPresent()) + return null; + if (pid.size() == 0) + return null; + for (StructuredProperty p : pid) { + if (p.getQualifier().getClassid().equals(ModelConstants.ORCID)) { + return new Tuple2<>(p.getValue(), Boolean.TRUE); + } + } + for (StructuredProperty p : pid) { + if (p.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING)) { + return new Tuple2<>(p.getValue(), Boolean.FALSE); + } + } + return null; + } + + public static String getIdentifier(Prefixes entity, String id){ + return entity.label + DHPUtils.md5(id); + + } +} diff --git a/dump/src/main/java/eu/dnetlib/dhp/skgif/beans/EmitPerManifestation.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/beans/EmitPerManifestation.java similarity index 95% rename from dump/src/main/java/eu/dnetlib/dhp/skgif/beans/EmitPerManifestation.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/beans/EmitPerManifestation.java index 6dc978f..a3345ff 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/skgif/beans/EmitPerManifestation.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/beans/EmitPerManifestation.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.skgif.beans; +package eu.dnetlib.dhp.oa.graph.dump.skgif.beans; import java.io.Serializable; diff --git a/dump/src/main/java/eu/dnetlib/dhp/skgif/beans/PartialResearchProduct.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/beans/PartialResearchProduct.java similarity index 86% rename from dump/src/main/java/eu/dnetlib/dhp/skgif/beans/PartialResearchProduct.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/beans/PartialResearchProduct.java index 3c52222..a4cd7cb 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/skgif/beans/PartialResearchProduct.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/beans/PartialResearchProduct.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.skgif.beans; +package eu.dnetlib.dhp.oa.graph.dump.skgif.beans; import eu.dnetlib.dhp.skgif.model.ResearchProduct; diff --git a/dump/src/main/java/eu/dnetlib/dhp/skgif/beans/RelationPerProduct.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/beans/RelationPerProduct.java similarity index 95% rename from dump/src/main/java/eu/dnetlib/dhp/skgif/beans/RelationPerProduct.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/beans/RelationPerProduct.java index ba7fcca..e164f54 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/skgif/beans/RelationPerProduct.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/beans/RelationPerProduct.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.skgif.beans; +package eu.dnetlib.dhp.oa.graph.dump.skgif.beans; import java.io.Serializable; import java.util.ArrayList; diff --git a/dump/src/main/java/eu/dnetlib/dhp/skgif/exception/NoAllowedTypeException.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/exception/NoAllowedTypeException.java similarity index 91% rename from dump/src/main/java/eu/dnetlib/dhp/skgif/exception/NoAllowedTypeException.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/exception/NoAllowedTypeException.java index fac91bf..f6c8196 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/skgif/exception/NoAllowedTypeException.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/exception/NoAllowedTypeException.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.skgif.exception; +package eu.dnetlib.dhp.oa.graph.dump.skgif.exception; public class NoAllowedTypeException extends Exception { public NoAllowedTypeException() { diff --git a/dump/src/main/java/eu/dnetlib/dhp/skgif/exception/NoTitleFoundException.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/exception/NoTitleFoundException.java similarity index 91% rename from dump/src/main/java/eu/dnetlib/dhp/skgif/exception/NoTitleFoundException.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/exception/NoTitleFoundException.java index 5cc7591..4c7a936 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/skgif/exception/NoTitleFoundException.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/exception/NoTitleFoundException.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.skgif.exception; +package eu.dnetlib.dhp.oa.graph.dump.skgif.exception; public class NoTitleFoundException extends Exception { public NoTitleFoundException() { diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/MasterDuplicate.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/MasterDuplicate.java deleted file mode 100644 index 5fed3cd..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/MasterDuplicate.java +++ /dev/null @@ -1,29 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset; - -import java.io.Serializable; - -/** - * @author miriam.baglioni - * @Date 21/07/22 - */ -public class MasterDuplicate implements Serializable { - private String duplicate; - private String master; - - public String getDuplicate() { - return duplicate; - } - - public void setDuplicate(String duplicate) { - this.duplicate = duplicate; - } - - public String getMaster() { - return master; - } - - public void setMaster(String master) { - this.master = master; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/ReadMasterDuplicateFromDB.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/ReadMasterDuplicateFromDB.java deleted file mode 100644 index d38df32..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/ReadMasterDuplicateFromDB.java +++ /dev/null @@ -1,97 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset; - -import java.io.BufferedWriter; -import java.io.Closeable; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.nio.charset.StandardCharsets; -import java.sql.ResultSet; -import java.sql.SQLException; -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 org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.mongodb.DBCursor; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.DbClient; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; - -public class ReadMasterDuplicateFromDB { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static final String QUERY = "SELECT id as master, duplicate FROM dsm_dedup_services; "; - - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - ReadMasterDuplicateFromDB.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/datasourcemaster_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 String hdfsNameNode = parser.get("hdfsNameNode"); - - Configuration conf = new Configuration(); - conf.set("fs.defaultFS", hdfsNameNode); - - FileSystem fileSystem = FileSystem.get(conf); - Path hdfsWritePath = new Path(hdfsPath); - FSDataOutputStream fsDataOutputStream = fileSystem.create(hdfsWritePath); - - execute(dbUrl, dbUser, dbPassword, fsDataOutputStream); - - } - - private static void execute(String dbUrl, String dbUser, String dbPassword, FSDataOutputStream fos) { - try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) { - try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8))) { - dbClient.processResults(QUERY, rs -> writeMap(datasourceMasterMap(rs), writer)); - } - - } catch (IOException e) { - e.printStackTrace(); - } - } - - public static MasterDuplicate datasourceMasterMap(ResultSet rs) { - try { - MasterDuplicate dm = new MasterDuplicate(); - String duplicate = rs.getString("duplicate"); - dm.setDuplicate(OafMapperUtils.createOpenaireId(10, duplicate, true)); - String master = rs.getString("master"); - dm.setMaster(OafMapperUtils.createOpenaireId(10, master, true)); - - return dm; - - } catch (final SQLException e) { - throw new RuntimeException(e); - } - } - - protected static void writeMap(final MasterDuplicate dm, BufferedWriter writer) { - try { - writer.write(OBJECT_MAPPER.writeValueAsString(dm)); - writer.newLine(); - } catch (final IOException e) { - throw new RuntimeException(e); - } - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkDumpResult.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkDumpResult.java deleted file mode 100644 index 2815468..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkDumpResult.java +++ /dev/null @@ -1,199 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.io.StringReader; -import java.util.*; -import java.util.stream.Collectors; - -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.Document; -import org.dom4j.DocumentException; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; -import com.jayway.jsonpath.DocumentContext; -import com.jayway.jsonpath.JsonPath; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.subset.criteria.VerbResolver; -import eu.dnetlib.dhp.oa.graph.dump.subset.criteria.VerbResolverFactory; -import eu.dnetlib.dhp.oa.graph.dump.subset.selectionconstraints.Param; -import eu.dnetlib.dhp.oa.graph.dump.subset.selectionconstraints.SelectionConstraints; -import eu.dnetlib.dhp.oa.model.graph.*; -import eu.dnetlib.dhp.schema.oaf.*; - -/** - * Spark Job that fires the dump for the entities - */ -public class SparkDumpResult implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkDumpResult.class); - private static final VerbResolver resolver = VerbResolverFactory.newInstance(); - public static final String COMPRESSION = "compression"; - public static final String GZIP = "gzip"; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpResult.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultType = parser.get("resultType"); - log.info("resultType: {}", resultType); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - Optional pathString = Optional.ofNullable(parser.get("pathMap")); - HashMap pathMap = null; - if (pathString.isPresent()) { - pathMap = new Gson().fromJson(parser.get("pathMap"), HashMap.class); - log.info("pathMap: {}", new Gson().toJson(pathMap)); - } - - final Optional parameter = Optional.ofNullable(parser.get("selectionCriteria")); - SelectionConstraints selectionConstraints = null; - if (parameter.isPresent()) { - selectionConstraints = new ObjectMapper().readValue(parameter.get(), SelectionConstraints.class); - selectionConstraints.addResolver(resolver); - - } - - Class inputClazz = (Class) Class - .forName(resultClassName); - - run( - isSparkSessionManaged, inputPath, outputPath, pathMap, selectionConstraints, inputClazz, - resultType); - - } - - private static void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, - HashMap pathMap, SelectionConstraints selectionConstraints, - Class inputClazz, String resultType) { - SparkConf conf = new SparkConf(); - - HashMap finalPathMap = pathMap; - SelectionConstraints finalSelectionConstraints = selectionConstraints; - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath + "/original/" + resultType); - Utils.removeOutputDir(spark, outputPath + "/dump/" + resultType); - resultDump( - spark, inputPath, outputPath, inputClazz, finalPathMap, - finalSelectionConstraints, resultType); - }); - - } - - public static void resultDump( - SparkSession spark, - String inputPath, - String outputPath, - Class inputClazz, - Map pathMap, - SelectionConstraints selectionConstraints, - String resultType) { - - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) value -> filterResult( - value, pathMap, selectionConstraints, inputClazz, resultType), - Encoders.bean(inputClazz)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/original/" + resultType); - - Utils - .readPath(spark, outputPath + "/original/" + resultType, inputClazz) - .map( - (MapFunction) value -> (GraphResult) ResultMapper - .map( - value, null, - Constants.DUMPTYPE.COMPLETE.getType()), - Encoders.bean(GraphResult.class)) - .map((MapFunction) r -> new ObjectMapper().writeValueAsString(r), Encoders.STRING()) - .write() - .mode(SaveMode.Overwrite) - .option(COMPRESSION, GZIP) - .text(outputPath + "/dump/" + resultType); - - } - - private static I filterResult(I value, Map pathMap, - SelectionConstraints selectionConstraints, Class inputClazz, - String resultType) { - Optional odInfo = Optional.ofNullable(value.getDataInfo()); - - if (Boolean.FALSE.equals(odInfo.isPresent())) { - return null; - } - if (Boolean.TRUE.equals(odInfo.get().getDeletedbyinference()) - || Boolean.TRUE.equals(odInfo.get().getInvisible())) { - return null; - } - - if (!isCompatible(value.getResulttype().getClassid(), resultType)) { - return null; - } - - if (selectionConstraints != null) { - Param param = new Param(); - String json = new Gson().toJson(value, inputClazz); - DocumentContext jsonContext = JsonPath.parse(json); - - for (String key : pathMap.keySet()) { - try { - param.insert(key, jsonContext.read(pathMap.get(key))); - } catch (com.jayway.jsonpath.PathNotFoundException e) { - param.insert(key, new ArrayList<>()); - } - } - if (!selectionConstraints.verifyCriteria(param)) { - return null; - } - } - - return value; - } - - private static boolean isCompatible(String classid, String resultType) { - return (classid.equals(resultType) || (classid.equals("other") && resultType.equals("otherresearchproduct"))); - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectSubset.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectSubset.java deleted file mode 100644 index 5c02498..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectSubset.java +++ /dev/null @@ -1,328 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; - -import javax.print.attribute.standard.MediaSize; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.*; -import org.apache.spark.sql.*; -import org.apache.spark.sql.Dataset; -import org.jetbrains.annotations.NotNull; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.graph.GraphResult; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import eu.dnetlib.dhp.utils.DHPUtils; -import scala.Function1; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 11/11/22 - */ -public class SparkSelectSubset implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkSelectSubset.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSelectSubset.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - Optional rs = Optional.ofNullable(parser.get("removeSet")); - final Set removeSet = new HashSet<>(); - if (rs.isPresent()) { - Collections.addAll(removeSet, rs.get().split(";")); - } - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - selectSubset(spark, inputPath, outputPath, removeSet); - - }); - - } - - private static void selectSubset(SparkSession spark, String inputPath, String outputPath, Set removeSet) { - Dataset relation = Utils - .readPath(spark, inputPath + "/relation", Relation.class) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() - && !removeSet.contains(r.getRelClass())); - - Dataset resultIds = Utils - .readPath(spark, outputPath + "/original/publication", Publication.class) - - .map((MapFunction) p -> p.getId(), Encoders.STRING()) - .union( - Utils - .readPath(spark, outputPath + "/original/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class) - - .map((MapFunction) d -> d.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, outputPath + "/original/software", Software.class) - - .map((MapFunction) s -> s.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, outputPath + "/original/otherresearchproduct", OtherResearchProduct.class) - - .map((MapFunction) o -> o.getId(), Encoders.STRING())); - - // select result -> result relations - Dataset relResultResult = relation - .joinWith(resultIds, relation.col("source").equalTo(resultIds.col("value"))) - .map((MapFunction, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class)); - - relResultResult - .joinWith(resultIds, relResultResult.col("target").equalTo(resultIds.col("value"))) - .map((MapFunction, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath + "/original/relation"); - - // save the relations among other entities and the results - Dataset otherIds = Utils - .readPath(spark, inputPath + "/organization", Organization.class) - .filter((FilterFunction) e -> !e.getDataInfo().getDeletedbyinference()) - .map((MapFunction) o -> o.getId(), Encoders.STRING()) - .union( - Utils - .readPath(spark, inputPath + "/project", Project.class) - .filter((FilterFunction) e -> !e.getDataInfo().getDeletedbyinference()) - .map((MapFunction) p -> p.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/datasource", Datasource.class) - .filter((FilterFunction) e -> !e.getDataInfo().getDeletedbyinference()) - .map((MapFunction) d -> d.getId(), Encoders.STRING())); - - Dataset relResultOther = relation - .joinWith(resultIds, relation.col("source").equalTo(resultIds.col("value"))) - .map((MapFunction, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class)); - - relResultOther - .joinWith(otherIds, relResultOther.col("target").equalTo(otherIds.col("value"))) - .map((MapFunction, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class)) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(outputPath + "/original/relation"); - - Dataset relOtherResult = relation - .joinWith(resultIds, relation.col("target").equalTo(resultIds.col("value"))) - .map((MapFunction, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class)); - - relOtherResult - .joinWith(otherIds, relOtherResult.col("source").equalTo(otherIds.col("value"))) - .map((MapFunction, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class)) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(outputPath + "/original/relation"); - - Dataset relAll = Utils - .readPath(spark, outputPath + "/original/relation", Relation.class) - .flatMap( - (FlatMapFunction) r -> Arrays.asList(r.getSource(), r.getTarget()).iterator(), - Encoders.STRING()) - .distinct(); - - // Save the entities in relations with at least one result - Dataset organization = Utils - .readPath(spark, inputPath + "/organization", Organization.class) - .filter((FilterFunction) o -> !o.getDataInfo().getDeletedbyinference()); - organization - .joinWith(relAll, organization.col("id").equalTo(relAll.col("value"))) - .map( - (MapFunction, Organization>) t2 -> t2._1(), - Encoders.bean(Organization.class)) - .groupByKey((MapFunction) v -> v.getId(), Encoders.STRING()) - .mapGroups( - (MapGroupsFunction) (k, it) -> it.next(), - Encoders.bean(Organization.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/original/organization"); - - Dataset datasource = Utils - .readPath(spark, inputPath + "/datasource", Datasource.class) - .filter((FilterFunction) d -> !d.getDataInfo().getDeletedbyinference()); - datasource - .joinWith(relAll, datasource.col("id").equalTo(relAll.col("value"))) - .map((MapFunction, Datasource>) t2 -> t2._1(), Encoders.bean(Datasource.class)) - .groupByKey((MapFunction) v -> v.getId(), Encoders.STRING()) - .mapGroups( - (MapGroupsFunction) (k, it) -> it.next(), - Encoders.bean(Datasource.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/original/datasource"); - - // plus we need to dump all the datasource in collectedfrom hostedby - Dataset cfhb_orig = Utils - .readPath(spark, outputPath + "/original/publication", Publication.class) - .flatMap( - (FlatMapFunction) p -> { - List ret = new ArrayList<>(); - p.getInstance().stream().forEach(i -> { - if (Optional.ofNullable(i.getHostedby()).isPresent() - && Optional.ofNullable(i.getHostedby().getKey()).isPresent()) - ret.add(i.getHostedby().getKey()); - }); - if (Optional.ofNullable(p.getCollectedfrom()).isPresent()) { - p.getCollectedfrom().stream().forEach(cf -> { - if (Optional.ofNullable(cf.getKey()).isPresent()) - ret.add(cf.getKey()); - }); - } - return ret.iterator(); - }, Encoders.STRING()) - .union( - Utils - .readPath(spark, outputPath + "/original/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class) - .flatMap( - (FlatMapFunction) p -> { - List ret = new ArrayList<>(); - p.getInstance().stream().forEach(i -> { - if (Optional.ofNullable(i.getHostedby()).isPresent() - && Optional.ofNullable(i.getHostedby().getKey()).isPresent()) - ret.add(i.getHostedby().getKey()); - }); - if (Optional.ofNullable(p.getCollectedfrom()).isPresent()) { - p.getCollectedfrom().stream().forEach(cf -> { - if (Optional.ofNullable(cf.getKey()).isPresent()) - ret.add(cf.getKey()); - }); - } - return ret.iterator(); - }, Encoders.STRING())) - .union( - Utils - .readPath(spark, outputPath + "/original/software", Software.class) - .flatMap( - (FlatMapFunction) p -> { - List ret = new ArrayList<>(); - p.getInstance().stream().forEach(i -> { - if (Optional.ofNullable(i.getHostedby()).isPresent() - && Optional.ofNullable(i.getHostedby().getKey()).isPresent()) - ret.add(i.getHostedby().getKey()); - }); - if (Optional.ofNullable(p.getCollectedfrom()).isPresent()) { - p.getCollectedfrom().stream().forEach(cf -> { - if (Optional.ofNullable(cf.getKey()).isPresent()) - ret.add(cf.getKey()); - }); - } - return ret.iterator(); - }, Encoders.STRING())) - .union( - Utils - .readPath(spark, outputPath + "/original/otherresearchproduct", OtherResearchProduct.class) - .flatMap( - (FlatMapFunction) p -> { - List ret = new ArrayList<>(); - p.getInstance().stream().forEach(i -> { - if (Optional.ofNullable(i.getHostedby()).isPresent() - && Optional.ofNullable(i.getHostedby().getKey()).isPresent()) - ret.add(i.getHostedby().getKey()); - }); - if (Optional.ofNullable(p.getCollectedfrom()).isPresent()) { - p.getCollectedfrom().stream().forEach(cf -> { - if (Optional.ofNullable(cf.getKey()).isPresent()) - ret.add(cf.getKey()); - }); - } - return ret.iterator(); - }, Encoders.STRING())) - .filter((FilterFunction) s -> !s.equals(ModelConstants.UNKNOWN_REPOSITORY.getKey())) - .distinct(); - - datasource - .joinWith(cfhb_orig, datasource.col("id").equalTo(cfhb_orig.col("value"))) - .map((MapFunction, Datasource>) t2 -> t2._1(), Encoders.bean(Datasource.class)) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(outputPath + "/original/datasource"); - - Dataset project = Utils - .readPath(spark, inputPath + "/project", Project.class) - .filter((FilterFunction) d -> !d.getDataInfo().getDeletedbyinference()); - project - .joinWith(relAll, project.col("id").equalTo(relAll.col("value"))) - .map((MapFunction, Project>) t2 -> t2._1(), Encoders.bean(Project.class)) - .groupByKey((MapFunction) v -> v.getId(), Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(Project.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/original/project"); - - // save the relations among entities different from the result - - Dataset selectedIDs = Utils - .readPath(spark, outputPath + "/original/project", Project.class) - .map((MapFunction) p -> p.getId(), Encoders.STRING()) - .union( - Utils - .readPath(spark, outputPath + "/original/organization", Organization.class) - .map((MapFunction) o -> o.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, outputPath + "/original/datasource", Datasource.class) - .map((MapFunction) d -> d.getId(), Encoders.STRING())); - - Dataset relOtherOther = relation - .joinWith(selectedIDs, relation.col("source").equalTo(selectedIDs.col("value"))) - .map((MapFunction, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class)); - - relOtherOther - .joinWith(selectedIDs, relOtherOther.col("target").equalTo(selectedIDs.col("value"))) - .map((MapFunction, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class)) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(outputPath + "/original/relation"); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidContext.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidContext.java deleted file mode 100644 index 0dcdbcd..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidContext.java +++ /dev/null @@ -1,133 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; -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.FlatMapFunction; -import org.apache.spark.api.java.function.ForeachFunction; -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.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.graph.ResearchCommunity; -import eu.dnetlib.dhp.schema.oaf.*; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 15/11/22 - */ -public class SparkSelectValidContext implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkSelectValidContext.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSelectValidContext.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_select_context.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String contextPath = parser.get("contextPath"); - log.info("contextPath: {}", contextPath); - - final String communityMapPath = parser.get("communityMapPath"); - log.info("communityMapPath: {}", communityMapPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - selectValidContext(spark, inputPath, contextPath, communityMapPath, outputPath); - - }); - - } - - private static void selectValidContext(SparkSession spark, String inputPath, String contextPath, - String communityMapPath, String outputPath) { - List keys = Arrays - .asList(Utils.getCommunityMap(spark, communityMapPath).keySet().stream().toArray(String[]::new)); - Dataset context = getFilter(spark, inputPath + "/publication", keys, Publication.class) - .union(getFilter(spark, inputPath + "/dataset", keys, eu.dnetlib.dhp.schema.oaf.Dataset.class)) - .union(getFilter(spark, inputPath + "/software", keys, Software.class)) - .union(getFilter(spark, inputPath + "/otherresearchproduct", keys, OtherResearchProduct.class)) - .distinct(); - - context.foreach((ForeachFunction) c -> System.out.println(c)); - - Dataset researchCommunity = Utils.readPath(spark, contextPath, ResearchCommunity.class); - - researchCommunity - .joinWith(context, researchCommunity.col("acronym").equalTo(context.col("value"))) - .map( - (MapFunction, ResearchCommunity>) t2 -> t2._1(), - Encoders.bean(ResearchCommunity.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - - } - - private static Dataset getFilter(SparkSession spark, String inputPath, - List keys, Class inputClazz) { - - return Utils - .readPath(spark, inputPath, inputClazz) - .filter((FilterFunction) r -> isPresentContext(r)) - .flatMap( - (FlatMapFunction) r -> r - .getContext() - .stream() - .map(c -> extract(c.getId(), keys)) - .collect(Collectors.toList()) - .iterator(), - Encoders.STRING()) - .filter(Objects::nonNull); - - } - - private static boolean isPresentContext(I r) { - return Optional.ofNullable(r.getContext()).isPresent(); - } - - private static String extract(String c, List keySet) { - if (keySet.contains(c)) - return c; - if (c.contains(":") && keySet.contains(c.substring(0, c.indexOf(":")))) - return c.substring(0, c.indexOf(":")); - return null; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidRelation.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidRelation.java deleted file mode 100644 index 022d6d6..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidRelation.java +++ /dev/null @@ -1,116 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.getEntitiesId; -import static eu.dnetlib.dhp.oa.graph.dump.Utils.getValidRelations; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -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.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.graph.GraphResult; -import eu.dnetlib.dhp.oa.model.graph.Relation; -import eu.dnetlib.dhp.oa.model.graph.ResearchCommunity; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 15/11/22 - */ -public class SparkSelectValidRelation implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelation.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSelectValidRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_select_valid_relation_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - // results dumped - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - // all relations plus those produced via context and extracted from results - final String relationPath = parser.get("relationPath"); - log.info("relationPath: {}", relationPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - selectValidRelation(spark, inputPath, relationPath); - - }); - - } - - private static void selectValidRelation(SparkSession spark, String inputPath, - String relationPath) { - // read the results - - getValidRelations( - Utils - .readPath(spark, relationPath, Relation.class), - getEntitiesId(spark, inputPath)) - -// Dataset> relJoinSource = relationSource -// .joinWith(dumpedIds, relationSource.col("_1").equalTo(dumpedIds.col("value"))) -// .map( -// (MapFunction, String>, Tuple2>) t2 -> new Tuple2<>( -// t2._1()._2().getTarget().getId(), t2._1()._2()), -// Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class))); -// -// relJoinSource -// .joinWith(dumpedIds, relJoinSource.col("_1").equalTo(dumpedIds.col("value"))) -// .map( -// (MapFunction, String>, Relation>) t2 -> t2._1()._2(), -// Encoders.bean(Relation.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(inputPath + "/relation"); - -// relJoinSource = relationSource -// .joinWith(dumpedIds, relationSource.col("_1").equalTo(dumpedIds.col("value"))) -// .map( -// (MapFunction, String>, Tuple2>) t2 -> new Tuple2<>( -// t2._1()._2().getTarget().getId(), t2._1()._2()), -// Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class))); -// -// relJoinSource -// .joinWith(dumpedIds, relJoinSource.col("_1").equalTo(dumpedIds.col("value"))) -// .map( -// (MapFunction, String>, Relation>) t2 -> t2._1()._2(), -// Encoders.bean(Relation.class)) -// .write() -// .mode(SaveMode.Append) -// .option("compression", "gzip") -// .json(inputPath + "/relation"); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidRelationContext.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidRelationContext.java deleted file mode 100644 index 779c4c2..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/SparkSelectValidRelationContext.java +++ /dev/null @@ -1,153 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.ForeachFunction; -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.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.graph.GraphResult; -import eu.dnetlib.dhp.oa.model.graph.Relation; -import eu.dnetlib.dhp.oa.model.graph.ResearchCommunity; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 15/11/22 - */ -public class SparkSelectValidRelationContext implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationContext.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSelectValidRelationContext.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_select_valid_relation_context_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - // results dumped - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String contextRelationPath = parser.get("contextRelationPath"); - log.info("contextRelationPath: {}", contextRelationPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - selectValidRelation(spark, inputPath, contextRelationPath); - - }); - - } - - private static void selectValidRelation(SparkSession spark, String inputPath, - String contextRelationPath) { - // read the results - Dataset dumpedIds = Utils - .readPath(spark, inputPath + "/publication", GraphResult.class) - .map((MapFunction) r -> r.getId(), Encoders.STRING()) - .union( - Utils - .readPath(spark, inputPath + "/dataset", GraphResult.class) - .map((MapFunction) r -> r.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/software", GraphResult.class) - .map((MapFunction) r -> r.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/otherresearchproduct", GraphResult.class) - .map((MapFunction) r -> r.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/organization", eu.dnetlib.dhp.oa.model.graph.Organization.class) - .map( - (MapFunction) o -> o.getId(), - Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.oa.model.graph.Project.class) - .map( - (MapFunction) o -> o.getId(), Encoders.STRING())) - .union( - Utils - .readPath(spark, inputPath + "/datasource", eu.dnetlib.dhp.oa.model.graph.Datasource.class) - .map( - (MapFunction) o -> o.getId(), - Encoders.STRING())); - - Dataset> relationSource = Utils - .readPath(spark, contextRelationPath + "/context", Relation.class) - .union(Utils.readPath(spark, contextRelationPath + "/contextOrg", Relation.class)) - .map( - (MapFunction>) r -> new Tuple2<>(r.getSource(), r), - Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class))); - - Dataset allowedContext = Utils - .readPath(spark, inputPath + "/communities_infrastructures", ResearchCommunity.class); - - Dataset> relJoinSource = relationSource - .joinWith(dumpedIds, relationSource.col("_1").equalTo(dumpedIds.col("value"))) - .map( - (MapFunction, String>, Tuple2>) t2 -> new Tuple2<>( - t2._1()._2().getTarget(), t2._1()._2()), - Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class))); - - relJoinSource - .joinWith(allowedContext, relJoinSource.col("_1").equalTo(allowedContext.col("id"))) - .map( - (MapFunction, ResearchCommunity>, Relation>) t2 -> t2._1()._2(), - Encoders.bean(eu.dnetlib.dhp.oa.model.graph.Relation.class)) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(inputPath + "/relation"); - - relJoinSource = relationSource - .joinWith(allowedContext, relationSource.col("_1").equalTo(allowedContext.col("id"))) - .map( - (MapFunction, ResearchCommunity>, Tuple2>) t2 -> new Tuple2<>( - t2._1()._2().getTarget(), t2._1()._2()), - Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class))); - - relJoinSource - .joinWith(dumpedIds, relJoinSource.col("_1").equalTo(dumpedIds.col("value"))) - .map( - (MapFunction, String>, Relation>) t2 -> t2._1()._2(), - Encoders.bean(Relation.class)) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .json(inputPath + "/relation"); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/ContainsVerb.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/ContainsVerb.java deleted file mode 100644 index 784f35d..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/ContainsVerb.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; - -@VerbClass("contains") -public class ContainsVerb implements Selection, Serializable { - - private String param; - - public ContainsVerb() { - } - - public ContainsVerb(final String param) { - this.param = param; - } - - @Override - public boolean apply(String value) { - return value.contains(param); - } - - public String getParam() { - return param; - } - - public void setParam(String param) { - this.param = param; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/ContainsVerbIgnoreCase.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/ContainsVerbIgnoreCase.java deleted file mode 100644 index cbfea55..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/ContainsVerbIgnoreCase.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; - -@VerbClass("contains_ignorecase") -public class ContainsVerbIgnoreCase implements Selection, Serializable { - - private String param; - - public ContainsVerbIgnoreCase() { - } - - public ContainsVerbIgnoreCase(final String param) { - this.param = param; - } - - @Override - public boolean apply(String value) { - return value.toLowerCase().contains(param.toLowerCase()); - } - - public String getParam() { - return param; - } - - public void setParam(String param) { - this.param = param; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/EqualVerb.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/EqualVerb.java deleted file mode 100644 index c0a2c4e..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/EqualVerb.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; - -@VerbClass("equals") -public class EqualVerb implements Selection, Serializable { - - private String param; - - public EqualVerb() { - } - - public EqualVerb(final String param) { - this.param = param; - } - - @Override - public boolean apply(String value) { - return value.equals(param); - } - - public String getParam() { - return param; - } - - public void setParam(String param) { - this.param = param; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/EqualVerbIgnoreCase.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/EqualVerbIgnoreCase.java deleted file mode 100644 index c2f34f5..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/EqualVerbIgnoreCase.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; - -@VerbClass("equals_ignorecase") -public class EqualVerbIgnoreCase implements Selection, Serializable { - - private String param; - - public EqualVerbIgnoreCase() { - } - - public EqualVerbIgnoreCase(final String param) { - this.param = param; - } - - @Override - public boolean apply(String value) { - return value.equalsIgnoreCase(param); - } - - public String getParam() { - return param; - } - - public void setParam(String param) { - this.param = param; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/GreatThanVerb.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/GreatThanVerb.java deleted file mode 100644 index c89ddb1..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/GreatThanVerb.java +++ /dev/null @@ -1,34 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; - -/** - * @author miriam.baglioni - * @Date 11/11/22 - */ -@VerbClass("greater_than") -public class GreatThanVerb implements Selection, Serializable { - - private String param; - - public GreatThanVerb() { - } - - public GreatThanVerb(final String param) { - this.param = param; - } - - @Override - public boolean apply(String value) { - return value.compareTo(param) > 0; - } - - public String getParam() { - return param; - } - - public void setParam(String param) { - this.param = param; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/InterfaceAdapter.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/InterfaceAdapter.java deleted file mode 100644 index 8ffbfe7..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/InterfaceAdapter.java +++ /dev/null @@ -1,43 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.lang.reflect.Type; - -import com.google.gson.*; - -public class InterfaceAdapter implements JsonSerializer, JsonDeserializer { - - private static final String CLASSNAME = "CLASSNAME"; - private static final String DATA = "DATA"; - - public Object deserialize( - JsonElement jsonElement, - Type type, - JsonDeserializationContext jsonDeserializationContext) - throws JsonParseException { - - JsonObject jsonObject = jsonElement.getAsJsonObject(); - JsonPrimitive prim = (JsonPrimitive) jsonObject.get(CLASSNAME); - String className = prim.getAsString(); - Class klass = getObjectClass(className); - return jsonDeserializationContext.deserialize(jsonObject.get(DATA), klass); - } - - public JsonElement serialize( - Object jsonElement, Type type, JsonSerializationContext jsonSerializationContext) { - JsonObject jsonObject = new JsonObject(); - jsonObject.addProperty(CLASSNAME, jsonElement.getClass().getName()); - jsonObject.add(DATA, jsonSerializationContext.serialize(jsonElement)); - return jsonObject; - } - - /** **** Helper method to get the className of the object to be deserialized **** */ - public Class getObjectClass(String className) { - try { - return Class.forName(className); - } catch (ClassNotFoundException e) { - // e.printStackTrace(); - throw new JsonParseException(e.getMessage()); - } - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/LessThanVerb.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/LessThanVerb.java deleted file mode 100644 index 8a99775..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/LessThanVerb.java +++ /dev/null @@ -1,34 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; - -/** - * @author miriam.baglioni - * @Date 11/11/22 - */ -@VerbClass("lesser_than") -public class LessThanVerb implements Selection, Serializable { - - private String param; - - public LessThanVerb() { - } - - public LessThanVerb(final String param) { - this.param = param; - } - - @Override - public boolean apply(String value) { - return value.compareTo(param) < 0; - } - - public String getParam() { - return param; - } - - public void setParam(String param) { - this.param = param; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotContainsVerb.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotContainsVerb.java deleted file mode 100644 index 5f10746..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotContainsVerb.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; - -@VerbClass("not_contains") -public class NotContainsVerb implements Selection, Serializable { - - private String param; - - public NotContainsVerb() { - } - - public NotContainsVerb(final String param) { - this.param = param; - } - - @Override - public boolean apply(String value) { - return !value.contains(param); - } - - public String getParam() { - return param; - } - - public void setParam(String param) { - this.param = param; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotContainsVerbIgnoreCase.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotContainsVerbIgnoreCase.java deleted file mode 100644 index 62e438b..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotContainsVerbIgnoreCase.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; - -@VerbClass("not_contains_ignorecase") -public class NotContainsVerbIgnoreCase implements Selection, Serializable { - - private String param; - - public NotContainsVerbIgnoreCase() { - } - - public NotContainsVerbIgnoreCase(final String param) { - this.param = param; - } - - @Override - public boolean apply(String value) { - return !(value.toLowerCase().contains(param.toLowerCase())); - } - - public String getParam() { - return param; - } - - public void setParam(String param) { - this.param = param; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotEqualVerb.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotEqualVerb.java deleted file mode 100644 index 43d964c..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotEqualVerb.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; - -@VerbClass("not_equals") -public class NotEqualVerb implements Selection, Serializable { - - private String param; - - public NotEqualVerb(final String param) { - this.param = param; - } - - public NotEqualVerb() { - } - - public String getParam() { - return param; - } - - public void setParam(String param) { - this.param = param; - } - - @Override - public boolean apply(String value) { - return !value.equals(param); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotEqualVerbIgnoreCase.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotEqualVerbIgnoreCase.java deleted file mode 100644 index 4750753..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/NotEqualVerbIgnoreCase.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; - -@VerbClass("not_equals_ignorecase") -public class NotEqualVerbIgnoreCase implements Selection, Serializable { - - private String param; - - public NotEqualVerbIgnoreCase(final String param) { - this.param = param; - } - - public NotEqualVerbIgnoreCase() { - } - - public String getParam() { - return param; - } - - public void setParam(String param) { - this.param = param; - } - - @Override - public boolean apply(String value) { - return !value.equalsIgnoreCase(param); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/Selection.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/Selection.java deleted file mode 100644 index 3da0112..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/Selection.java +++ /dev/null @@ -1,9 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; - -public interface Selection extends Serializable { - - boolean apply(String value); -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/VerbClass.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/VerbClass.java deleted file mode 100644 index 4b93454..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/VerbClass.java +++ /dev/null @@ -1,14 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.lang.annotation.ElementType; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; - -@Retention(RetentionPolicy.RUNTIME) -@Target(ElementType.TYPE) -@interface VerbClass { - - String value(); -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/VerbResolver.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/VerbResolver.java deleted file mode 100644 index 2a43636..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/VerbResolver.java +++ /dev/null @@ -1,54 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -import java.io.Serializable; -import java.lang.reflect.InvocationTargetException; -import java.util.Map; -import java.util.stream.Collectors; - -import io.github.classgraph.ClassGraph; -import io.github.classgraph.ClassInfoList; -import io.github.classgraph.ScanResult; - -public class VerbResolver implements Serializable { - - private Map> map = null; - - public VerbResolver() { - - final ClassGraph classgraph = new ClassGraph(); - try (ScanResult scanResult = // Assign scanResult in try-with-resources - classgraph // Create a new ClassGraph instance - .verbose() // If you want to enable logging to stderr - .enableAllInfo() // Scan classes, methods, fields, annotations - .whitelistPackages( - "eu.dnetlib.dhp.oa.graph.dump.subset.criteria") // Scan com.xyz and subpackages - .scan()) { // Perform the scan and return a ScanResult - - ClassInfoList routeClassInfoList = scanResult - .getClassesWithAnnotation( - "eu.dnetlib.dhp.oa.graph.dump.subset.criteria.VerbClass"); - - this.map = routeClassInfoList - .stream() - .collect( - Collectors - .toMap( - value -> (String) value - .getAnnotationInfo() - .get(0) - .getParameterValues() - .get(0) - .getValue(), - value -> (Class) value.loadClass())); - } - } - - public Selection getSelectionCriteria(String name, String param) - throws NoSuchMethodException, IllegalAccessException, InvocationTargetException, - InstantiationException { - - // return Class.forName(tmp_map.get(name)). - return map.get(name).getDeclaredConstructor((String.class)).newInstance(param); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/VerbResolverFactory.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/VerbResolverFactory.java deleted file mode 100644 index 370855d..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/criteria/VerbResolverFactory.java +++ /dev/null @@ -1,13 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.criteria; - -public class VerbResolverFactory { - - private VerbResolverFactory() { - } - - public static VerbResolver newInstance() { - - return new VerbResolver(); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/Constraint.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/Constraint.java deleted file mode 100644 index 47ef317..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/Constraint.java +++ /dev/null @@ -1,53 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.selectionconstraints; - -import java.io.Serializable; -import java.lang.reflect.InvocationTargetException; - -import eu.dnetlib.dhp.oa.graph.dump.subset.criteria.Selection; -import eu.dnetlib.dhp.oa.graph.dump.subset.criteria.VerbResolver; - -public class Constraint implements Serializable { - private String verb; - private String field; - private String value; - private Selection selection; - - public String getVerb() { - return verb; - } - - public void setVerb(String verb) { - this.verb = verb; - } - - public String getField() { - return field; - } - - public void setField(String field) { - this.field = field; - } - - public String getValue() { - return value; - } - - public void setValue(String value) { - this.value = value; - } - -// public void setSelection(Selection sel) { -// selection = sel; -// } - - public void setSelection(VerbResolver resolver) - throws InvocationTargetException, NoSuchMethodException, InstantiationException, - IllegalAccessException { - selection = resolver.getSelectionCriteria(verb, value); - } - - public boolean verifyCriteria(String metadata) { - return selection.apply(metadata); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/Constraints.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/Constraints.java deleted file mode 100644 index 9b1cc17..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/Constraints.java +++ /dev/null @@ -1,65 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.selectionconstraints; - -import java.io.Serializable; -import java.lang.reflect.InvocationTargetException; -import java.lang.reflect.Type; -import java.util.Collection; -import java.util.List; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -import com.google.gson.Gson; -import com.google.gson.reflect.TypeToken; - -import eu.dnetlib.dhp.oa.graph.dump.subset.criteria.VerbResolver; - -/** Created by miriam on 02/08/2018. */ -public class Constraints implements Serializable { - private static final Log log = LogFactory.getLog(Constraints.class); - - private List constraint; - - public List getConstraint() { - return constraint; - } - - public void setConstraint(List constraint) { - this.constraint = constraint; - } - - public void setSc(String json) { - Type collectionType = new TypeToken>() { - }.getType(); - constraint = new Gson().fromJson(json, collectionType); - } - - void setSelection(VerbResolver resolver) { - for (Constraint st : constraint) { - - try { - st.setSelection(resolver); - } catch (NoSuchMethodException | IllegalAccessException | InvocationTargetException - | InstantiationException e) { - log.error(e.getMessage()); - } - } - } - - // Constraint in and - public boolean verifyCriteria(final Param param) { - - for (Constraint sc : constraint) { - boolean verified = false; - for (String value : param.get(sc.getField())) { - if (sc.verifyCriteria(value.trim())) { - verified = true; - } - } - if (!verified) - return verified; - } - return true; - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/Param.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/Param.java deleted file mode 100644 index 3734723..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/Param.java +++ /dev/null @@ -1,32 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.selectionconstraints; - -import java.io.Serializable; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashMap; -import java.util.function.BiFunction; - -import scala.xml.PrettyPrinter; - -/** - * @author miriam.baglioni - * @Date 11/11/22 - */ -public class Param extends HashMap> implements Serializable { - public Param() { - super(); - } - - public void insert(String key, Object value) { - if (value instanceof ArrayList) - super.put(key, (ArrayList) value); - if (value instanceof String) { - ArrayList al = new ArrayList<>(); - al.add((String) value); - super.put(key, al); - } - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/ProtoMap.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/ProtoMap.java deleted file mode 100644 index 0a86438..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/ProtoMap.java +++ /dev/null @@ -1,15 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.selectionconstraints; - -import java.io.Serializable; -import java.util.HashMap; - -/** - * @author miriam.baglioni - * @Date 11/11/22 - */ -public class ProtoMap extends HashMap implements Serializable { - public ProtoMap() { - super(); - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/SelectionConstraints.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/SelectionConstraints.java deleted file mode 100644 index 53396b0..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/subset/selectionconstraints/SelectionConstraints.java +++ /dev/null @@ -1,47 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset.selectionconstraints; - -import java.io.Serializable; -import java.lang.reflect.Type; -import java.util.Collection; -import java.util.List; - -import com.google.gson.Gson; -import com.google.gson.reflect.TypeToken; - -import eu.dnetlib.dhp.oa.graph.dump.subset.criteria.VerbResolver; - -public class SelectionConstraints implements Serializable { - private List criteria; - - public List getCriteria() { - return criteria; - } - - public void setCriteria(List criteria) { - this.criteria = criteria; - } - - public void setSc(String json) { - Type collectionType = new TypeToken>() { - }.getType(); - criteria = new Gson().fromJson(json, collectionType); - } - - // Constraints in or - public boolean verifyCriteria(final Param param) { - for (Constraints selc : criteria) { - if (selc.verifyCriteria(param)) { - return true; - } - } - return false; - } - - public void addResolver(VerbResolver resolver) { - - for (Constraints cs : criteria) { - cs.setSelection(resolver); - } - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/InputStreamRequestBody.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/InputStreamRequestBody.java similarity index 96% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/InputStreamRequestBody.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/InputStreamRequestBody.java index bbb1e70..0f37da0 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/InputStreamRequestBody.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/InputStreamRequestBody.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi; +package eu.dnetlib.dhp.oa.zenodoapi; /** * @author miriam.baglioni diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/MissingConceptDoiException.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/MissingConceptDoiException.java similarity index 77% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/MissingConceptDoiException.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/MissingConceptDoiException.java index dc3819c..6bfdba6 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/MissingConceptDoiException.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/MissingConceptDoiException.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi; +package eu.dnetlib.dhp.oa.zenodoapi; public class MissingConceptDoiException extends Throwable { public MissingConceptDoiException(String message) { diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/ZenodoAPIClient.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/ZenodoAPIClient.java similarity index 98% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/ZenodoAPIClient.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/ZenodoAPIClient.java index 6a206b3..e75fdb4 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/ZenodoAPIClient.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/ZenodoAPIClient.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi; +package eu.dnetlib.dhp.oa.zenodoapi; import java.io.*; import java.net.HttpURLConnection; @@ -14,8 +14,8 @@ import org.slf4j.LoggerFactory; import com.google.gson.Gson; -import eu.dnetlib.dhp.common.zenodoapi.model.ZenodoModel; -import eu.dnetlib.dhp.common.zenodoapi.model.ZenodoModelList; +import eu.dnetlib.dhp.oa.zenodoapi.model.ZenodoModel; +import eu.dnetlib.dhp.oa.zenodoapi.model.ZenodoModelList; import okhttp3.*; public class ZenodoAPIClient implements Serializable { diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Community.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Community.java similarity index 84% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Community.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Community.java index 8ab58b2..008737b 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Community.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Community.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi.model; +package eu.dnetlib.dhp.oa.zenodoapi.model; /** * @author miriam.baglioni diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Creator.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Creator.java similarity index 94% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Creator.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Creator.java index dd74f40..9e6eab8 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Creator.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Creator.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi.model; +package eu.dnetlib.dhp.oa.zenodoapi.model; /** * @author miriam.baglioni diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/File.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/File.java similarity index 94% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/File.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/File.java index 1931345..540bc7c 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/File.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/File.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi.model; +package eu.dnetlib.dhp.oa.zenodoapi.model; /** * @author miriam.baglioni diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Grant.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Grant.java similarity index 89% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Grant.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Grant.java index 185054e..3a9ddd2 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Grant.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Grant.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi.model; +package eu.dnetlib.dhp.oa.zenodoapi.model; /** * @author miriam.baglioni diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Links.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Links.java similarity index 97% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Links.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Links.java index 7d5aa13..e2c3a74 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Links.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Links.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi.model; +package eu.dnetlib.dhp.oa.zenodoapi.model; /** * @author miriam.baglioni diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Metadata.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Metadata.java similarity index 98% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Metadata.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Metadata.java index 74d6d2c..0aaf9b6 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/Metadata.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/Metadata.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi.model; +package eu.dnetlib.dhp.oa.zenodoapi.model; /** * @author miriam.baglioni diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/PrereserveDoi.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/PrereserveDoi.java similarity index 90% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/PrereserveDoi.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/PrereserveDoi.java index 05d523a..a38b338 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/PrereserveDoi.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/PrereserveDoi.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi.model; +package eu.dnetlib.dhp.oa.zenodoapi.model; /** * @author miriam.baglioni diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/RelatedIdentifier.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/RelatedIdentifier.java similarity index 94% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/RelatedIdentifier.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/RelatedIdentifier.java index 3eae11a..d128993 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/RelatedIdentifier.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/RelatedIdentifier.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi.model; +package eu.dnetlib.dhp.oa.zenodoapi.model; /** * @author miriam.baglioni diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/ZenodoModel.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/ZenodoModel.java similarity index 97% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/ZenodoModel.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/ZenodoModel.java index 4b2aa13..1a0a1a9 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/ZenodoModel.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/ZenodoModel.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi.model; +package eu.dnetlib.dhp.oa.zenodoapi.model; /** * @author miriam.baglioni diff --git a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/ZenodoModelList.java b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/ZenodoModelList.java similarity index 81% rename from dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/ZenodoModelList.java rename to dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/ZenodoModelList.java index 2f1229e..858eff8 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/common/zenodoapi/model/ZenodoModelList.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/model/ZenodoModelList.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.common.zenodoapi.model; +package eu.dnetlib.dhp.oa.zenodoapi.model; /** * @author miriam.baglioni diff --git a/dump/src/main/java/eu/dnetlib/dhp/skgif/DumpResult.java b/dump/src/main/java/eu/dnetlib/dhp/skgif/DumpResult.java deleted file mode 100644 index 9825950..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/skgif/DumpResult.java +++ /dev/null @@ -1,304 +0,0 @@ - -package eu.dnetlib.dhp.skgif; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.skgif.Utils.getOrcid; - -import java.io.Serializable; -import java.util.*; -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.FlatMapFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.*; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.types.DataTypes; -import org.apache.spark.sql.types.StructType; -import org.jetbrains.annotations.NotNull; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.common.EntityType; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.skgif.beans.EmitPerManifestation; -import eu.dnetlib.dhp.skgif.beans.PartialResearchProduct; -import eu.dnetlib.dhp.skgif.beans.RelationPerProduct; -import eu.dnetlib.dhp.skgif.model.*; -import eu.dnetlib.dhp.skgif.model.AccessRight; -import eu.dnetlib.dhp.utils.DHPUtils; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 06/02/24 - */ -public class DumpResult implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(DumpResult.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - PrepareResultRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/dump_result_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String workingDir = parser.get("workingDir"); - log.info("workingDir: {}", workingDir); - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - mapResult(spark, inputPath, outputPath, workingDir); - }); - } - -//per ogni result emetto id + journal se esiste + istanza + hosted by dell'istanza - public static void mapResult(SparkSession spark, String inputPath, String outputPath, - String workingDir) { - - // selection of the relevant relations from result type to other entity. Only teh semantic relevant ones are - // considered - selectRelations(spark, inputPath, workingDir); - - // merge of relations and manifestation for the same result - getRelationAndManifestation(spark, workingDir, inputPath); - - // dump of the result and enrichment with relevant information for relations and manifestations - dumpResult(spark, inputPath, workingDir); - - } - - private static void getRelationAndManifestation(SparkSession spark, String workingDir, String inputPath) { - Dataset aggRelations = Utils - .readPath(spark, workingDir + "aggrelation", RelationPerProduct.class); - ModelSupport.entityTypes - .keySet() - .parallelStream() - .filter(ModelSupport::isResult) - .forEach(e -> { - Dataset datasource = Utils - .readPath(spark, inputPath + "/datasource", Datasource.class) - .filter( - (FilterFunction) d -> Optional.ofNullable(d.getEosctype()).isPresent() && - d.getEosctype().getClassname().equalsIgnoreCase("Journal archive")); - - Dataset man = Utils - .readPath(spark, workingDir + e.name() + "/manifestation", EmitPerManifestation.class); - man - .joinWith(aggRelations, man.col("resultId").equalTo(aggRelations.col("resultId")), "left") - .groupByKey( - (MapFunction, String>) t2 -> t2 - ._1() - .getResultId(), - Encoders.STRING()) - .mapGroups( - (MapGroupsFunction, PartialResearchProduct>) ( - k, v) -> { - PartialResearchProduct prp = new PartialResearchProduct(); - prp.setResultId(k); - List epms = new ArrayList<>(); - Tuple2 first = v.next(); - RelationPerProduct rpp = first._2(); - epms.add(first._1()); - v.forEachRemaining(t2 -> epms.add(t2._1())); - Dataset emitformanifestation = spark - .createDataset(epms, Encoders.bean(EmitPerManifestation.class)); - prp.setManifestations(getManifestationList(emitformanifestation, datasource)); - prp.setRelatedProducts(rpp.getRelatedProduct()); - prp.setRelevantOrganizations(rpp.getOrganizations()); - prp.setFunding(rpp.getFunding()); - return prp; - }, Encoders.bean(PartialResearchProduct.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingDir + e.name() + "/partialResearchproduct"); - - }); - } - - private static List getManifestationList(Dataset emitformanifestation, - Dataset datasource) { - return emitformanifestation - .joinWith( - datasource, emitformanifestation - .col("hostedBy") - .equalTo(datasource.col("id")), - "left") - .map((MapFunction, Manifestation>) t2 -> { - // se il lato sinistro c'e' allora ho la biblio e la venue - // se non c'e' allora ho solo gli altri valori - EmitPerManifestation epm = t2._1(); - Manifestation manifestation = new Manifestation(); - manifestation.setProductLocalTypeSchema(epm.getInstance().getInstancetype().getClassname()); - manifestation.setProductLocalTypeSchema(epm.getInstance().getInstancetype().getSchemename()); - manifestation - .setDates( - Arrays - .asList( - Dates.newInstance(epm.getInstance().getDateofacceptance().getValue(), "publishing"))); - if (Optional.ofNullable(epm.getInstance().getRefereed()).isPresent()) - switch (epm.getInstance().getRefereed().getClassid()) { - case "0000": - manifestation.setPeerReview(PeerReview.UNAVAILABLE.label); - break; - case "0001": - manifestation.setPeerReview(PeerReview.PEER_REVIEWED.label); - break; - case "0002": - manifestation.setPeerReview(PeerReview.NON_PEER_REVIEWED.label); - break; - } - - manifestation.setMetadataCuration("unavailable"); - if (Optional.ofNullable(epm.getInstance().getAccessright()).isPresent()) - switch (epm.getInstance().getAccessright().getClassid()) { - case "OPEN": - case "OPEN DATA": - case "OPEN SOURCE": - manifestation.setAccessRight(AccessRight.OPEN.label); - break; - case "CLOSED": - manifestation.setAccessRight(AccessRight.CLOSED.label); - break; - case "RESTRICTED": - manifestation.setAccessRight(AccessRight.RESTRICTED.label); - break; - case "EMBARGO": - case "12MONTHS": - case "6MONTHS": - manifestation.setAccessRight(AccessRight.EMBARGO.label); - break; - default: - manifestation.setAccessRight(AccessRight.UNAVAILABLE.label); - - } - manifestation.setLicence(epm.getInstance().getLicense().getValue()); - manifestation.setUrl(epm.getInstance().getUrl().get(0)); - if (Optional.ofNullable(epm.getInstance().getPid()).isPresent()) { - manifestation.setPid(epm.getInstance().getPid().get(0).getValue()); - } - if (Optional.ofNullable(t2._2()).isPresent()) - manifestation.setBiblio(getBiblio(epm)); - manifestation.setVenue("venue_______::" + DHPUtils.md5(epm.getInstance().getHostedby().getKey())); - manifestation - .setHostingDatasource("datasource__::" + DHPUtils.md5(epm.getInstance().getHostedby().getKey())); - return manifestation; - }, Encoders.bean(Manifestation.class)) - .collectAsList(); - } - - private static Biblio getBiblio(EmitPerManifestation epm) { - Biblio biblio = new Biblio(); - biblio.setEdition(epm.getJournal().getEdition()); - biblio.setIssue(epm.getJournal().getIss()); - biblio.setPublisher(epm.getPublisher()); - biblio.setVolume(epm.getJournal().getVol()); - biblio.setEndPage(epm.getJournal().getEp()); - biblio.setStartPage(epm.getJournal().getSp()); - return biblio; - } - - private static void dumpResult(SparkSession spark, String inputPath, String workingDir) { - ModelSupport.entityTypes - .keySet() - .parallelStream() - .filter(ModelSupport::isResult) - .forEach(e -> { - Class resultClazz = ModelSupport.entityTypes.get(e); - - Dataset results = Utils.readPath(spark, inputPath + e.name(), resultClazz); - Dataset prr = Utils - .readPath(spark, workingDir + e.name() + "/partialresearchproduct", PartialResearchProduct.class); - - results - .joinWith(prr, results.col("id").equalTo(prr.col("resultId")), "left") - .map((MapFunction, ResearchProduct>) t2 -> { - ResearchProduct rp = ResultMapper.map(t2._1()); - rp.setRelatedProducts(t2._2().getRelatedProducts()); - rp.setFunding(t2._2().getFunding()); - rp.setRelevantOrganizations(t2._2().getRelevantOrganizations()); - rp.setManifestations(rp.getManifestations()); - return rp; - }, Encoders.bean(ResearchProduct.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingDir + e.name() + "/researchproduct"); - - }); - - } - - private static void selectRelations(SparkSession spark, String inputPath, String workingDir) { - Dataset relation = spark - .read() - .json(inputPath + "/relation") - .as(Encoders.bean(Relation.class)) - .filter("dataInfo.deletedbyinference != true and dataInfo.invisible != true") - .filter( - "relClass == 'HasAuthorInstitution' or relClass == 'IsProducedBy' or " + - "relClass == 'IsSupplementedBy' or relClass == 'IsDocumentedBy' or relClass == 'IsPartOf' " + - "relClass == 'IsNewVersionOf' or relClass == 'Cites'"); - - relation - .groupByKey((MapFunction) r -> r.getSource(), Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, v) -> { - RelationPerProduct rpp = new RelationPerProduct(); - rpp.setResultId(k); - Map> remainignRelations = new HashMap<>(); - while (v.hasNext()) { - Relation rel = v.next(); - String target = rel.getTarget(); - String relClass = rel.getRelClass(); - switch (rel.getRelClass().toLowerCase()) { - case "hasauthorinstitution": - rpp.getOrganizations().add("organization::" + DHPUtils.md5(target)); - break; - case "isproducedby": - rpp.getFunding().add("grant_______::" + DHPUtils.md5(target)); - break; - default: - if (!remainignRelations.keySet().contains(relClass)) - remainignRelations.put(relClass, new ArrayList<>()); - remainignRelations.get(relClass).add("product_____::" + DHPUtils.md5(target)); - } - } - for (String key : remainignRelations.keySet()) - rpp.getRelatedProduct().add(Relations.newInstance(key, remainignRelations.get(key))); - return rpp; - }, Encoders.bean(RelationPerProduct.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingDir + "/aggrelation"); - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/skgif/ExtendResult.java b/dump/src/main/java/eu/dnetlib/dhp/skgif/ExtendResult.java deleted file mode 100644 index 09647df..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/skgif/ExtendResult.java +++ /dev/null @@ -1,134 +0,0 @@ - -package eu.dnetlib.dhp.skgif; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.*; -import org.apache.spark.sql.types.StructType; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.skgif.model.RelationType; -import eu.dnetlib.dhp.skgif.model.Relations; -import eu.dnetlib.dhp.skgif.model.ResearchProduct; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 05/09/23 - */ -public class ExtendResult implements Serializable { - private static final Logger log = LoggerFactory.getLogger(ExtendResult.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - PrepareResultRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/extend_result_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - extendResult(spark, inputPath, outputPath); - }); - } - - private static void extendResult(SparkSession spark, String inputPath, String outputPath) { - ObjectMapper mapper = new ObjectMapper(); - Dataset result = spark - .read() - .json(inputPath + "/result") - .as(Encoders.bean(ResearchProduct.class)); - final StructType structureSchema = new StructType() - .fromDDL("`resultId` STRING, `target` STRING, `resultClass` STRING"); - - Dataset relations = spark - .read() - .schema(structureSchema) - .json(inputPath + "/preparedRelations"); - - result - .joinWith( - relations, result - .col("localIdentifier") - .equalTo(relations.col("resultId")), - "left") - .groupByKey( - (MapFunction, String>) t2 -> t2._1().getLocalIdentifier(), - Encoders.STRING()) - .mapGroups((MapGroupsFunction, ResearchProduct>) (key, it) -> { - Tuple2 first = it.next(); - ResearchProduct rp = first._1(); - addRels(rp, first._2()); - it.forEachRemaining(t2 -> addRels(rp, t2._2())); - return rp; - }, Encoders.bean(ResearchProduct.class)) - .map((MapFunction) r -> mapper.writeValueAsString(r), Encoders.STRING()) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .text(outputPath); - - } - - private static void addRels(ResearchProduct rp, Row row) { - String relClass = row.getAs("relClass"); - Map> relations = new HashMap<>(); - if (relClass.equals(RelationType.OUTCOME.label)) { - if (!Optional.ofNullable(rp.getFunding()).isPresent()) { - rp.setFunding(new ArrayList<>()); - } - rp.getFunding().add(row.getAs("target")); - } else if (relClass.equals(RelationType.AFFILIATION)) { - if (!Optional.ofNullable(rp.getRelevantOrganizations()).isPresent()) - rp.setRelevantOrganizations(new ArrayList<>()); - rp.getRelevantOrganizations().add(row.getAs("target")); - } else { - if (!relations.containsKey(relClass)) { - relations.put(relClass, new ArrayList<>()); - } - relations.get(relClass).add(row.getAs("target")); - } - if (relations.size() > 0) { - rp.setRelatedProducts(new ArrayList<>()); - for (String key : relations.keySet()) { - Relations rel = new Relations(); - rel.setRelationType(key); - rel.setProductList(relations.get(key)); - } - } - - } -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/skgif/PrepareResultRelation.java b/dump/src/main/java/eu/dnetlib/dhp/skgif/PrepareResultRelation.java deleted file mode 100644 index 203104a..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/skgif/PrepareResultRelation.java +++ /dev/null @@ -1,106 +0,0 @@ - -package eu.dnetlib.dhp.skgif; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.sql.*; -import org.apache.spark.sql.types.DataTypes; -import org.apache.spark.sql.types.StructType; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.oaf.Relation; - -/** - * @author miriam.baglioni - * @Date 04/09/23 - */ -public class PrepareResultRelation implements Serializable { - private static final Logger log = LoggerFactory.getLogger(PrepareResultRelation.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - PrepareResultRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/result_relation_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - prepareResultRelationList(spark, inputPath, outputPath); - }); - } - - private static void prepareResultRelationList(SparkSession spark, String inputPath, String outputPath) { - - final StructType structureSchema = new StructType() - .add( - "dataInfo", new StructType() - .add("deletedbyinference", DataTypes.BooleanType) - .add("invisible", DataTypes.BooleanType)) - .add("id", DataTypes.StringType); - - Dataset relation = spark - .read() - .json(inputPath) - .as(Encoders.bean(Relation.class)) - .filter("dataInfo.deletedbyinference != true and dataInfo.invisible != true") - .filter( - "subRelType == 'affiliation' or subRelType == 'outcome' or " + - "relClass == 'IsSupplementedBy' or relClass == 'IsDocumentedBy' or relClass == 'IsPartOf' " + - "relClass == 'IsNewVersionOf' or relClass == 'Cites'"); - - org.apache.spark.sql.Dataset df = spark.createDataFrame(new ArrayList(), structureSchema); - List entities = Arrays - .asList( - "publication", "dataset", "otherresearchproduct", "software"); - for (String e : entities) - df = df - .union( - spark - .read() - .schema(structureSchema) - .json(inputPath + "/" + e) - .filter("dataInfo.deletedbyinference != true and dataInfo.invisible != true")); - - relation - .joinWith(df, relation.col("source").equalTo(df.col("id"))) - .select( - new Column("id").as("resultId"), - new Column("target"), - new Column("relClass")) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - - } - -} diff --git a/dump/src/main/java/eu/dnetlib/dhp/skgif/Utils.java b/dump/src/main/java/eu/dnetlib/dhp/skgif/Utils.java deleted file mode 100644 index 4684c2a..0000000 --- a/dump/src/main/java/eu/dnetlib/dhp/skgif/Utils.java +++ /dev/null @@ -1,36 +0,0 @@ - -package eu.dnetlib.dhp.skgif; - -import java.io.Serializable; -import java.util.List; -import java.util.Optional; - -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import scala.Tuple2; - -/** - * @author miriam.baglioni - * @Date 16/02/24 - */ -public class Utils implements Serializable { - - public static Tuple2 getOrcid(List pid) { - if (!Optional.ofNullable(pid).isPresent()) - return null; - if (pid.size() == 0) - return null; - for (StructuredProperty p : pid) { - if (p.getQualifier().getClassid().equals(ModelConstants.ORCID)) { - return new Tuple2<>(p.getValue(), Boolean.TRUE); - } - } - for (StructuredProperty p : pid) { - if (p.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING)) { - return new Tuple2<>(p.getValue(), Boolean.FALSE); - } - } - return null; - } - -} diff --git a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/copygraph_parameters.json b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/copygraph_parameters.json deleted file mode 100644 index cf76eb0..0000000 --- a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/copygraph_parameters.json +++ /dev/null @@ -1,21 +0,0 @@ -[ - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName":"hp", - "paramLongName":"hivePath", - "paramDescription": "the name of the result table we are currently working on", - "paramRequired": true - }, - { - "paramName":"issm", - "paramLongName":"isSparkSessionManaged", - "paramDescription": "the name of the result table we are currently working on", - "paramRequired": false -} -] - diff --git a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/datasourcemaster_parameters.json b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/datasourcemaster_parameters.json deleted file mode 100644 index 9b8d482..0000000 --- a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/datasourcemaster_parameters.json +++ /dev/null @@ -1,32 +0,0 @@ -[ - { - "paramName":"hdp", - "paramLongName":"hdfsPath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "pp", - "paramLongName": "postgresPassword", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "pu", - "paramLongName": "postgresUser", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": true - }, - { - "paramName": "purl", - "paramLongName": "postgresUrl", - "paramDescription": "the relationPath", - "paramRequired": true - }, - { - "paramName": "hdnn", - "paramLongName": "hdfsNameNode", - "paramDescription": "the relationPath", - "paramRequired": true - } -] \ No newline at end of file diff --git a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_datasource_parameters.json b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_datasource_parameters.json new file mode 100644 index 0000000..b1f618c --- /dev/null +++ b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_datasource_parameters.json @@ -0,0 +1,27 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "wd", + "paramLongName": "workingDir", + "paramDescription": "the relationPath", + "paramRequired": false + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the relationPath", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_grant_parameters.json b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_grant_parameters.json new file mode 100644 index 0000000..b1f618c --- /dev/null +++ b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_grant_parameters.json @@ -0,0 +1,27 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "wd", + "paramLongName": "workingDir", + "paramDescription": "the relationPath", + "paramRequired": false + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the relationPath", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_organization_parameters.json b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_organization_parameters.json new file mode 100644 index 0000000..33ec33f --- /dev/null +++ b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_organization_parameters.json @@ -0,0 +1,22 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the relationPath", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_result_parameters.json b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_result_parameters.json new file mode 100644 index 0000000..b1f618c --- /dev/null +++ b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/dump_result_parameters.json @@ -0,0 +1,27 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "wd", + "paramLongName": "workingDir", + "paramDescription": "the relationPath", + "paramRequired": false + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the relationPath", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/emit_biblio_parameters.json similarity index 90% rename from dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json rename to dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/emit_biblio_parameters.json index 5669dca..fad451a 100644 --- a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/emit_biblio_parameters.json @@ -18,8 +18,8 @@ "paramRequired": false }, { - "paramName": "gp", - "paramLongName": "graphPath", + "paramName": "wd", + "paramLongName": "workingDir", "paramDescription": "the relationPath", "paramRequired": false } diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java deleted file mode 100644 index 2496219..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ /dev/null @@ -1,1102 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; -import java.util.Optional; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; - -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts; -import eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob; -import eu.dnetlib.dhp.oa.model.*; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; -import eu.dnetlib.dhp.oa.model.graph.GraphResult; -import eu.dnetlib.dhp.schema.common.ModelConstants; - -//@Disabled -public class DumpJobTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class); - - private static final CommunityMap map = new CommunityMap(); - - static { - map.put("egi", "EGI Federation"); - map.put("fet-fp7", "FET FP7"); - map.put("fet-h2020", "FET H2020"); - map.put("clarin", "CLARIN"); - map.put("fam", "Fisheries and Aquaculture Management"); - map.put("ni", "Neuroinformatics"); - map.put("mes", "European Marine Scinece"); - map.put("instruct", "Instruct-Eric"); - map.put("rda", "Research Data Alliance"); - map.put("elixir-gr", "ELIXIR GR"); - map.put("aginfra", "Agricultural and Food Sciences"); - map.put("dariah", "DARIAH EU"); - map.put("risis", "RISI"); - map.put("ee", "SDSN - Greece"); - map.put("oa-pg", "EC Post-Grant Open Access Pilot"); - map.put("beopen", "Transport Research"); - map.put("euromarine", "Euromarine"); - map.put("ifremer", "Ifremer"); - map.put("dh-ch", "Digital Humanities and Cultural Heritage"); - map.put("science-innovation-policy", "Science and Innovation Policy Studies"); - map.put("covid-19", "COVID-19"); - map.put("enrmaps", "Energy Research"); - map.put("epos", "EPOS"); - - } - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(DumpJobTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(DumpJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void testMap() { - System.out.println(new Gson().toJson(map)); - } - - @Test - public void testDumpIndicators() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publicationWithMeasures") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - GraphResult gr = verificationDataset.first(); - - Assertions.assertTrue(Optional.ofNullable(gr.getIndicators().getUsageCounts()).isPresent()); - Assertions.assertFalse(Optional.ofNullable(gr.getIndicators().getBipIndicators()).isPresent()); - - } - - @Test - public void testPublicationDump() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - GraphResult gr = verificationDataset.first(); - - System.out.println(new ObjectMapper().writeValueAsString(gr)); - - Assertions.assertEquals(6, gr.getAuthor().size()); - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Nikolaidou,Charitini") && - a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou") - && a.getRank() == 1 && a.getPid() == null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Votsi,Nefta") && - a.getName().equals("Nefta") && a.getSurname().equals("Votsi") - && a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Sgardelis,Steanos") && - a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis") - && a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Halley,John") && - a.getName().equals("John") && a.getSurname().equals("Halley") - && a.getRank() == 4 && a.getPid() == null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Pantis,John") && - a.getName().equals("John") && a.getSurname().equals("Pantis") - && a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Tsiafouli,Maria") && - a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli") - && a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions.assertEquals("publication", gr.getType()); - - Assertions.assertEquals("eng", gr.getLanguage().getCode()); - Assertions.assertEquals("English", gr.getLanguage().getLabel()); - - Assertions.assertEquals(1, gr.getCountry().size()); - Assertions.assertEquals("IT", gr.getCountry().get(0).getCode()); - Assertions.assertEquals("Italy", gr.getCountry().get(0).getLabel()); - Assertions.assertTrue(gr.getCountry().get(0).getProvenance() == null); - - Assertions.assertEquals(12, gr.getSubjects().size()); - Assertions - .assertTrue( - gr - .getSubjects() - .stream() - .anyMatch( - s -> s.getSubject().getValue().equals("Ecosystem Services hotspots") - && s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null && - s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); - Assertions - .assertTrue( - gr - .getSubjects() - .stream() - .anyMatch( - s -> s.getSubject().getValue().equals("Natura 2000") - && s.getSubject().getScheme().equals("") && s.getProvenance() != null && - s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); - - Assertions - .assertEquals( - "Ecosystem Service capacity is higher in areas of multiple designation types", - gr.getMaintitle()); - - Assertions.assertEquals(null, gr.getSubtitle()); - - Assertions.assertEquals(1, gr.getDescription().size()); - - Assertions - .assertTrue( - gr - .getDescription() - .get(0) - .startsWith("The implementation of the Ecosystem Service (ES) concept into practice")); - Assertions - .assertTrue( - gr - .getDescription() - .get(0) - .endsWith( - "start complying with new standards and demands for nature conservation and environmental management.")); - - Assertions.assertEquals("2017-01-01", gr.getPublicationdate()); - - Assertions.assertEquals("Pensoft Publishers", gr.getPublisher()); - - Assertions.assertEquals(null, gr.getEmbargoenddate()); - - Assertions.assertEquals(1, gr.getSource().size()); - Assertions.assertEquals("One Ecosystem 2: e13718", gr.getSource().get(0)); - - Assertions.assertEquals(1, gr.getFormat().size()); - Assertions.assertEquals("text/html", gr.getFormat().get(0)); - - Assertions.assertEquals(0, gr.getContributor().size()); - - Assertions.assertEquals(0, gr.getCoverage().size()); - - Assertions.assertEquals(ModelConstants.ACCESS_RIGHT_OPEN, gr.getBestaccessright().getLabel()); - Assertions - .assertEquals( - Constants.ACCESS_RIGHTS_COAR_MAP.get(ModelConstants.ACCESS_RIGHT_OPEN), - gr.getBestaccessright().getCode()); - - Assertions.assertEquals("One Ecosystem", gr.getContainer().getName()); - Assertions.assertEquals("2367-8194", gr.getContainer().getIssnOnline()); - Assertions.assertEquals("", gr.getContainer().getIssnPrinted()); - Assertions.assertEquals("", gr.getContainer().getIssnLinking()); - - Assertions.assertTrue(null == gr.getDocumentationUrl() || gr.getDocumentationUrl().size() == 0); - - Assertions.assertTrue(null == gr.getCodeRepositoryUrl()); - - Assertions.assertEquals(null, gr.getProgrammingLanguage()); - - Assertions.assertTrue(null == gr.getContactperson() || gr.getContactperson().size() == 0); - - Assertions.assertTrue(null == gr.getContactgroup() || gr.getContactgroup().size() == 0); - - Assertions.assertTrue(null == gr.getTool() || gr.getTool().size() == 0); - - Assertions.assertEquals(null, gr.getSize()); - - Assertions.assertEquals(null, gr.getVersion()); - - Assertions.assertTrue(null == gr.getGeolocation() || gr.getGeolocation().size() == 0); - - Assertions.assertEquals("pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId()); - - Assertions.assertEquals(1, gr.getOriginalId().size()); - Assertions - .assertTrue( - gr.getOriginalId().contains("10.3897/oneeco.2.e13718")); - - Assertions.assertEquals(1, gr.getPid().size()); - Assertions - .assertTrue( - gr.getPid().get(0).getScheme().equals("doi") - && gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004")); - - Assertions.assertEquals("2020-03-23T00:20:51.392Z", gr.getDateofcollection()); - - Assertions.assertTrue(Optional.ofNullable(gr.getIndicators().getUsageCounts()).isPresent()); - Assertions.assertTrue(Optional.ofNullable(gr.getIndicators().getBipIndicators()).isPresent()); - - Assertions - .assertEquals(5, gr.getIndicators().getBipIndicators().size()); - - Assertions - .assertTrue(gr.getIndicators().getUsageCounts() != null); - Assertions - .assertTrue(Integer.valueOf(gr.getIndicators().getUsageCounts().getDownloads()) >= 0); - Assertions - .assertTrue(Integer.valueOf(gr.getIndicators().getUsageCounts().getViews()) >= 0); - - List bip = gr.getIndicators().getBipIndicators(); - for (Score in : bip) { - switch (in.getIndicator()) { - case "influence": - Assertions.assertEquals("6.01504990349e-09", in.getScore()); - Assertions.assertEquals("C", in.getClazz()); - break; - case "popularity_alt": - Assertions.assertEquals("2.304", in.getScore()); - Assertions.assertEquals("C", in.getClazz()); - break; - case "popularity": - Assertions.assertEquals("1.81666032463e-08", in.getScore()); - Assertions.assertEquals("C", in.getClazz()); - break; - case "influence_alt": - Assertions.assertEquals("8.0", in.getScore()); - Assertions.assertEquals("C", in.getClazz()); - break; - case "impulse": - Assertions.assertEquals("8.0", in.getScore()); - Assertions.assertEquals("C", in.getClazz()); - } - - } - - Assertions.assertEquals("0", gr.getIndicators().getUsageCounts().getDownloads()); - Assertions.assertEquals("1", gr.getIndicators().getUsageCounts().getViews()); - - Assertions.assertEquals(1, gr.getInstance().size()); - - Instance instance = gr.getInstance().get(0); - Assertions.assertEquals(0, instance.getPid().size()); - Assertions.assertEquals(1, instance.getAlternateIdentifier().size()); - Assertions - .assertTrue( - instance.getAlternateIdentifier().get(0).getScheme().equals("doi") - && instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718")); - Assertions.assertEquals(null, instance.getLicense()); - Assertions - .assertTrue( - instance - .getAccessright() - .getCode() - .equals( - Constants.ACCESS_RIGHTS_COAR_MAP - .get(ModelConstants.ACCESS_RIGHT_OPEN))); - Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN)); - Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green)); - Assertions.assertTrue(instance.getType().equals("Article")); - Assertions.assertEquals(2, instance.getUrl().size()); - Assertions - .assertTrue( - instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718") - && instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/")); - Assertions.assertEquals("2017-01-01", instance.getPublicationdate()); - Assertions.assertEquals(null, instance.getArticleprocessingcharge()); - Assertions.assertEquals("peerReviewed", instance.getRefereed()); - } - - @Test - public void testDatasetDump() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count()); - - // the common fields in the result have been already checked. Now checking only - // community specific fields - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(2, gr.getGeolocation().size()); - Assertions.assertEquals(2, gr.getGeolocation().stream().filter(gl -> gl.getBox().equals("")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("")).count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> gl.getPlace().equals("18 York St, Ottawa, ON K1N 5S6; Ottawa; Ontario; Canada")) - .count()); - Assertions - .assertEquals( - 1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("45.427242 -75.693904")).count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> gl.getPoint().equals("") && !gl.getPlace().equals("")) - .count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> !gl.getPoint().equals("") && gl.getPlace().equals("")) - .count()); - - Assertions.assertEquals("1024Gb", gr.getSize()); - - Assertions.assertEquals("1.01", gr.getVersion()); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); - Assertions.assertEquals(null, gr.getProgrammingLanguage()); - Assertions.assertEquals(null, gr.getDocumentationUrl()); - Assertions.assertEquals(null, gr.getContactperson()); - Assertions.assertEquals(null, gr.getContactgroup()); - Assertions.assertEquals(null, gr.getTool()); - - } - - @Test - public void testSoftwareDump() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'software'").count()); - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(2, gr.getDocumentationUrl().size()); - Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_1")); - Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_2")); - - Assertions.assertEquals("code_repo", gr.getCodeRepositoryUrl()); - - Assertions.assertEquals("perl", gr.getProgrammingLanguage()); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getContactperson()); - Assertions.assertEquals(null, gr.getContactgroup()); - Assertions.assertEquals(null, gr.getTool()); - Assertions.assertEquals(null, gr.getGeolocation()); - Assertions.assertEquals(null, gr.getSize()); - Assertions.assertEquals(null, gr.getVersion()); - - } - - @Test - public void testOrpDump() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'other'").count()); - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(2, gr.getContactperson().size()); - Assertions.assertTrue(gr.getContactperson().contains(("contact_person1"))); - Assertions.assertTrue(gr.getContactperson().contains(("contact_person2"))); - - Assertions.assertEquals(1, gr.getContactgroup().size()); - Assertions.assertTrue(gr.getContactgroup().contains(("contact_group"))); - - Assertions.assertEquals(2, gr.getTool().size()); - Assertions.assertTrue(gr.getTool().contains("tool1")); - Assertions.assertTrue(gr.getTool().contains("tool2")); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getDocumentationUrl()); - Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); - Assertions.assertEquals(null, gr.getProgrammingLanguage()); - Assertions.assertEquals(null, gr.getGeolocation()); - Assertions.assertEquals(null, gr.getSize()); - Assertions.assertEquals(null, gr.getVersion()); - - } - - @Test - public void testPublicationDumpCommunity() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count()); - - // the common fields in the result have been already checked. Now checking only - // community specific fields - - CommunityResult cr = verificationDataset.first(); - - Assertions.assertEquals(1, cr.getContext().size()); - Assertions.assertEquals("dh-ch", cr.getContext().get(0).getCode()); - Assertions.assertEquals("Digital Humanities and Cultural Heritage", cr.getContext().get(0).getLabel()); - Assertions.assertEquals(1, cr.getContext().get(0).getProvenance().size()); - Assertions.assertEquals("Inferred by OpenAIRE", cr.getContext().get(0).getProvenance().get(0).getProvenance()); - Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust()); - - Assertions.assertEquals(1, cr.getCollectedfrom().size()); - Assertions - .assertEquals("openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey()); - Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue()); - - Assertions.assertEquals(1, cr.getInstance().size()); - Assertions - .assertEquals( - "openaire____::fdc7e0400d8c1634cdaf8051dbae23db", - cr.getInstance().get(0).getCollectedfrom().getKey()); - Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue()); - Assertions - .assertEquals( - "openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey()); - Assertions.assertEquals("One Ecosystem", cr.getInstance().get(0).getHostedby().getValue()); - - } - - @Test - public void testDataset() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(90, verificationDataset.count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset - .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_16ec'").count() == verificationDataset - .filter("bestAccessright.code = 'c_16ec' and bestAccessright.label = 'RESTRICTED'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_14cb'").count() == verificationDataset - .filter("bestAccessright.code = 'c_14cb' and bestAccessright.label = 'CLOSED'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_f1cf'").count() == verificationDataset - .filter("bestAccessright.code = 'c_f1cf' and bestAccessright.label = 'EMBARGO'") - .count()); - - Assertions.assertTrue(verificationDataset.filter("size(context) > 0").count() == 90); - - Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); - - } - - @Test - public void testDataset2All() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(5, verificationDataset.count()); - - } - - @Test - public void testDataset2Communities() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(0, verificationDataset.count()); - - } - - @Test - public void testPublication() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(74, verificationDataset.count()); - verificationDataset.show(false); - - Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count()); - - } - - @Test - public void testSoftware() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(6, verificationDataset.count()); - - Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count()); - - } - - @Test - public void testORP() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(3, verificationDataset.count()); - - Assertions.assertEquals(3, verificationDataset.filter("type = 'other'").count()); - - } - - @Test - public void testRecord() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(2, verificationDataset.count()); - verificationDataset.show(false); - - Assertions.assertEquals(2, verificationDataset.filter("type = 'publication'").count()); - - } - - @Test - public void testArticlePCA() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(23, verificationDataset.count()); - - Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count()); - - verificationDataset.createOrReplaceTempView("check"); - - org.apache.spark.sql.Dataset temp = spark - .sql( - "select id " + - "from check " + - "lateral view explode (instance) i as inst " + - "where inst.articleprocessingcharge is not null"); - - Assertions.assertTrue(temp.count() == 2); - - Assertions.assertTrue(temp.filter("id = 'datacite____::05c611fdfc93d7a2a703d1324e28104a'").count() == 1); - - Assertions.assertTrue(temp.filter("id = 'dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); - - temp = spark - .sql( - "select id, inst.articleprocessingcharge.amount, inst.articleprocessingcharge.currency " + - "from check " + - "lateral view explode (instance) i as inst " + - "where inst.articleprocessingcharge is not null"); - - Assertions - .assertEquals( - "3131.64", - temp - .filter("id = 'datacite____::05c611fdfc93d7a2a703d1324e28104a'") - .collectAsList() - .get(0) - .getString(1)); - Assertions - .assertEquals( - "EUR", - temp - .filter("id = 'datacite____::05c611fdfc93d7a2a703d1324e28104a'") - .collectAsList() - .get(0) - .getString(2)); - - Assertions - .assertEquals( - "2578.35", - temp - .filter("id = 'dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'") - .collectAsList() - .get(0) - .getString(1)); - Assertions - .assertEquals( - "EUR", - temp - .filter("id = 'dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'") - .collectAsList() - .get(0) - .getString(2)); - } - - @Test - public void testresultNotDumped() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/resultNotDumped.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - Assertions.assertEquals(0, tmp.count()); - - } - -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java deleted file mode 100644 index 9522a97..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ /dev/null @@ -1,347 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import static org.junit.jupiter.api.Assertions.assertEquals; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -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.AfterAll; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; -import eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject; - -public class PrepareResultProjectJobTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(PrepareResultProjectJobTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(PrepareResultProjectJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(PrepareResultProjectJobTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(PrepareResultProjectJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testNoMatch() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(0, verificationDataset.count()); - - } - - @Test - void testMatchOne() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(1, verificationDataset.count()); - - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - - verificationDataset.createOrReplaceTempView("table"); - - Dataset check = spark - .sql( - "Select projList.provenance.provenance " + - "from table " + - "lateral view explode (projectsList) pl as projList"); - - assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); - - verificationDataset.show(false); - - } - - @Test - void testMatch() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(2, verificationDataset.count()); - - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; - - Dataset resultExplodedProvenance = spark.sql(query); - assertEquals(3, resultExplodedProvenance.count()); - assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); - - assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); - - } - - @Test - public void testMatchValidated() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(2, verificationDataset.count()); - - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " - + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; - - Dataset resultExplodedProvenance = spark.sql(query); - assertEquals(3, resultExplodedProvenance.count()); - assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); - assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); - - assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); - - assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); - - } - - @Test - void testMatchx() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); - } - -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java deleted file mode 100644 index 1d48eda..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java +++ /dev/null @@ -1,167 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; - -public class SplitForCommunityTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(SplitForCommunityTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(SplitForCommunityTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(SplitForCommunityTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testCommunitySplit2() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityResult") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - CommunitySplit split = new CommunitySplit(); - - split.run(false, sourcePath, workingDir.toString() + "/split", communityMapPath); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/Digital_Humanities_and_Cultural_Heritage") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - System.out.println(tmp.count()); - } - - @Test - void testCommunitySplit() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/splitForCommunity") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - CommunitySplit split = new CommunitySplit(); - - split.run(false, sourcePath, workingDir.toString() + "/split", communityMapPath); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/Digital_Humanities_and_Cultural_Heritage") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(19, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - tmp = sc - .textFile(workingDir.toString() + "/split/EGI_Federation") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - - tmp = sc - .textFile(workingDir.toString() + "/split/Neuroinformatics") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(5, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count()); - - tmp = sc - .textFile(workingDir.toString() + "/split/Science_and_Innovation_Policy_Studies") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(4, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0347b1cd516fc59e41ba92e0d74e4e9f'").count()); - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::1432beb6171baa5da8a85a7f99545d69'").count()); - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::1c8bd19e633976e314b88ce5c3f92d69'").count()); - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - } -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java deleted file mode 100644 index b352d5f..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java +++ /dev/null @@ -1,232 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; -import java.util.stream.Collectors; - -import org.apache.commons.io.FileUtils; -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.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; -import eu.dnetlib.dhp.oa.model.community.Project; - -public class UpdateProjectInfoTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(UpdateProjectInfoTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(UpdateProjectInfoTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(UpdateProjectInfoTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(UpdateProjectInfoTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") - .getPath(); - - SparkUpdateProjectInfo.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-preparedInfoPath", sourcePath + "/preparedInfo", - "-outputPath", workingDir.toString() + "/result", - "-sourcePath", sourcePath + "/software.json" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - verificationDataset.show(false); - - Assertions.assertEquals(6, verificationDataset.count()); - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, " - + - "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream " - + "from dataset " + - "lateral view explode(projects) p as MyT "; - - org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); - - Assertions.assertEquals(3, resultExplodedProvenance.count()); - resultExplodedProvenance.show(false); - - Assertions - .assertEquals( - 2, - resultExplodedProvenance.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '123455'") - .count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '119027'") - .count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' and code = '123455'") - .count()); - - resultExplodedProvenance.show(false); - } - - @Test - public void testValidatedRelation() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") - .getPath(); - - SparkUpdateProjectInfo.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-preparedInfoPath", sourcePath + "/preparedInfoValidated", - "-outputPath", workingDir.toString() + "/result", - "-sourcePath", sourcePath + "/publication_extendedmodel" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - verificationDataset.show(false); - - Assertions.assertEquals(2, verificationDataset.count()); - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, " - + - "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream, MyT.validated " - + "from dataset " + - "lateral view explode(projects) p as MyT "; - - org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); - - Assertions.assertEquals(2, resultExplodedProvenance.count()); - resultExplodedProvenance.show(false); - - Assertions - .assertEquals( - 2, - resultExplodedProvenance.filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2'").count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '123455'") - .count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '119027'") - .count()); - - Project project = verificationDataset - .map( - (MapFunction) cr -> cr - .getProjects() - .stream() - .filter(p -> p.getValidated() != null) - .collect(Collectors.toList()) - .get(0), - Encoders.bean(Project.class)) - .first(); - - Assertions.assertTrue(project.getFunder().getName().equals("Academy of Finland")); - Assertions.assertTrue(project.getFunder().getShortName().equals("AKA")); - Assertions.assertTrue(project.getFunder().getJurisdiction().equals("FI")); - Assertions.assertTrue(project.getFunder().getFundingStream() == null); - Assertions.assertTrue(project.getValidated().getValidationDate().equals("2021-08-06")); - - project = verificationDataset - .map( - (MapFunction) cr -> cr - .getProjects() - .stream() - .filter(p -> p.getValidated() == null) - .collect(Collectors.toList()) - .get(0), - Encoders.bean(Project.class)) - .first(); - - Assertions.assertTrue(project.getFunder().getName().equals("European Commission")); - Assertions.assertTrue(project.getFunder().getShortName().equals("EC")); - Assertions.assertTrue(project.getFunder().getJurisdiction().equals("EU")); - Assertions.assertTrue(project.getFunder().getFundingStream().equals("H2020")); - - } - -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java index 9c384b4..d18f36a 100644 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java +++ b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java @@ -7,6 +7,7 @@ import java.io.IOException; import java.io.InputStream; import java.nio.file.Files; +import eu.dnetlib.dhp.oa.graph.dump.skgif.EmitFromResultJobTest; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.*; import org.junit.jupiter.api.Assertions; @@ -16,9 +17,9 @@ import org.junit.jupiter.api.Test; import com.google.gson.Gson; -import eu.dnetlib.dhp.common.zenodoapi.MissingConceptDoiException; -import eu.dnetlib.dhp.common.zenodoapi.ZenodoAPIClient; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.zenodoapi.MissingConceptDoiException; +import eu.dnetlib.dhp.oa.zenodoapi.ZenodoAPIClient; + @Disabled public class ZenodoUploadTest { @@ -31,63 +32,63 @@ public class ZenodoUploadTest { @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory(UpdateProjectInfoTest.class.getSimpleName()) + .createTempDirectory(EmitFromResultJobTest.class.getSimpleName()) .toString(); } - @Test - void testNewDeposition() throws IOException { - CommunityMap communityMap = new CommunityMap(); - communityMap.put("ni", "Neuroinformatics"); - communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage"); - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") - .getPath()), - new Path(workingDir + "/zenodo/ni/ni")); - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") - .getPath()), - new Path(workingDir + "/zenodo/dh-ch/dh-ch")); - - ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, - ACCESS_TOKEN); - client.newDeposition(); - - // the second boolean parameter here sets the recursion to true - RemoteIterator fileStatusListIterator = fs - .listFiles( - new Path(workingDir + "/zenodo"), true); - while (fileStatusListIterator.hasNext()) { - LocatedFileStatus fileStatus = fileStatusListIterator.next(); - - String p_string = fileStatus.getPath().toString(); - - int index = p_string.lastIndexOf("/"); - String community = p_string.substring(0, index); - community = community.substring(community.lastIndexOf("/") + 1); - String community_name = communityMap.get(community).replace(" ", "_"); - // fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name)); - System.out.println(community); - - // File f = new File("/tmp/" + community_name); - FSDataInputStream inputStream = fs.open(fileStatus.getPath()); - System.out.println(client.uploadIS(inputStream, community_name)); - - } - - String metadata = "{\"metadata\":{\"access_right\":\"open\",\"communities\":[{\"identifier\":\"openaire-research-graph\"}],\"creators\":[{\"affiliation\":\"CNR - ISTI\",\"name\":\"Manghi, Paolo\",\"orcid\":\"0000-0001-7291-3210\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Atzori, Claudio\",\"orcid\":\"0000-0001-9613-6639\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Bardi, Alessia\",\"orcid\":\"0000-0002-1112-1292\"},{\"affiliation\":\"ISTI - CNR\",\"name\":\"Baglioni, Miriam\",\"orcid\":\"0000-0002-2273-9004\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Shirrwagen, Jochen\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Dimitropoulos, Harry\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"La Bruzzo, Sandro\",\"orcid\":\"0000-0003-2855-1245\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Foufoulas, Ioannis\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Löhden, Aenne\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Bäcker, Amelie\",\"orcid\":\"0000-0001-6015-2063\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Mannocci, Andrea\",\"orcid\":\"0000-0002-5193-7851\"},{\"affiliation\":\"University of Warsaw\",\"name\":\"Horst, Marek\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Czerniak, Andreas\",\"orcid\":\"0000-0003-3883-4169\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kiatropoulou, Katerina\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kokogiannaki, Argiro\",\"orcid\":\"0000-0002-3880-0244\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"De Bonis, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Artini, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Ottonello, Enrico\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Lempesis, Antonis\"},{\"affiliation\":\"CERN\",\"name\":\"Ioannidis, Alexandros\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Summan, Friedrich\"}],\"description\":\"\\u003cp\\u003eThis dataset contains dumps of the OpenAIRE Research Graph containing metadata records relevant for the research communities and initiatives collaborating with OpenAIRE\\u003c/p\\u003e. \\u003cp\\u003eEach dataset is a zip containing a file with one json per line. Each json is compliant to the schema available at XXXX\\u003c/p\\u003e Note that the file that is offered is not a typical json file: each line contains a separate, self-contained json object. For more information please see http://jsonlines.org\",\"grants\":[{\"id\":\"777541\"},{\"id\":\"824091\"},{\"id\":\"824323\"}],\"keywords\":[\"Open Science\",\"Scholarly Communication\",\"Information Science\"],\"language\":\"eng\",\"license\":\"CC-BY-4.0\",\"title\":\"OpenAIRE Research Graph: Dumps for research communities and initiatives.\",\"upload_type\":\"dataset\",\"version\":\"1.0\"}}"; - - System.out.println(client.sendMretadata(metadata)); - - // System.out.println(client.publish()); - - } +// @Test +// void testNewDeposition() throws IOException { +// CommunityMap communityMap = new CommunityMap(); +// communityMap.put("ni", "Neuroinformatics"); +// communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage"); +// LocalFileSystem fs = FileSystem.getLocal(new Configuration()); +// +// fs +// .copyFromLocalFile( +// false, new Path(getClass() +// .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") +// .getPath()), +// new Path(workingDir + "/zenodo/ni/ni")); +// fs +// .copyFromLocalFile( +// false, new Path(getClass() +// .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") +// .getPath()), +// new Path(workingDir + "/zenodo/dh-ch/dh-ch")); +// +// ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, +// ACCESS_TOKEN); +// client.newDeposition(); +// +// // the second boolean parameter here sets the recursion to true +// RemoteIterator fileStatusListIterator = fs +// .listFiles( +// new Path(workingDir + "/zenodo"), true); +// while (fileStatusListIterator.hasNext()) { +// LocatedFileStatus fileStatus = fileStatusListIterator.next(); +// +// String p_string = fileStatus.getPath().toString(); +// +// int index = p_string.lastIndexOf("/"); +// String community = p_string.substring(0, index); +// community = community.substring(community.lastIndexOf("/") + 1); +// String community_name = communityMap.get(community).replace(" ", "_"); +// // fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name)); +// System.out.println(community); +// +// // File f = new File("/tmp/" + community_name); +// FSDataInputStream inputStream = fs.open(fileStatus.getPath()); +// System.out.println(client.uploadIS(inputStream, community_name)); +// +// } +// +// String metadata = "{\"metadata\":{\"access_right\":\"open\",\"communities\":[{\"identifier\":\"openaire-research-graph\"}],\"creators\":[{\"affiliation\":\"CNR - ISTI\",\"name\":\"Manghi, Paolo\",\"orcid\":\"0000-0001-7291-3210\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Atzori, Claudio\",\"orcid\":\"0000-0001-9613-6639\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Bardi, Alessia\",\"orcid\":\"0000-0002-1112-1292\"},{\"affiliation\":\"ISTI - CNR\",\"name\":\"Baglioni, Miriam\",\"orcid\":\"0000-0002-2273-9004\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Shirrwagen, Jochen\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Dimitropoulos, Harry\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"La Bruzzo, Sandro\",\"orcid\":\"0000-0003-2855-1245\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Foufoulas, Ioannis\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Löhden, Aenne\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Bäcker, Amelie\",\"orcid\":\"0000-0001-6015-2063\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Mannocci, Andrea\",\"orcid\":\"0000-0002-5193-7851\"},{\"affiliation\":\"University of Warsaw\",\"name\":\"Horst, Marek\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Czerniak, Andreas\",\"orcid\":\"0000-0003-3883-4169\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kiatropoulou, Katerina\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kokogiannaki, Argiro\",\"orcid\":\"0000-0002-3880-0244\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"De Bonis, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Artini, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Ottonello, Enrico\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Lempesis, Antonis\"},{\"affiliation\":\"CERN\",\"name\":\"Ioannidis, Alexandros\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Summan, Friedrich\"}],\"description\":\"\\u003cp\\u003eThis dataset contains dumps of the OpenAIRE Research Graph containing metadata records relevant for the research communities and initiatives collaborating with OpenAIRE\\u003c/p\\u003e. \\u003cp\\u003eEach dataset is a zip containing a file with one json per line. Each json is compliant to the schema available at XXXX\\u003c/p\\u003e Note that the file that is offered is not a typical json file: each line contains a separate, self-contained json object. For more information please see http://jsonlines.org\",\"grants\":[{\"id\":\"777541\"},{\"id\":\"824091\"},{\"id\":\"824323\"}],\"keywords\":[\"Open Science\",\"Scholarly Communication\",\"Information Science\"],\"language\":\"eng\",\"license\":\"CC-BY-4.0\",\"title\":\"OpenAIRE Research Graph: Dumps for research communities and initiatives.\",\"upload_type\":\"dataset\",\"version\":\"1.0\"}}"; +// +// System.out.println(client.sendMretadata(metadata)); +// +// // System.out.println(client.publish()); +// +// } @Test void testNewVersion() throws Exception, MissingConceptDoiException { @@ -161,19 +162,7 @@ public class ZenodoUploadTest { } - @Test - void readCommunityMap() throws IOException { - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - System.out - .println( - new Gson() - .toJson( - Utils - .readCommunityMap( - fs, getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath()))); - } + @Test void depositBigFile() throws MissingConceptDoiException, IOException { diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java deleted file mode 100644 index 32ed39b..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ /dev/null @@ -1,152 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static org.mockito.Mockito.lenient; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.nio.charset.StandardCharsets; -import java.nio.file.Files; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.function.Consumer; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.LocalFileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.io.compress.CompressionCodec; -import org.apache.hadoop.io.compress.CompressionCodecFactory; -import org.codehaus.jackson.map.ObjectMapper; -import org.junit.jupiter.api.*; -import org.junit.jupiter.api.extension.ExtendWith; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; - -import com.google.gson.Gson; - -import eu.dnetlib.dhp.communityapi.QueryCommunityAPI; -import eu.dnetlib.dhp.communityapi.model.CommunityModel; -import eu.dnetlib.dhp.oa.graph.dump.UtilCommunityAPI; -import eu.dnetlib.dhp.oa.model.graph.ResearchCommunity; -import eu.dnetlib.dhp.oa.model.graph.ResearchInitiative; -import eu.dnetlib.dhp.utils.DHPUtils; - -@ExtendWith(MockitoExtension.class) -public class CreateEntityTest { - - private static final String validCommunities = "[{\"id\":\"eut\",\"name\":\"EUt+\",\"description\":\"

EUt+ is an " - + - "alliance of 8 universities: Technological University Dublin, Riga Technical University, Cyprus University " + - "of Technology, Technical University of Cluj-Napoca, Polytechnic University of Cartagena, University of " + - "Technology of Troyes, Technical University of Sofia and Hochschule Darmstadt.

\",\"status\":\"all\"," + - "\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"\"},{\"id\":\"knowmad\",\"name\":\"Knowmad Institut\",\"description\":\"

\\\"\\\"

The Knowmad Research Gateway facilitates researchers, policymakers, activists, and experts to discover publications, data, software, and other research products  related to Human Rights, Sustainable Development, Drug Policy, New Technologies, Ethnobotany, and Special Populations. 

The European Institute for Multidisciplinary Studies on Human Rights & Science - Knowmad Institut is an independent Think & Do Tank based in Brandenburg, Germany, promoting Human Dignity and Open Science in Public and Private Policies....Click Here For More Information.

  • If you would like to suggest research inputs with bibliographic information, Please Use This Form.

El Knowmad Research Gateway facilita a investigadores, responsables políticos, activistas y expertos el descubrimiento de publicaciones, datos, software y otros productos de investigación relacionados con los Derechos Humanos, el Desarrollo Sostenible, las Políticas de Drogas, las Nuevas Tecnologías, la Etnobotánica y las Poblaciones Especiales.

El Instituto Europeo de Estudios Multidisciplinares sobre Derechos Humanos y Ciencia - Knowmad Institut es un Think & Do Tank independiente con sede en Brandenburgo, Alemania, que promueve la Dignidad Humana y la Ciencia Abierta en las Políticas Públicas y Privadas....Haga clic aquí para obtener más información.

Si desea sugerir aportaciones de investigación con información bibliográfica, Utilice Este Formulario.

Das Knowmad Research Gateway ermöglicht Forschern, politischen Entscheidungsträgern, Aktivisten und Experten die Entdeckung von Publikationen, Daten, Software und anderen Forschungsprodukten im Zusammenhang mit Menschenrechten, nachhaltiger Entwicklung, Drogenpolitik, neuen Technologien, Ethnobotanik und speziellen Bevölkerungsgruppen.

Das Europäische Institut für multidisziplinäre Studien zu Menschenrechten und Wissenschaft - Knowmad Institut ist ein unabhängiger Think & Do Tank mit Sitz in Brandenburg (Deutschland), der sich für Menschenwürde und Open Science in öffentlichen und privaten Politiken einsetzt… Klicken Sie hier für weitere Informationen.

Wenn Sie Forschungseingaben mit bibliographischen Informationen vorschlagen möchten, nutzen Sie bitte dieses Formular.

 

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"knowmadinstitut\"},{\"id\":\"netherlands\",\"name\":\"Netherlands Research Portal\",\"description\":\"

All Dutch Research,
In One Place.

A comprehensive and open dataset of research information covering 3m publications, 500k research data, 100 research software items, from 48 data sources, linked to 3K grants and 900 organizations.
All linked together through citations and semantics.
 
Try browsing by:
\\\"SDGsSustainable Development Goals (SDGs)\\\"FOSFields of Science (FoS)

 

Welcome to the Portal of Research Output from the Netherlands. This has been developed as part of a collaboration between UKB, SURF and OpenAIRE. This portal presents Dutch research results and research projects as a sub-section found in the OpenAIRE Graph. This Research Graph is actively fed by Dutch institutional repositories, data and software repositories, and Research Information Systems (CRIS's) that comply with the OpenAIRE metadata guidelines. In addition, this portal also includes research output and research projects from other sources that have an affiliation with one or more Dutch research performing organisations and research funders found in the OpenAIRE Graph.

In Dutch:

Welkom bij het Portaal van het Nederlandse Onderzoeks Resultaten. Dit is ontwikkeld als onderdeel van een samenwerking tussen UKB, SURF and OpenAIRE.  Dit portaal presenteert Nederlandse onderzoeksresultaten en onderzoeksprojecten als een sub-sectie die zijn gevonden in de OpenAIRE Graph. Deze Research Graph wordt actief gevoed door Nederlandse institutionele repositories, data- en software-repositories, en onderzoeksinformatiesystemen (CRISen) die voldoen aan de OpenAIRE metadata richtlijnen. Daarnaast bevat dit portaal ook onderzoeksresultaten en onderzoeksprojecten uit andere bronnen die een affiliatie hebben met een of meer Nederlandse onderzoeksuitvoeringsorganisaties en onderzoeksfinanciers gevonden in de OpenAIRE Graph.

\\\"OpenAIRE

Share your research.

\\\"Linking\\\"
Link your work.
Connect all your research. If you can’t find your research results in OpenAIRE, don’t worry! Use our Link Out service , that reaches out to many external sources via APIs, to connect your research results and claim them to your project.
Learn More
\\\"Deposit\\\"
Deposit your research.
Whether it’s publications, data or software, select an OpenAIRE compatible repository and share using community standards. Alternatively use Zenodo, a catch-all repository hosted by CERN. All results will be indexed, discoverable and accessible via this portal.
Learn More

 

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"\"},{\"id\":\"tunet\",\"name\":\"TU-NET\",\"description\":\"

The Technological University Network (TU-NET) is an affiliation of the Technological Universities in Ireland: Technological University Dublin (TU Dublin), Technological University of the South-East (SETU), Munster Technological University (MTU), Technological University of the Shannon: Midlands Midwest (TUS) and Atlantic Technological University (ATU).  TU-NET is a network for the Irish Technological Universities to share expertise, information and resources where possible.

This portal harvests data from the following Open Access Repositories: ARROW (TU Dublin), SETU Waterford Libraries Repository and Research@THEA (SETU Carlow, TUS, ATU & IADT).

 

Background photo by  Pietro Jeng on Unsplash

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"\"},{\"id\":\"forthem\",\"name\":\"FORTHEM Alliance\",\"description\":\"FORTHEM: Fostering Outreach within European Regions, Transnational Higher Education and Mobility\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"\"},{\"id\":\"neanias-space\",\"name\":\"NEANIAS Space Research Community\",\"description\":\"

The NEANIAS Space Research Community engages Open Science practices through the European Open Science Cloud (EOSC), targeting a wide variety of scientific and professional communities related to Astrophysics and Planetary Science engaging also computer scientists and software engineers interested in computer vision and machine learning. NEANIAS Space Services data and products may also have a high impact in planetary mining and robotics, space weather and mobile telecommunications.

The NEANIAS Space Research services  are aimed at supporting management and analysis of large data volumes in astrophysics and planetary sciences through visualization (SPACE-VIS services), efficiently generating large multidimensional maps and mosaics (SPACE-MOS services), and, finally, supporting mechanisms for automatic detection of structures within maps through machine learning (SPACE-ML services). 

The SPACE-VIS services provide an integrated operational solution for astrophysics and planetary data management aided by advanced visualization mechanisms, including visual analytics and virtual reality, and it is underpinned by FAIR principles.  

  • The ViaLactea service accesses astrophysical surveys to aid understanding of the star formation process of the Milky Way. ViaLactea Visual Analytics (VLVA) combine different types of visualization to perform analysis by exploring correlations managed in the ViaLactea Knowledge Base (VLKB). VLKB includes 2D and 3D (velocity cubes) surveys, numerical model outputs, point-like and diffuse object catalogues and allows for retrieval of all available datasets as well as cut-outs on the positional and/or velocity axis.  
  • The  Astra Data Navigator (ADN) is a virtual reality environment for visualizing large stellar catalogues. The first prototype has been customised to access cloud services for interactive data exploration and navigation with the ability of exploring advanced virtual reality mechanisms providing full immersion.  
  • Finally, the ADAM-Space Service (Advanced Geospatial Data Management platform) accesses a large variety of environmental data and is customised in NEANIAS to access planetary data. 

The SPACE-MOS services provide tools for making high quality images from raw data (map making) and for assembling such images into custom mosaics (mosaicing). 

  • The AstroMapMerging service exploits Montage (http://montage.ipac.caltech.edu/) and is integrated with the ViaLactea service for merging adjacent datasets.  

  • The ISIS3 and ASP under ADAM-DPS service allows integration with data processing pipelines in ADAM which offers tools for planetary data analysis and for producing cartographic products, such as Digital Elevation Models (DEMs) and 3D models from stereo imagery. 

  

The SPACE-ML services provide advanced solutions for pattern and structure detection in astronomical surveys as well as in planetary surface composition, topography and morphometry. The service integrates cutting-edge machine learning algorithms to perform automatic classification of compact and extended sky structures or planetary surfaces. 

  • CAESAR service allows to extract and parametrize compact and extended sources from astronomical radio interferometric maps. The processing pipeline consists of a series of distinct stages that can be run on multiple cores and processors.  

  • AstroML service has been developed to integrate a deep learning mechanism to significantly improve source identification, classification, and characterization of sources in large-scale radio surveys. 

  • The Latent Space Explorer service performs unsupervised representation learning of astronomical images using deep learning techniques (e.g., autoencoders) and interactive visualization of the representations with the chance to apply clustering methods in order to help the domain expert to understand the structure of the representation space. 

Please visit also the NEANIAS Space thematic portal for more info on the Space Services and the research community.

NEANIAS web portal: https://www.neanias.eu/

Please consider acknowledging the NEANIAS project if you use the results of this service in any paper or communication: NEANIAS is funded by European Union under Horizon 2020 research and innovation programme via grant agreement No. 863448.

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"neanias\"},{\"id\":\"aurora\",\"name\":\"Aurora Universities Network\",\"description\":\"

Aurora consists of research-intensive universities deeply committed to the social impact of our activities, and with a history of engagement with the communities in which we operate. Our overall vision is to use our academic excellence to influence societal change through our research and education – aiming to contribute to the achievement of the United Nations’ Sustainable Development Goals.

All our research output is combines via this Aurora Connect Gateway, and put on the Aurora Monitor Dashboard.

More about Aurora: https://aurora-universities.eu/

 

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"\"},{\"id\":\"argo-france\",\"name\":\"Argo France\",\"description\":\"

Argo France brings together all French contributions to the international Argo programme, i.e. scientific and technical coordination, float purchase and deployment, data processing and interfaces with the user community (operational oceanography with Mercator Ocean and research).

\",\"status\":\"all\",\"type\":\"ri\",\"subjects\":null,\"zenodoCommunity\":\"\"},{\"id\":\"dariah\",\"name\":\"DARIAH EU\",\"description\":\"The Digital Research Infrastructure for the Arts and Humanities (DARIAH) aims to enhance and support digitally-enabled research and teaching across the arts and humanities. It develops, maintains and operates an infrastructure in support of ICT-based research practices and sustains researchers in using them to build, analyse and interpret digital resources. DARIAH was established as a European Research Infrastructure Consortium (ERIC) in August 2014. Currently, DARIAH has 18 Members and several cooperating partners in eight non-member countries. Here you will find a growing collection of DARIAH-affiliated research outputs and other documents.\",\"status\":\"all\",\"type\":\"ri\",\"subjects\":null,\"zenodoCommunity\":\"dariah\"},{\"id\":\"north-american-studies\",\"name\":\"North American Studies\",\"description\":\"

North American Studies was born in the context of collaboration between CISAN, the Center for Research on North America and the multi and interdisciplinary research Unit of Universidad National Autonoma de Mexico UNAM, and OpenAIRE. The aim of this collaboration is to strengthen the integration and automated intercommunication between digital platforms in North America and Europe and become a leading platform for North America Studies which will facilitate communication among the community.

In this community scholars, teachers, students, policy stakeholders, journalists and anyone interested in the validated information of the region will be very welcome and able to find easy and directly research outputs on North American Studies, enriching and updating their knowledge from very diverse perspectives and origins in a single portal.

The platform is managed by MiCISAN, the institutional repository of CISAN, whose purpose is collecting research on North American research findings. With OpenAIRE collaboration, it will be possible the integration, organization, protection and dissemination of the CISAN’s scientific products, and similar scientific sources and resources by following the OpenAIRE guidelines and FAIR Principles, in the frame of Open Science.

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"redancommunity\"},{\"id\":\"dth\",\"name\":\"Digital Twins in Health\",\"description\":\"

Open Research Gateway on Digital Twins in Health.

Virtual Human Twin (VHT) is an integrated multiscale, multi-time, and multi-discipline representation of quantitative human physiology and pathology. Its realisation through a collaborative distributed knowledge and resource platform is specifically designed to accelerate the development, integration, and adoption of patient-specific predictive computer models, which will be used as clinical decision support systems, for personal health forecasting or as methodologies for the development and de-risking of personalised medical products. The vision of EDITH is to facilitate the realisation of the opportunities presented by VHTs for the benefit of patients, healthcare providers, regulatory bodies and industry, both within Europe and globally.

Objectives

 

ECOSYSTEM

EDITH has the objective to frame an inclusive ecosystem of digital twins in healthcare within the EU Member States and associated countries. It will start with a comprehensive mapping of the existing relevant actors, initiatives, resources (i.e., models, data sets, methods, good practices, infrastructures, solutions, services), and barriers in the digital twins. This will ensure adequate clinical representation, while fostering collaboration and integration of all relevant stakeholders, such as solution developers, technology providers, infrastructure providers, end-users (healthcare professionals and patients), regulatory agencies, and Health Technology Assessment (HTA) bodies.

 

ROADMAP

EDITH has the objective to build a roadmap with all the necessary conditions to evolve towards an integrated Virtual Human Twin (VHT). The roadmap will identify the necessary building blocks to ensure the VHT’s clinical application and formulate clear short- and mid-term policy recommendations. It will also address aspects of interoperability, computability, health information integration from various sources. It will identify any possible implementation needs and barriers, including the development of a strategic approach for clinical deployment of the VHT model. This will foster the uptake of personalised clinical decision-making, with a particular focus on areas of unmet medical needs.

 

REPOSITORY

EDITH has the objective to develop a federated and cloud-based repository of digital twins (data, models, algorithms, and good practices) in healthcare. The repository will provide a virtual collaboration environment for multiple users and organisations, that will pool together existing digital twin resources across Europe. The ecosystem will be leveraged to create a repository catalogue with available resources and recruit resources into the repository from the consortium and external contributors. Through a federated approach, links will be established with ongoing initiatives that have complementary objectives.

 

SIMULATION PLATFORM

EDITH has the objective to develop the architecture of a simulation platform that will support the transition towards an integrated Virtual Human Twin (VHT). EDITH’s platform, based on a personal user account with specific permissions, will outline how to provide users with a one-stop shop to design, develop, test, and validate single organ digital twins, and combine them with other twins to build integrated VHT models. Five use-cases (cancer, cardiovascular, intensive care, osteoporosis, brain) have been pre-selected to be developed as prototypes, representing the variety of functionalities to be provided by the platform.

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"\"},{\"id\":\"elixir-gr\",\"name\":\"The Greek National Node of the ESFRI European RI ELIXIR\",\"description\":\"ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.\",\"status\":\"all\",\"type\":\"ri\",\"subjects\":null,\"zenodoCommunity\":\"oaa_elixir-gr\"},{\"id\":\"rural-digital-europe\",\"name\":\"Assessing the socio-economic impact of digitalisation in rural areas\",\"description\":\"The scope of this community is to provide access to publications, research data, projects and software for assessing the socio-economic impact of digitalisation in rural areas in Europe\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"\"},{\"id\":\"mes\",\"name\":\"European Marine Science\",\"description\":\"This community was initially defined to include a very broad range of topics, with the intention to generate a number of more focused and sustainable dashboards for research communities and initiatives. As outlined in the logo of this community, we intend to setup a community dashboard for EuroMarine (a consortium of 56 research and academic organisations) and monitoring dashboards for marine research initiatives, including infrastructures (e.g. EMBRC & EMSO), advisory boards (e.g. Marine Boards & ICES), and transnational funding bodies (e.g. JPI-Oceans and Tara Foundation).\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"oac_mes\"},{\"id\":\"neanias-underwater\",\"name\":\"NEANIAS Underwater Research Community\",\"description\":\"

NEANIAS Underwater Research Community engages Open Science practices through the European Open Science Cloud (EOSC), targeting a wide variety of scientific and professional communities related to  the marine environment. NEANIAS Underwater group provides three user-friendly, cloud-based solutions addressing bathymetry processing, seafloor mosaicking and classification (https://www.neanias.eu/index.php/services/underwater). More specifically:

  • Bathymetry Mapping from Acoustic Data service delivers an advanced, user-friendly, cloud-based version of the popular open-source MB-System software for post-processing bathymetry through Jupyter notebooks with additional functionalities .
  • The Seafloor Mosaicing from Optical Data service provides an operational solution for large area representation (in the order of tens of thousands of images) of the predominantly flat, seafloor, also addressing visibility limitations from the underwater medium (https://marketplace.eosc-portal.eu/services/uw-mos).
  • The Seabed Classification from Multispectral, Multibeam Data service delivers a user-friendly cloud-based solution integrating cutting-edge machine learning frameworks for mapping several seabed classes, validated for archaeological, geo-hazards, energy, and other applications (https://marketplace.eosc-portal.eu/services/uw-map).

NEANIAS: https://www.neanias.eu/

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"neanias\"},{\"id\":\"neanias-atmospheric\",\"name\":\"NEANIAS Atmospheric Research Community\",\"description\":\"

NEANIAS Atmospheric Research Community engages Open Science practices through the European Open Science Cloud (EOSC), targeting a wide variety of sectors related to the atmosphere. The sectors it targets include, among others, meteorologists, industrial air pollutant emitters, ecologists, geologists, rural urban planners and air quality authorities, geohazards, civil protection, insurance or health agencies.

More in detail, NEANIAS Atmospheric group offers the following services on the EOSC platform:

  • The Greenhouse Gases Flux Density Monitoring service (A1 - ATMO-FLUD) delivers an operational workflow for estimating flux density and fluxes of gases, aerosol, energy from data obtained from specifically set meteorological stations, validated towards standardized, regularized processes.
  • The Atmospheric Perturbations and Components Monitoring service (A2, divided in two services, ATMO-STRESS and ATMO-SEISM) performs all required analyses of atmospheric and geological data in order to estimate possible correlations of gaseous and particulate components of the atmosphere with earthquake and volcanic processes.
  • The Air Quality Estimation, Monitoring and Forecasting service (A3 – ATMO-4CAST) delivers a novel cloud-based solution providing crucial information and products to a variety of stakeholder in agriculture, urban/ city authorities, health, insurance agencies and relative governmental authorities.

NEANIAS: https://www.neanias.eu/

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"neanias\"},{\"id\":\"beopen\",\"name\":\"Transport Research\",\"description\":\"Welcome to the Open Research Gateway for Transport Research. This gateway is part of the TOPOS Observatory (https://www.topos-observatory.eu). The TOPOS aims to showcase the status and progress of open science uptake in transport research. It focuses on promoting territorial and cross border cooperation and contributing in the optimization of open science in transport research. The TOPOS Observatory is supported by the EC H2020 BEOPEN project (824323)\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"be-open-transport\"},{\"id\":\"heritage-science\",\"name\":\"Heritage Science\",\"description\":\"

Heritage Science community gateway is managed by the IPERION HS Research Infrastructure EU project. 

Heritage science is the interdisciplinary domain of scientific  study  of  cultural  or  natural  heritage. Heritage science draws on  diverse  humanities, sciences  and  engineering  disciplines. It  focuses  on  enhancing  the  understanding,  care  and  sustainable  use  of  heritage  so it  can enrich people's lives, both today and in the future. Heritage science is an umbrella term encompassing all forms of scientific enquiry into human works and the combined works of nature and humans, of value to people.

The gateway aims at including all the relevant research outcomes in  this  field.

 

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"\"},{\"id\":\"ni\",\"name\":\"Neuroinformatics\",\"description\":\"The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"oac_ni\"},{\"id\":\"dh-ch\",\"name\":\"Digital Humanities and Cultural Heritage\",\"description\":\"This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"oac_dh-ch\"},{\"id\":\"eutopia\",\"name\":\"EUTOPIA Open Research Portal\",\"description\":\"

EUTOPIA is an ambitious alliance of 10 like-minded universities ready to reinvent themselves: the Babeș-Bolyai University in Cluj-Napoca (Romania), the Vrije Universiteit Brussel (Belgium), the Ca'Foscari University of Europe (Italy), CY Cergy Paris Université (France), the Technische Universität Dresden (Germany), the University of Gothenburg (Sweden), the University of Ljubljana (Slovenia), the NOVA University Lisbon (Portugal), the University of Pompeu Fabra (Spain) and the University of Warwick (United Kingdom). Together, these 10 pioneers join forces to build the university of the future.

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"\"},{\"id\":\"sdsn-gr\",\"name\":\"Sustainable Development Solutions Network - Greece\",\"description\":\"The UN Sustainable Development Solutions Network (SDSN) has been operating since 2012 under the auspices of the UN Secretary-General. SDSN mobilizes global scientific and technological expertise to promote practical solutions for sustainable development, including the implementation of the Sustainable Development Goals (SDGs) and the Paris Climate Agreement. The Greek hub of SDSN has been included in the SDSN network in 2017 and is co-hosted by ICRE8: International Center for Research on the Environment and the Economy and the Political Economy of Sustainable Development Lab.\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"oac_sdsn-greece\"},{\"id\":\"covid-19\",\"name\":\"Corona Virus Disease\",\"description\":\"

This portal provides access to publications, research data, projects and software that may be relevant to the Corona Virus Disease (COVID-19). The OpenAIRE COVID-19 Gateway aggregates COVID-19 related records, links them and provides a single access point for discovery and navigation. We tag content from the OpenAIRE Research Graph (10,000+ data sources) and additional sources. All COVID-19 related research results are linked to people, organizations and projects, providing a contextualized navigation.

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"covid-19\"},{\"id\":\"enermaps\",\"name\":\"Welcome to EnerMaps Gateway! Find the latest scientific data.\",\"description\":\"

EnerMaps Open Data Management Tool aims to  improve data management  and  accessibility  in the field of  energy research  for the  renewable energy industry.

EnerMaps’ tool accelerates and facilitates the energy transition offering a qualitative and user-friendly digital platform to the energy professionals.

The project is based on the  FAIR data principle  which requires data to be  Findable,  Accessible,  Interoperable and  Reusable.

EnerMaps project  coordinates and enriches existing energy databases to promote  trans-disciplinary research  and to develop partnerships between researchers and the energy professionals.

The EnerMaps project has received funding from the European Union’s Horizon 2020 research and innovation program under   grant agreement N°884161. 

 

Website:  https://enermaps.eu/ 

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"\"},{\"id\":\"eu-conexus\",\"name\":\"European University for Smart Urban Coastal Sustainability\",\"description\":\"

The European University for Smart Urban Coastal Sustainability - EU-CONEXUS promotes common European values and a strengthened European identity by bringing together a new generation of Europeans, who can cooperate and work within different European cultures, in different languages and across borders, sectors and academic disciplines. EU-CONEXUS is committed to creating a new institutional framework for higher education in Europe that allows for a truly European way of studying and carrying out research through institutional alignment and seamless mobility for all. 

The thematic framework Smart Urban Coastal Sustainability (SmUCS) means for EU-CONEXUS to focus its research & innovation, education and knowledge sharing activities on societal challenges that are linked to a specific geographical location – the urban and semi-urbanised coastal (rivers and oceans) regions. SmUCS is not a subject-driven thematic framework, but a challenge-driven education and research domain.

\",\"status\":\"all\",\"type\":\"community\",\"subjects\":null,\"zenodoCommunity\":\"\"}]"; - - private static String workingDir; - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(CreateEntityTest.class.getSimpleName()) - .toString(); - } - - @Test - void test1() throws IOException { - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - UtilCommunityAPI queryCommunityAPI = new UtilCommunityAPI(); - new ObjectMapper() - .readValue(validCommunities, CommunityModelList.class) - .forEach(ri -> consumer.accept(queryCommunityAPI.getContext(ri))); - - List riList = new ArrayList<>(); - cInfoList.forEach(cInfo -> riList.add(Process.getEntity(cInfo))); - - Assertions.assertEquals(25, riList.size()); - - riList.stream().forEach(c -> { - switch (c.getAcronym()) { - case "mes": - Assertions - .assertTrue(c.getType().equals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_COMMUNITY)); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().size() == 5); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("marine")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("ocean")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("fish")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("aqua")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("sea")); - Assertions - .assertTrue( - c - .getId() - .equals( - String - .format( - "%s::%s", Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5(c.getAcronym())))); - Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_mes")); - Assertions.assertTrue("mes".equals(c.getAcronym())); - break; - case "clarin": - Assertions - .assertTrue(c.getType().equals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_INFRASTRUCTURE)); - Assertions - .assertTrue( - c - .getId() - .equals( - String - .format( - "%s::%s", Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5(c.getAcronym())))); - Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_clarin")); - Assertions.assertTrue("clarin".equals(c.getAcronym())); - break; - } - // TODO add check for all the others Entities - - }); - - riList.forEach(c -> System.out.println(new Gson().toJson(c))); - } - - @Test - @Disabled - void test2() throws IOException { - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - - Path hdfsWritePath = new Path(workingDir + "/prova"); - FSDataOutputStream fsDataOutputStream = null; - if (fs.exists(hdfsWritePath)) { - fsDataOutputStream = fs.append(hdfsWritePath); - } else { - fsDataOutputStream = fs.create(hdfsWritePath); - } - CompressionCodecFactory factory = new CompressionCodecFactory(fs.getConf()); - CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); - - BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), - StandardCharsets.UTF_8)); - - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - UtilCommunityAPI queryCommunityAPI = new UtilCommunityAPI(); - queryCommunityAPI.getContextInformation().forEach(ci -> consumer.accept(ci)); - - for (ContextInfo cInfo : cInfoList) { - writer.write(new Gson().toJson(Process.getEntity(cInfo))); - } - writer.close(); - - } -} - -class CommunityModelList extends ArrayList { - public CommunityModelList() { - super(); - } -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java deleted file mode 100644 index d399ec7..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java +++ /dev/null @@ -1,194 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.util.*; -import java.util.function.Consumer; -import java.util.stream.Collectors; - -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; - -import eu.dnetlib.dhp.communityapi.QueryCommunityAPI; -import eu.dnetlib.dhp.oa.graph.dump.UtilCommunityAPI; -import eu.dnetlib.dhp.oa.graph.dump.subset.MasterDuplicate; -import eu.dnetlib.dhp.oa.model.graph.Relation; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.utils.DHPUtils; - -class CreateRelationTest { - - String contextInfo1 = "{\"id\":\"eut\",\"description\":null,\"type\":null,\"zenodocommunity\":null,\"name\":null,\"projectList\":[],\"datasourceList\":[\"opendoar____::39e4973ba3321b80f37d9b55f63ed8b8\",\"opendoar____::cda72177eba360ff16b7f836e2754370\",\"opendoar____::71f6278d140af599e06ad9bf1ba03cb0\",\"opendoar____::f5c59267dae7d123f54b741a76f28f84\",\"opendoar____::532a082cc38eaffa923d73bce41b4061\",\"opendoar____::00a03ec6533ca7f5c644d198d815329c\",\"opendoar____::33a854e247155d590883b93bca53848a\"],\"subject\":null}"; - String contextInfo2 = "{\"id\":\"knowmad\",\"description\":null,\"type\":null,\"zenodocommunity\":null,\"name\":null,\"projectList\":[],\"datasourceList\":[\"issn___print::81db6614a3fa07becf706193d4754f30\",\"doajarticles::71eae002613af3569ea42b7093eefdbd\",\"doajarticles::daf53452e1199952d6c95ee7d0088d35\",\"issn___print::ff1a02f622ff006edc668e55fc865ae8\",\"doajarticles::14c007581eb12d843050ebf0493f2254\",\"issn__online::14c007581eb12d843050ebf0493f2254\",\"doajarticles::19a7308c7287b3784aacdb1979141c50\",\"doajarticles::c28985d2363f1ed20048dfd682ee14be\",\"issn__online::c28985d2363f1ed20048dfd682ee14be\",\"doajarticles::81db6614a3fa07becf706193d4754f30\",\"doajarticles::588fc0f98218e9f29a0dabe1182851c4\",\"doajarticles::5ccbe475390dfa642a356c7fd678b70a\",\"doajarticles::cf63b988539f8d28ed366220691f751b\",\"doajarticles::c03353a080ac66c37a1f6aa2de05ca63\",\"issn__online::efec4cc1b1143f69d7d0954a2e9b18b6\",\"doajarticles::25ddd7bb737fc8b027b455f6712111a0\",\"doajarticles::ca2e3cc507ff73298333ed53177e9916\",\"doajarticles::220ab67f748963b6932600585452ad83\",\"doajarticles::b718013941a35a86b17b9b57aca9d260\",\"doajarticles::934e4b68deaeee0781f18a6a6e4fd906\",\"doajarticles::43587737046be23d692860e3212d6966\",\"doajarticles::23a27fb45b9af1f2b57632b7ceb98448\",\"doajarticles::9d32313b109db4f024eb1c802ad4e353\",\"fairsharing_::b4944963b5c83d545c3d3022bcf03282\",\"doajarticles::b5a2cadc830f94ceb2f8035369cf66a1\",\"doajarticles::8d64614210c51d4bc9e1470bbe1b5607\",\"doajarticles::e258604e7e1132683570d4178e9bec8f\",\"doajarticles::260c4ba804c4c08842ad39a6e8fd2a97\",\"doajarticles::8c9f0a0c20cb062a0ab7823af8262d0e\",\"issn__online::ef2866d8e4561162a1b115c24ebd7887\",\"doajarticles::de16206a48e58e344ef049670a1a0134\",\"doajarticles::96621c5056169f56ff3131ea90aa07c9\",\"issn__online::4558a062701b28ec0b4a6b2f0fbe8d09\",\"issn___print::5571b62bd2e69e2311990fceb7fe2e3a\",\"doajarticles::c61ecda4a5a75b94a28b1c782008e64c\",\"doajarticles::fd825a036d04fcdf0ab805d87e16d1de\",\"issn___print::61d35d3f7e7f635fa9818eb5c5724833\",\"doajarticles::685e5ac5fb55c74ee8a2b266923e1f1d\",\"doajarticles::b99614718f7a6545b1eed9b68d3441de\",\"doajarticles::7d2d2e0095bf1ec755bf3e39d31a5bcb\",\"doajarticles::6124a1bc19d8f538c1bb45da8fda914b\",\"issn___print::6f2e006697b7a4f9d6e2e4d61d9e87c2\",\"issn___print::24d6c4cc60c9446680a4bf6464f232cc\",\"issn___print::0482ed6012f16fa029dd0434b644cb90\",\"issn___print::74d68388e8ad50f80b754f5036c80fcf\",\"issn__online::22b586e63e4962054a332a538e5d2b71\",\"issn___print::4bceffb60baed7f1e3f25b171b8fcf63\",\"issn__online::4074709fc410b3be61ea1769634ae8ff\",\"issn__online::d787423124beb54d12945b8fb6effe17\",\"issn__online::92d6a58173da7e479557acb8701da9dc\",\"issn___print::36813e86616b329b06101afab0f2d115\",\"issn___print::60f102cf59ddbfc2297dbfd2efe1c006\",\"issn__online::e2bedb8ffd0dd9a05af59c2651eb4200\",\"issn___print::3a5263873041ce993d856c3a08b87e66\",\"issn___print::c0118216b90b4ec13c4344c302eb1cc2\",\"issn___print::36cb3b21af46a23327d120d848ac5256\",\"issn___print::f6528b255fa5b915efddf5bdd4b12bef\",\"issn___print::50ae07b765e6c893d93701b63dc885eb\",\"issn___print::1efd4ac736f64f83bc537339bf112882\",\"issn___print::f46704a2eb1338c3524391c7fcdc5f50\",\"issn__online::6e823cb8d73afda60e12a0ce7ec65fe3\",\"doajarticles::df6746f5d17a6c27cf1033e2888b934d\",\"issn___print::8a8a700ac926378b330e57d7faf5948e\",\"issn___print::6fbc352ab2267a17490b922033c2ce8c\",\"issn___print::692e57ca190e52967683bca19dcc6200\",\"issn___print::4f657189126a3c51cf8f2d58410d09b8\",\"issn___print::2fd71afb352b4ec1ee58b2bfa4d536da\",\"doajarticles::e91e4788bfb04277b61416fd184416b2\",\"issn__online::3097c43f11470b27e74f040cf267eedf\",\"doajarticles::942ba9d488531f3a60633b716db0b05c\",\"doajarticles::1aefeb2e98d29b17473e3f4dbcc5000e\",\"issn___print::223b857892c5de7247b3f906e1e1b96a\",\"doajarticles::b64f9c27d2c8899df904930cd6d2316a\"],\"subject\":null}"; - String contextInfo3 = "{\"id\":\"ni\",\"description\":null,\"type\":null,\"zenodocommunity\":null,\"name\":null,\"projectList\":[\"nih_________::412379d1e2683a9571405e6621d3cdeb\",\"nsf_________::1e685a3d3ca1d62192bb51d42d44c6d1\",\"nsf_________::8ff441b675f2c62061f15210b05c1584\",\"nih_________::2d8bd32ed8cb2f0b0d4508df61d494dd\",\"nsf_________::e71b0a0f6a347d76816adb29b322441c\",\"nih_________::c27d60d28c9bc5cf17dd7ae7ad2d4ab4\",\"nih_________::b28919975c85cfee114e442c30c918c6\",\"wt__________::d709ac8e1ed393d036c895d239d825a4\"],\"datasourceList\":[\"re3data_____::5b9bf9171d92df854cf3c520692e9122\",\"doajarticles::c7d3de67dc77af72f6747157441252ec\",\"re3data_____::8515794670370f49c1d176c399c714f5\",\"doajarticles::d640648c84b10d425f96f11c3de468f3\",\"doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a\",\"rest________::fb1a3d4523c95e63496e3bc7ba36244b\",\"opendoar____::7e7757b1e12abcb736ab9a754ffb617a\"],\"subject\":null}"; - - @Test - void test1() throws IOException { - ObjectMapper mapper = new ObjectMapper(); - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - - consumer.accept(mapper.readValue(contextInfo1, ContextInfo.class)); - consumer.accept(mapper.readValue(contextInfo2, ContextInfo.class)); - consumer.accept(mapper.readValue(contextInfo3, ContextInfo.class)); - - List rList = new ArrayList<>(); - - cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add)); - - Assertions.assertEquals(190, rList.size()); - - Assertions - .assertTrue( - rList - .stream() - .map(r -> r.getSource()) - .collect(Collectors.toSet()) - .contains( - String - .format( - "%s::%s", - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("eut")))); - - Assertions - .assertEquals( - 7, - rList - .stream() - .filter( - r -> r - .getSource() - - .equals( - String - .format( - "%s::%s", - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("eut")))) - .collect(Collectors.toList()) - .size()); - - Assertions - .assertEquals( - 7, - rList - .stream() - .filter( - r -> r - .getTarget() - - .equals( - String - .format( - "%s::%s", - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("eut")))) - .collect(Collectors.toList()) - .size()); - - Set tmp = rList - .stream() - .filter( - r -> r - .getSource() - - .equals( - String - .format( - "%s::%s", - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("eut")))) - .map(r -> r.getTarget()) - .collect(Collectors.toSet()); - - Assertions - .assertTrue( - tmp.contains("opendoar____::532a082cc38eaffa923d73bce41b4061") && - tmp.contains("opendoar____::00a03ec6533ca7f5c644d198d815329c") && - tmp.contains("opendoar____::33a854e247155d590883b93bca53848a") && - tmp.contains("opendoar____::71f6278d140af599e06ad9bf1ba03cb0") && - tmp.contains("opendoar____::f5c59267dae7d123f54b741a76f28f84") && - tmp.contains("opendoar____::cda72177eba360ff16b7f836e2754370") && - tmp.contains("opendoar____::39e4973ba3321b80f37d9b55f63ed8b8")); - - Assertions - .assertTrue( - rList - .stream() - .filter( - r -> r - .getSource() - - .equals( - String - .format( - "%s::%s", - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("eut")))) - .map(r -> r.getTargetType()) - .collect(Collectors.toSet()) - .stream() - .allMatch(t -> t.equals("datasource"))); - - Assertions - .assertEquals( - 15, - rList - .stream() - .filter( - r -> r - .getTarget() - - .equals( - String - .format( - "%s::%s", - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("ni")))) - .collect(Collectors.toList()) - .size()); - - Assertions - .assertEquals( - 7, rList - .stream() - .filter( - r -> r - .getSource() - .equals( - String - .format( - "%s::%s", - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("ni"))) - && - r.getTargetType().equals("datasource")) - .count()); - - Assertions - .assertEquals( - 8, rList - .stream() - .filter( - r -> r - .getSource() - .equals( - String - .format( - "%s::%s", - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("ni"))) - && - r.getTargetType().equals("project")) - .count()); - } - -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java deleted file mode 100644 index 58fae3c..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java +++ /dev/null @@ -1,267 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -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.ForeachFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; -import eu.dnetlib.dhp.oa.model.Indicator; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.Project; - -public class DumpOrganizationProjectDatasourceTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(DumpOrganizationProjectDatasourceTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(DumpOrganizationProjectDatasourceTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(DumpOrganizationProjectDatasourceTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(DumpOrganizationProjectDatasourceTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void dumpOrganizationTest() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/organization") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Organization", - "-outputPath", workingDir.toString() + "/dump" - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.oa.model.graph.Organization.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.oa.model.graph.Organization.class)); - - Assertions.assertEquals(15, verificationDataset.count()); - - // TODO write significant assertions -// verificationDataset -// .foreach( -// (ForeachFunction) o -> System.out -// .println(OBJECT_MAPPER.writeValueAsString(o))); - - } - - @Test - public void dumpProjectTest() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/project") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Project", - "-outputPath", workingDir.toString() + "/dump" - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.oa.model.graph.Project.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.oa.model.graph.Project.class)); - - Assertions.assertEquals(12, verificationDataset.count()); - - Assertions.assertEquals(10, verificationDataset.filter("indicators is NULL").count()); - Assertions.assertEquals(2, verificationDataset.filter("indicators is not NULL").count()); - Assertions - .assertEquals( - 1, - verificationDataset - .filter("indicators is not NULL AND id == 'aka_________::01bb7b48e29d732a1c7bc5150b9195c4'") - .count()); - Assertions - .assertEquals( - 1, - verificationDataset - .filter("indicators is not NULL AND id == 'aka_________::9d1af21dbd0f5bc719f71553d19a6b3a'") - .count()); - -// eu.dnetlib.dhp.oa.model.graph.Project p = tmp -// .filter(pr -> pr.getId().equals("aka_________::01bb7b48e29d732a1c7bc5150b9195c4")) -// .first(); -// Assertions.assertEquals("2019", p.getIndicators().getUsageCounts().getDownloads()); -// Assertions.assertEquals("1804", p.getIndicators().getUsageCounts().getViews()); -// Assertions.assertNull(p.getIndicators().getImpactMeasures()); - -// p = tmp.filter(pr -> pr.getId().equals("aka_________::9d1af21dbd0f5bc719f71553d19a6b3a")).first(); -// Assertions.assertEquals("139", p.getIndicators().getUsageCounts().getDownloads()); -// Assertions.assertEquals("53", p.getIndicators().getUsageCounts().getViews()); -// Assertions.assertNull(p.getIndicators().getImpactMeasures()); - // TODO write significant assertions -// verificationDataset -// .foreach( -// (ForeachFunction) o -> System.out -// .println(OBJECT_MAPPER.writeValueAsString(o))); - - } - - @Test - public void dumpDatasourceTest() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/datasource") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Datasource", - "-outputPath", workingDir.toString() + "/dump" - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.oa.model.graph.Datasource.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.oa.model.graph.Datasource.class)); - - Assertions.assertEquals(5, verificationDataset.count()); - - Assertions.assertEquals(3, verificationDataset.filter("indicators is NULL").count()); - Assertions.assertEquals(2, verificationDataset.filter("indicators is not NULL").count()); - Assertions - .assertEquals( - 1, - verificationDataset - .filter("indicators is not NULL AND id == 'doajarticles::1fa6859d71faa77b32d82f278c6ed1df'") - .count()); - Assertions - .assertEquals( - 1, - verificationDataset - .filter("indicators is not NULL AND id == 'doajarticles::9c4b678901e5276d9e3addee566816af'") - .count()); - -// eu.dnetlib.dhp.oa.model.graph.Datasource p = tmp -// .filter(pr -> pr.getId().equals("doajarticles::1fa6859d71faa77b32d82f278c6ed1df")) -// .first(); -// Assertions.assertEquals("47542", p.getIndicators().getUsageCounts().getDownloads()); -// Assertions.assertEquals("36485", p.getIndicators().getUsageCounts().getViews()); -// Assertions.assertNull(p.getIndicators().getImpactMeasures()); -// -// p = tmp.filter(pr -> pr.getId().equals("doajarticles::9c4b678901e5276d9e3addee566816af")).first(); -// Assertions.assertEquals("981357", p.getIndicators().getUsageCounts().getDownloads()); -// Assertions.assertEquals("646539", p.getIndicators().getUsageCounts().getViews()); -// Assertions.assertNull(p.getIndicators().getImpactMeasures()); - - // TODO write significant assertions -// verificationDataset -// .foreach( -// (ForeachFunction) o -> System.out -// .println(OBJECT_MAPPER.writeValueAsString(o))); - } - - @Test - public void dumpDatasourceNotDumpedTest() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/datasourcenotdumped") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Datasource", - "-outputPath", workingDir.toString() + "/dump" - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.oa.model.graph.Datasource.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.oa.model.graph.Datasource.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - // TODO write significant assertions -// verificationDataset -// .foreach( -// (ForeachFunction) o -> System.out -// .println(OBJECT_MAPPER.writeValueAsString(o))); - } - -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java deleted file mode 100644 index 2ac7afd..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java +++ /dev/null @@ -1,305 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -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.ForeachFunction; -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.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.model.graph.Relation; - -public class DumpRelationTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(DumpRelationTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(DumpRelationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(DumpRelationTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(DumpRelationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source, sourceType stype, target,targetType ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 22, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count()); - Assertions - .assertEquals( - 7, check - .filter( - "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + - "and provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); - Assertions - .assertEquals( - 1, check - .filter( - "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + - "and provenance = 'Inferred by OpenAIRE'") - .count()); - } - - @Test - public void test2() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source, sourceType stype, target,targetType ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(20, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 20, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count()); - Assertions - .assertEquals( - 7, check - .filter( - "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + - "and provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); - Assertions - .assertEquals( - 1, check - .filter( - "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + - "and provenance = 'Inferred by OpenAIRE'") - .count()); - - Assertions.assertEquals(2, check.filter("name = 'isProducedBy'").count()); - Assertions - .assertEquals( - 2, check - .filter( - "name = 'isProducedBy' and stype = 'project' and ttype = 'result' " + - "and provenance = 'Harvested' and validated = true " + - "and validationDate = '2021-08-06'") - .count()); - } - - @Test - public void test3() throws Exception {// - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath, - "-removeSet", "isParticipant" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source, sourceType stype, target,targetType ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 22, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(0, check.filter("name = 'isParticipant'").count()); - - Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); - Assertions - .assertEquals( - 1, check - .filter( - "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + - "and provenance = 'Inferred by OpenAIRE'") - .count()); - } - - @Test - public void test4() throws Exception {// - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath, - "-removeSet", "isParticipant;isAuthorInstitutionOf" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source, sourceType stype, target,targetType ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 22, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(0, check.filter("name = 'isParticipant'").count()); - - Assertions.assertEquals(0, check.filter("name = 'isAuthorInstitutionOf'").count()); - - } - -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/ExtractRelationFromEntityTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/ExtractRelationFromEntityTest.java deleted file mode 100644 index 01a9f5d..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/ExtractRelationFromEntityTest.java +++ /dev/null @@ -1,200 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -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.FilterFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.model.graph.Relation; - -public class ExtractRelationFromEntityTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(ExtractRelationFromEntityTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(ExtractRelationFromEntityTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(ExtractRelationFromEntityTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(ExtractRelationFromEntityTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - Extractor ex = new Extractor(); - ex - .run( - false, sourcePath, workingDir.toString() + "/relation", - // eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); - eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.show(false); - - Assertions - .assertEquals( - 9, - verificationDataset.filter("source = 'dedup_wf_001::15270b996fa8fd2fb5723daeab3685c3'").count()); - - Assertions - .assertEquals( - 9, - verificationDataset.filter("source = 'dedup_wf_001::15270b996fa8fd2fb5723daxab3685c3'").count()); - - Assertions - .assertEquals( - "IsRelatedTo", verificationDataset - .filter((FilterFunction) row -> row.getSourceType().equals("context")) - .collectAsList() - .get(0) - .getReltype() - .getName()); - - Assertions - .assertEquals( - "relationship", verificationDataset - .filter((FilterFunction) row -> row.getSourceType().equals("context")) - .collectAsList() - .get(0) - .getReltype() - .getType()); - - Assertions - .assertEquals( - "context", verificationDataset - .filter((FilterFunction) row -> row.getSourceType().equals("context")) - .collectAsList() - .get(0) - .getSourceType()); - - Assertions - .assertEquals( - "result", verificationDataset - .filter((FilterFunction) row -> row.getSourceType().equals("context")) - .collectAsList() - .get(0) - .getTargetType()); - Assertions - .assertEquals( - "IsRelatedTo", verificationDataset - .filter((FilterFunction) row -> row.getTargetType().equals("context")) - .collectAsList() - .get(0) - .getReltype() - .getName()); - - Assertions - .assertEquals( - "relationship", verificationDataset - .filter((FilterFunction) row -> row.getTargetType().equals("context")) - .collectAsList() - .get(0) - .getReltype() - .getType()); - - Assertions - .assertEquals( - "context", verificationDataset - .filter((FilterFunction) row -> row.getTargetType().equals("context")) - .collectAsList() - .get(0) - .getTargetType()); - - Assertions - .assertEquals( - "result", verificationDataset - .filter((FilterFunction) row -> row.getTargetType().equals("context")) - .collectAsList() - .get(0) - .getSourceType()); - } - - @Test - void sdsdTest() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/sdsn-gr_publication.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - Extractor ex = new Extractor(); - ex - .run( - false, sourcePath, workingDir.toString() + "/relation", - // eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); - eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); - - } -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/FunderParsingTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/FunderParsingTest.java deleted file mode 100644 index b64df6e..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/FunderParsingTest.java +++ /dev/null @@ -1,70 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import org.dom4j.DocumentException; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.Test; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.oa.model.graph.Funder; - -class FunderParsingTest { - - @Test - void testFunderTwoLevels() throws DocumentException { - - String funding_Stream = "nsf_________::NSFNSFNational Science " - + - "FoundationUSnsf_________::NSF::CISE/OAD::CISE/CCFDivision " - + - "of Computing and Communication FoundationsDivision of Computing and Communication " + - "Foundationsnsf_________::NSF::CISE/OADDirectorate for " - + - "Computer & Information Science & EngineeringDirectorate for Computer & " + - "Information Science & Engineeringnsf:fundingStream"; - - Funder f = SparkDumpEntitiesJob.getFunder(funding_Stream); - - Assertions.assertEquals("NSF", f.getShortName()); - Assertions.assertEquals("National Science Foundation", f.getName()); - Assertions.assertEquals("US", f.getJurisdiction()); - - Assertions.assertEquals("NSF::CISE/OAD::CISE/CCF", f.getFunding_stream().getId()); - Assertions - .assertEquals( - "Directorate for Computer & Information Science & Engineering - Division of Computing and Communication Foundations", - f.getFunding_stream().getDescription()); - - } - - @Test - void testFunderThreeeLevels() throws DocumentException, SAXException { - String funding_stream = "ec__________::EC" + - "EC" + - "European Commission" + - "EU" + - "" + - "ec__________::EC::H2020::ERC::ERC-COG" + - "Consolidator Grant" + - "ERC-COGec:h2020toas" + - "ec__________::EC::H2020::ERC" + - "European Research Council" + - "ERCec:h2020fundings" + - "ec__________::EC::H2020H2020" + - "Horizon 2020 Framework Programme" + - "ec:h2020fundings"; - - Funder f = SparkDumpEntitiesJob.getFunder(funding_stream); - - Assertions.assertEquals("EC", f.getShortName()); - Assertions.assertEquals("European Commission", f.getName()); - Assertions.assertEquals("EU", f.getJurisdiction()); - - Assertions.assertEquals("EC::H2020::ERC::ERC-COG", f.getFunding_stream().getId()); - Assertions - .assertEquals( - "Horizon 2020 Framework Programme - European Research Council - Consolidator Grant", - f.getFunding_stream().getDescription()); - - } -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/RelationFromOrganizationTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/RelationFromOrganizationTest.java deleted file mode 100644 index 78b1374..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/RelationFromOrganizationTest.java +++ /dev/null @@ -1,123 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; -import java.util.regex.Matcher; -import java.util.regex.Pattern; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.model.graph.Relation; - -public class RelationFromOrganizationTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(RelationFromOrganizationTest.class); - - private static final HashMap map = new HashMap<>(); - - String organizationCommunityMap = "{\"20|grid________::afaa39865943381c51f76c08725ffa75\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e8dbe14cca9bf6fce09d468872f813f8\":[\"mes\",\"euromarine\"], \"20|snsf________::9b253f265e3bef5cae6d881fdf61aceb\":[\"mes\",\"euromarine\"],\"20|rcuk________::e054eea0a47665af8c3656b5785ccf76\":[\"mes\",\"euromarine\"],\"20|corda__h2020::edc18d67c9b11fb616ca9f6e1db1b151\":[\"mes\",\"euromarine\"],\"20|rcuk________::d5736d9da90521ddcdc7828a05a85e9a\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f5d418d3aa1cf817ddefcc3fdc039f27\":[\"mes\",\"euromarine\"],\"20|snsf________::8fa091f8f25a846779acb4ea97b50aef\":[\"mes\",\"euromarine\"],\"20|corda__h2020::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|corda_______::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|snsf________::31d0a100e54e3cdb3c6f52d91e638c78\":[\"mes\",\"euromarine\"],\"20|corda__h2020::ea379ef91b8cc86f9ac5edc4169292db\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f75ee2ee48e5cb0ec8c8d30aaa8fef70\":[\"mes\",\"euromarine\"],\"20|rcuk________::e16010089551a1a9182a94604fc0ea59\":[\"mes\",\"euromarine\"],\"20|corda__h2020::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|corda_______::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|grid________::b2cbbf5eadbbf87d534b022bad3191d7\":[\"mes\",\"euromarine\"],\"20|snsf________::74730ef1439d7f7636a8be58a6b471b8\":[\"mes\",\"euromarine\"],\"20|nsf_________::ad72e19043a5a467e35f9b444d11563e\":[\"mes\",\"euromarine\"],\"20|rcuk________::0fc3e92500290902a2d38ec2445e74c3\":[\"mes\",\"euromarine\"],\"20|grid________::ad2c29905da0eb3c06b3fa80cacd89ea\":[\"mes\",\"euromarine\"],\"20|corda__h2020::30b53e4d63d3724f00acb9cbaca40860\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f60f84bee14ad93f0db0e49af1d5c317\":[\"mes\",\"euromarine\"], \"20|corda__h2020::7bf251ac3765b5e89d82270a1763d09f\":[\"mes\",\"euromarine\"], \"20|corda__h2020::65531bd11be9935948c7f2f4db1c1832\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e0e98f86bbc76638bbb72a8fe2302946\":[\"mes\",\"euromarine\"], \"20|snsf________::3eb43582ac27601459a8d8b3e195724b\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af2481dab65d06c8ea0ae02b5517b9b6\":[\"mes\",\"euromarine\"], \"20|corda__h2020::c19d05cfde69a50d3ebc89bd0ee49929\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af0bfd9fc09f80d9488f56d71a9832f0\":[\"mes\",\"euromarine\"], \"20|rcuk________::f33c02afb0dc66c49d0ed97ca5dd5cb0\":[\"beopen\"], " - + - "\"20|grid________::a867f78acdc5041b34acfe4f9a349157\":[\"beopen\"], \"20|grid________::7bb116a1a9f95ab812bf9d2dea2be1ff\":[\"beopen\"], \"20|corda__h2020::6ab0e0739dbe625b99a2ae45842164ad\":[\"beopen\"], \"20|corda__h2020::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda_______::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda__h2020::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::15911e01e9744d57205825d77c218737\":[\"beopen\"], \"20|opendoar____::056a41e24e2a9a67215e87bbee6a80ab\":[\"beopen\"], \"20|opendoar____::7f67f2e6c6fbb0628f8160fcd3d92ae3\":[\"beopen\"], \"20|grid________::a8ecfd7c084e561168bcbe6bf0daf3e3\":[\"beopen\"], \"20|corda_______::7bbe6cc5d8ec1864739a04b0d020c9e9\":[\"beopen\"], \"20|corda_______::3ff558e30c2e434d688539548300b050\":[\"beopen\"], \"20|corda__h2020::5ffee5b3b83b33a8cf0e046877bd3a39\":[\"beopen\"], \"20|corda__h2020::5187217e2e806a6df3579c46f82401bc\":[\"beopen\"], \"20|grid________::5fa7e2709bcd945e26bfa18689adeec1\":[\"beopen\"], \"20|corda_______::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|corda__h2020::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|rcuk________::23a79ebdfa59790864e4a485881568c1\":[\"beopen\"], \"20|corda__h2020::b76cf8fe49590a966953c37e18608af9\":[\"beopen\"], \"20|grid________::d2f0204126ee709244a488a4cd3b91c2\":[\"beopen\"], \"20|corda__h2020::05aba9d2ed17533d15221e5655ac11e6\":[\"beopen\"], \"20|grid________::802401579481dc32062bdee69f5e6a34\":[\"beopen\"], \"20|corda__h2020::3f6d9d54cac975a517ba6b252c81582d\":[\"beopen\"]}"; - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(RelationFromOrganizationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(RelationFromOrganizationTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(RelationFromOrganizationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymapservices.json") - .getPath(); - - SparkOrganizationRelation.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath, - "-organizationCommunityMap", organizationCommunityMap, - "-communityMapPath", communityMapPath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - // Assertions.assertEquals(170, verificationDataset.count()); - Assertions.assertEquals(0, verificationDataset.count()); - -// Dataset checkDs = spark -// .sql( -// "Select source.id, source.type " + -// "from table "); -// -// Assertions.assertEquals(2, checkDs.filter("substr(id, 4, 5) = 'dedup' ").count()); -// -// Assertions.assertEquals(0, checkDs.filter("id = '20|grid________::afaa39865943381c51f76c08725ffa75'").count()); -// -// Assertions.assertEquals(25, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("beopen") + "'").count()); -// -// Assertions -// .assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("euromarine") + "'").count()); -// -// Assertions.assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("mes") + "'").count()); - } - -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java deleted file mode 100644 index d430376..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java +++ /dev/null @@ -1,95 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.oaf.Relation; - -public class SelectRelationTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(SelectRelationTest.class); - - private static HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(SelectRelationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(SelectRelationTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(SelectRelationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/selectrelations") - .getPath(); - - SparkSelectValidRelationsJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - Assertions.assertTrue(verificationDataset.count() == 7); - - } - -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/country/FindResultRelatedToCountryTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/country/FindResultRelatedToCountryTest.java deleted file mode 100644 index b5991bb..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/country/FindResultRelatedToCountryTest.java +++ /dev/null @@ -1,96 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.country; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.neethi.Assertion; -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.FilterFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -/** - * @author miriam.baglioni - * @Date 02/05/23 - */ -public class FindResultRelatedToCountryTest { - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(FindResultRelatedToCountryTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(FindResultRelatedToCountryTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(FindResultRelatedToCountryTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(FindResultRelatedToCountryTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/country/graph") - .getPath(); - - SparkFindResultsRelatedToCountry.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/resultWithCountry", - "-sourcePath", sourcePath, - "-country", "PT" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/resultWithCountry"); - - Assertions.assertEquals(3, tmp.count()); - - Assertions.assertTrue(tmp.collect().contains("50|06cdd3ff4700::136eb030ccb020e170df9627fa1a70af")); - Assertions.assertTrue(tmp.collect().contains("50|06cdd3ff4700::93859bd27121c3ee7c6ee4bfb1790cbb")); - Assertions.assertTrue(tmp.collect().contains("50|06cdd3ff4700::136eb030ccb020e170df9627fa1a70ag")); - - } -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/country/FindResultWithCountryTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/country/FindResultWithCountryTest.java deleted file mode 100644 index b1c0331..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/country/FindResultWithCountryTest.java +++ /dev/null @@ -1,115 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.country; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.security.PublicKey; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -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.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.model.graph.Relation; -import eu.dnetlib.dhp.schema.oaf.Publication; - -/** - * @author miriam.baglioni - * @Date 02/05/23 - */ -public class FindResultWithCountryTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(FindResultWithCountryTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(FindResultWithCountryTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(FindResultWithCountryTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(FindResultWithCountryTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/country/graph/publication") - .getPath(); - - spark - .read() - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/country/resultWithCountry") - .getPath()) - .write() - .text(workingDir.toString() + "/resWithCountry"); - - SparkFindResultWithCountry.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/out", - "-sourcePath", sourcePath, - "-resultType", "publication", - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-resultWithCountry", workingDir.toString() + "/resWithCountry" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/out/original/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - - Assertions.assertEquals(2, tmp.count()); - - Assertions - .assertTrue( - tmp.map(p -> p.getId()).collect().contains("50|06cdd3ff4700::136eb030ccb020e170df9627fa1a70af")); - Assertions - .assertTrue( - tmp.map(p -> p.getId()).collect().contains("50|06cdd3ff4700::136eb030ccb020e170df9627fa1a70ag")); - - } -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/DumpCommunitiesTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/DumpCommunitiesTest.java deleted file mode 100644 index 605f1ec..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/DumpCommunitiesTest.java +++ /dev/null @@ -1,9 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv; - -/** - * @author miriam.baglioni - * @Date 11/05/23 - */ -public class DumpCommunitiesTest { -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/DumpResultTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/DumpResultTest.java deleted file mode 100644 index fa37c1b..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/DumpResultTest.java +++ /dev/null @@ -1,358 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv; - -import static org.apache.commons.lang3.StringUtils.split; - -import java.io.IOException; -import java.io.StringReader; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; -import java.util.Optional; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.ForeachFunction; -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.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Element; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVAuthor; -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVResult; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.utils.DHPUtils; -import scala.Function1; - -/** - * @author miriam.baglioni - * @Date 11/05/23 - */ -public class DumpResultTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(DumpResultTest.class); - - private static HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(DumpResultTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(DumpResultTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(DumpResultTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void testDumpResult() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/input/") - .getPath(); - - spark - .read() - .text( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/working/resultIds") - .getPath()) - .write() - .text(workingDir.toString() + "/working/resultIds/"); - - SparkDumpResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - - "-workingPath", workingDir.toString() + "/working", - "-resultType", "publication", - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - Dataset tmp = Utils - .readPath(spark, workingDir.toString() + "/working/publication/result", CSVResult.class); - - tmp.show(false); - - Assertions.assertEquals(5, tmp.count()); - CSVResult row = tmp - .filter( - (FilterFunction) r -> r.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) - .first(); - Assertions.assertEquals(ModelConstants.OPEN_ACCESS_RIGHT().getClassid(), row.getAccessright()); - Assertions.assertEquals("FI", row.getCountry()); - Assertions.assertEquals("Lit.opg., bijl.", row.getDescription()); - Assertions.assertEquals(3, split(row.getKeywords(), ", ").length); - Assertions.assertTrue(row.getKeywords().toString().contains("archeologie")); - Assertions.assertTrue(row.getKeywords().toString().contains("prospectie")); - Assertions.assertTrue(row.getKeywords().toString().contains("archaeology")); - Assertions.assertEquals("nl", row.getLanguage()); - Assertions.assertEquals("2007-01-01", row.getPublication_date()); - Assertions.assertEquals("FakePublisher1", row.getPublisher()); - Assertions - .assertEquals( - "Inventariserend veldonderzoek d.m.v. boringen (karterende fase) : Raadhuisstraat te Dirkshorn, gemeente Harenkarspel", - row.getTitle()); - Assertions.assertEquals("publication", row.getType()); - - row = tmp - .filter( - (FilterFunction) r -> r.getId().equals("50|doi_________::715fec7723208e6f17e855c204656e2f")) - .first(); - - System.out.println(row.getPublisher()); - String a = row.getPublisher().replace("\\n", " "); - System.out.println(a); -// row = tmp -// .where("id = '50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9'") -// .first(); -// Assertions.assertEquals(ModelConstants.OPEN_ACCESS_RIGHT().getClassid(), row.getAs("accessright")); -// Assertions.assertEquals(2, split(row.getAs("country"), ", ").length); -// Assertions.assertNull(row.getAs("description")); -// Assertions.assertEquals(2, split(row.getAs("keywords"), ", ").length); -// Assertions.assertTrue(row.getAs("keywords").toString().contains("archeologie")); -// Assertions.assertTrue(row.getAs("keywords").toString().contains("archaeology")); -// Assertions.assertEquals("UNKNOWN", row.getAs("language")); -// Assertions.assertNull(row.getAs("publication_date")); -// Assertions.assertNull(row.getAs("publisher")); -// Assertions.assertEquals("None", row.getAs("title")); -// Assertions.assertEquals("publication", row.getAs("type")); -// -// row = tmp -// .where("id = '50|DansKnawCris::26780065282e607306372abd0d808245'") -// .first(); -// Assertions.assertEquals(ModelConstants.OPEN_ACCESS_RIGHT().getClassid(), row.getAs("accessright")); -// Assertions.assertNull(row.getAs("country")); -// Assertions.assertNull(row.getAs("description")); -// Assertions.assertEquals(2, split(row.getAs("keywords"), ", ").length); -// Assertions.assertTrue(row.getAs("keywords").toString().contains("archeologie")); -// Assertions.assertTrue(row.getAs("keywords").toString().contains("archaeology")); -// Assertions.assertEquals("UNKNOWN", row.getAs("language")); -// Assertions.assertNull(row.getAs("publication_date")); -// Assertions.assertNull(row.getAs("publisher")); -// Assertions.assertEquals("None", row.getAs("title")); -// Assertions.assertEquals("publication", row.getAs("type")); - - } - - @Test - public void testDumpAuthor() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/input/") - .getPath(); - - spark - .read() - .text( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/working/resultIds") - .getPath()) - .write() - .text(workingDir.toString() + "/working/resultIds/"); - - SparkDumpResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - - "-workingPath", workingDir.toString() + "/working", - "-resultType", "publication", - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - Dataset tmp = Utils - .readPath(spark, workingDir.toString() + "/working/publication/author", CSVAuthor.class); - - Assertions.assertEquals(13, tmp.count()); - - Assertions.assertEquals(1, tmp.where("firstName == 'Maryam'").count()); - - Assertions - .assertEquals( - DHPUtils.md5("50|DansKnawCris::0224aae28af558f21768dbc6439c7a951"), - tmp.where("firstName == 'Maryam'").first().getId()); - Assertions - .assertEquals(DHPUtils.md5("0000-0003-2914-2734"), tmp.where("firstName == 'Michael'").first().getId()); - Assertions - .assertEquals( - DHPUtils.md5("0000-0002-6660-5673"), - tmp.where("firstName == 'Mikhail'").first().getId()); - - } - - @Test - public void testDumpResultAuthorRelations() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/input/") - .getPath(); - - spark - .read() - .text( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/working/resultIds") - .getPath()) - .write() - .text(workingDir.toString() + "/working/resultIds/"); - - SparkDumpResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/output", - "-workingPath", workingDir.toString() + "/working", - "-resultType", "publication", - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - Dataset tmp = spark - .read() - .option("header", "true") - .option("delimiter", Constants.SEP) - .csv(workingDir.toString() + "/working/publication/result_author"); - - Assertions.assertEquals(6, tmp.count()); - - Assertions.assertEquals(2, tmp.where("author_id == '" + DHPUtils.md5("0000-0003-2914-2734") + "'").count()); - Assertions - .assertEquals( - 1, tmp - .where("author_id == '" + DHPUtils.md5("0000-0003-2914-2734") + "'") - .where("result_id == '50|DansKnawCris::0224aae28af558f21768dbc6439c7a95'") - .count()); - Assertions - .assertEquals( - 1, tmp - .where("author_id == '" + DHPUtils.md5("0000-0003-2914-2734") + "'") - .where("result_id == '50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9'") - .count()); - - } - - @Test - public void testDumpResultPid() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/input/") - .getPath(); - - spark - .read() - .text( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/working/resultIds") - .getPath()) - .write() - .text(workingDir.toString() + "/working/resultIds/"); - - SparkDumpResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/output", - "-workingPath", workingDir.toString() + "/working", - "-resultType", "publication", - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - Dataset tmp = spark - .read() - .option("header", "true") - .option("delimiter", Constants.SEP) - .csv(workingDir.toString() + "/working/publication/result_pid"); - - tmp.show(false); - Assertions.assertEquals(4, tmp.count()); - - Assertions - .assertEquals(2, tmp.where("result_id == '50|DansKnawCris::0224aae28af558f21768dbc6439c7a95'").count()); - Assertions - .assertEquals( - "10.1023/fakedoi", - tmp - .where("result_id == '50|DansKnawCris::0224aae28af558f21768dbc6439c7a95' and type == 'doi'") - .first() - .getAs("pid")); - - } - - @Test - public void prova() throws DocumentException { - String input = "" + - " This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields." - + - ""; - - final Document doc; - final SAXReader reader = new SAXReader(); - - doc = reader.read(new StringReader(input)); - Element root = doc.getRootElement(); - StringBuilder builder = new StringBuilder(); - builder.append(DHPUtils.md5(root.attribute("id").getValue())); - builder.append(Constants.SEP); - builder.append(root.attribute("label").getValue()); - builder.append(Constants.SEP); - builder.append(root.attribute("id").getValue()); - builder.append(Constants.SEP); - builder.append(((Node) (root.selectNodes("//description").get(0))).getText()); - System.out.println(builder.toString()); - } - - @Test - public void provaReplacement() { - String st = "\"Person in the sand " + "\""; - System.out.println(st); - - System.out.println(st.replace("\\\"", " ")); - } -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/MoveOnSingleDirTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/MoveOnSingleDirTest.java deleted file mode 100644 index 279ba40..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/MoveOnSingleDirTest.java +++ /dev/null @@ -1,119 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv; - -import static org.apache.commons.lang3.StringUtils.split; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.common.ModelConstants; - -/** - * @author miriam.baglioni - * @Date 25/05/23 - */ -public class MoveOnSingleDirTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(MoveOnSingleDirTest.class); - - private static HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(MoveOnSingleDirTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(MoveOnSingleDirTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(MoveOnSingleDirTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void testDMoveSingleDir() throws Exception { - - final String workingPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/working") - .getPath(); - - spark - .read() - .text( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/working/resultIds") - .getPath()) - .write() - .text(workingDir.toString() + "/working/resultIds/"); - - SparkMoveOnSigleDir.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/output", - "-workingPath", workingPath - }); - - Dataset tmp = spark - .read() - .option("header", "true") - .option("delimiter", Constants.SEP) - .csv(workingDir.toString() + "/output/result"); - - Assertions.assertEquals(22, tmp.count()); - Assertions.assertEquals(12, tmp.filter("type == 'dataset'").count()); - Assertions.assertEquals(4, tmp.filter("type == 'other'").count()); - Assertions.assertEquals(5, tmp.filter("type == 'publication'").count()); - Assertions.assertEquals(1, tmp.filter("type == 'software'").count()); - - tmp.filter("type == 'publication'").show(false); - - Assertions - .assertEquals( - 8, spark - .read() - .option("header", "true") - .option("delimiter", Constants.SEP) - .csv(workingDir.toString() + "/output/author") - .count()); - - } -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/SelectResultAndDumpRelationTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/SelectResultAndDumpRelationTest.java deleted file mode 100644 index a4eed68..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/SelectResultAndDumpRelationTest.java +++ /dev/null @@ -1,221 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.csv; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -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.ForeachFunction; -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.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVRELCommunityResult; -import eu.dnetlib.dhp.utils.DHPUtils; - -/** - * @author miriam.baglioni - * @Date 11/05/23 - */ -public class SelectResultAndDumpRelationTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(SelectResultAndDumpRelationTest.class); - - private static HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(SelectResultAndDumpRelationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(SelectResultAndDumpRelationTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(SelectResultAndDumpRelationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/input/") - .getPath(); - - SparkSelectResultsAndDumpRelations.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/output", - "-workingPath", workingDir.toString() + "/working", - "-communities", "enermaps;dh-ch", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - Assertions.assertEquals(2, sc.textFile(workingDir.toString() + "/working/communityResultIds").count()); - - Assertions - .assertEquals( - 1, sc - .textFile(workingDir.toString() + "/working/communityResultIds") - .filter(v -> v.equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) - .count()); - - Assertions - .assertEquals( - 1, sc - .textFile(workingDir.toString() + "/working/communityResultIds") - .filter(v -> v.equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) - .count()); - - // verify that the association is correct with the communityid and result id - spark - .read() - .option("header", "true") - .option("delimiter", Constants.SEP) - .csv(workingDir.toString() + "/output/result_community") - .createOrReplaceTempView("result_community"); - - Assertions.assertEquals(3, spark.sql("SELECT * FROM result_community").count()); - - Assertions - .assertEquals( - 1, spark - .sql( - "SELECT * " + - "FROM result_community " + - "WHERE community_id = '" + DHPUtils.md5("dh-ch") + "'") - .count()); - - Assertions - .assertEquals( - 1, spark - .sql( - "SELECT * " + - "FROM result_community" + - " WHERE result_id = '50|DansKnawCris::0224aae28af558f21768dbc6439c7a95' " + - "AND community_id = '" + DHPUtils.md5("dh-ch") + "'") - .count()); - - Assertions - .assertEquals( - 2, spark - .sql( - "SELECT * " + - "FROM result_community " + - "WHERE community_id = '" + DHPUtils.md5("enermaps") + "'") - .count()); - Assertions - .assertEquals( - 1, spark - .sql( - "SELECT * " + - "FROM result_community " + - "WHERE result_id = '50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9' " + - "AND community_id = '" + DHPUtils.md5("enermaps") + "'") - .count()); - Assertions - .assertEquals( - 1, spark - .sql( - "SELECT * " + - "FROM result_community " + - "WHERE result_id = '50|DansKnawCris::0224aae28af558f21768dbc6439c7a95' " + - "AND community_id = '" + DHPUtils.md5("enermaps") + "'") - .count()); - - Assertions.assertEquals(3, spark.read().textFile(workingDir.toString() + "/working/resultIds").count()); - - Assertions - .assertEquals( - 1, sc - .textFile(workingDir.toString() + "/working/resultIds") - .filter(v -> v.equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) - .count()); - - Assertions - .assertEquals( - 1, sc - .textFile(workingDir.toString() + "/working/resultIds") - .filter(v -> v.equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) - .count()); - - Assertions - .assertEquals( - 1, sc - .textFile(workingDir.toString() + "/working/resultIds") - .filter(v -> v.equals("50|DansKnawCris::26780065282e607306372abd0d808245")) - .count()); - - spark - .read() - .option("header", "true") - .option("delimiter", Constants.SEP) - .csv(workingDir.toString() + "/output/relation") - .createOrReplaceTempView("relation"); - - Assertions.assertEquals(2, spark.sql("SELECT * FROM relation").count()); - - Assertions - .assertEquals( - 1, spark - .sql( - "SELECT * FROM relation WHERE id = '" + - DHPUtils - .md5( - ("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9cites50|DansKnawCris::26780065282e607306372abd0d808245")) - + "'") - .count()); - - Assertions - .assertEquals( - 1, spark - .sql( - "SELECT * FROM relation WHERE id = '" + - DHPUtils - .md5( - ("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9cites50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) - + "'") - .count()); - - } - -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java deleted file mode 100644 index a26772f..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ /dev/null @@ -1,139 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresult; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; - -public class ResultLinkedToProjectTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(ResultLinkedToProjectTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory( - ResultLinkedToProjectTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(ResultLinkedToProjectTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testNoMatch() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); - - final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); - - SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - Assertions.assertEquals(0, tmp.count()); - - } - - @Test - void testMatchOne() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); - - final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); - - SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - Assertions.assertEquals(1, tmp.count()); - - } - -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java deleted file mode 100644 index 6d7739c..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ /dev/null @@ -1,147 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresult; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; - -public class SplitPerFunderTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(SplitPerFunderTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") - .getPath(); - - SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - // FP7 3 and H2020 3 - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(3, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); - - // CIHR 2 - tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(2, tmp.count()); - - // NWO 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // NIH 3 - tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(2, tmp.count()); - - // NSF 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // SNSF 1 - tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // NHMRC 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // H2020 3 - tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(3, tmp.count()); - - tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - // MZOS 1 - tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - } - -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java deleted file mode 100644 index ffbe8ce..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java +++ /dev/null @@ -1,124 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.projectssubset; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.model.graph.Project; - -public class ProjectSubsetTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; - private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(ProjectSubsetTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory( - ProjectSubsetTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(ProjectSubsetTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(ProjectSubsetTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testAllNew() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(12, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); - Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); - } - - @Test - void testMatchOne() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(11, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); - Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); - } -} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpDatasourceTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpDatasourceTest.java new file mode 100644 index 0000000..79bebdd --- /dev/null +++ b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpDatasourceTest.java @@ -0,0 +1,172 @@ +package eu.dnetlib.dhp.oa.graph.dump.skgif; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.skgif.model.Datasource; +import eu.dnetlib.dhp.skgif.model.Organization; +import org.apache.commons.io.FileUtils; +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.ForeachFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.io.Serializable; +import java.nio.file.Files; +import java.nio.file.Path; + +/** + * @author miriam.baglioni + * @Date 22/02/24 + */ +public class DumpDatasourceTest implements Serializable { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(DumpDatasourceTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpDatasourceTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpDatasourceTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpDatasourceTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testDumpDatasource() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph/") + .getPath(); + + + DumpDatasource.main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-outputPath", workingDir.toString() + "/" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD datasource = sc + .textFile(workingDir.toString() + "/Datasource") + .map(item -> OBJECT_MAPPER.readValue(item, Datasource.class)); + + Dataset datasourceDataset = spark.createDataset(datasource.rdd(), Encoders.bean(Datasource.class)); +Assertions.assertEquals(5,datasourceDataset.count()); + datasourceDataset.show(false); +// Assertions.assertEquals(7, relationDataset.count()); +// RelationPerProduct temp = relationDataset.filter((FilterFunction) r -> r.getResultId().equalsIgnoreCase("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).first(); +// Assertions.assertEquals(3, temp.getFunding().size()+temp.getRelatedProduct().size()+temp.getOrganizations().size()); +// Assertions.assertEquals(1, temp.getFunding().size()); +// Assertions.assertEquals(2, temp.getRelatedProduct().size()); +// Assertions.assertEquals(1, temp.getRelatedProduct().stream().filter(rp -> rp.getRelation_type().equalsIgnoreCase("issupplementedby")).count()); +// Assertions.assertEquals(1, temp.getRelatedProduct().stream().filter(rp -> rp.getRelation_type().equalsIgnoreCase("isdocumentedby")).count()); +// +// JavaRDD researchProduct = sc +// .textFile(workingDir.toString() + "/publication/researchproduct") +// .map(item -> OBJECT_MAPPER.readValue(item, ResearchProduct.class)); +// +// org.apache.spark.sql.Dataset researchProductDataset = spark +// .createDataset(researchProduct.rdd(), Encoders.bean(ResearchProduct.class)); +// +// Assertions.assertEquals(1, researchProductDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, "50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))).count()); +// ResearchProduct product = researchProductDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, "50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))).first(); +// Assertions.assertEquals(2, product.getRelevant_organizations().size()); +// Assertions.assertEquals(1, product.getFunding().size()); +// Assertions.assertEquals(0, product.getRelated_products().size()); +// Assertions.assertEquals(1, product.getContributions().size()); +// Assertions.assertEquals(2, product.getManifestations().size()); +// +// researchProductDataset.show(false); +// +// + + } + + @Test + public void testDumpDatasourceComplete() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph_complete_entities/") + .getPath(); + + + DumpDatasource.main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-outputPath", workingDir.toString() + "/" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD datasource = sc + .textFile(workingDir.toString() + "/Datasource") + .map(item -> OBJECT_MAPPER.readValue(item, Datasource.class)); + + Dataset datasourceDataset = spark.createDataset(datasource.rdd(), Encoders.bean(Datasource.class)); + + datasourceDataset.foreach((ForeachFunction) d -> System.out.println(OBJECT_MAPPER.writeValueAsString(d))); +// Assertions.assertEquals(7, relationDataset.count()); +// RelationPerProduct temp = relationDataset.filter((FilterFunction) r -> r.getResultId().equalsIgnoreCase("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).first(); +// Assertions.assertEquals(3, temp.getFunding().size()+temp.getRelatedProduct().size()+temp.getOrganizations().size()); +// Assertions.assertEquals(1, temp.getFunding().size()); +// Assertions.assertEquals(2, temp.getRelatedProduct().size()); +// Assertions.assertEquals(1, temp.getRelatedProduct().stream().filter(rp -> rp.getRelation_type().equalsIgnoreCase("issupplementedby")).count()); +// Assertions.assertEquals(1, temp.getRelatedProduct().stream().filter(rp -> rp.getRelation_type().equalsIgnoreCase("isdocumentedby")).count()); +// +// JavaRDD researchProduct = sc +// .textFile(workingDir.toString() + "/publication/researchproduct") +// .map(item -> OBJECT_MAPPER.readValue(item, ResearchProduct.class)); +// +// org.apache.spark.sql.Dataset researchProductDataset = spark +// .createDataset(researchProduct.rdd(), Encoders.bean(ResearchProduct.class)); +// +// Assertions.assertEquals(1, researchProductDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, "50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))).count()); +// ResearchProduct product = researchProductDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, "50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))).first(); +// Assertions.assertEquals(2, product.getRelevant_organizations().size()); +// Assertions.assertEquals(1, product.getFunding().size()); +// Assertions.assertEquals(0, product.getRelated_products().size()); +// Assertions.assertEquals(1, product.getContributions().size()); +// Assertions.assertEquals(2, product.getManifestations().size()); +// +// researchProductDataset.show(false); +// +// + + } +} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpGrantTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpGrantTest.java new file mode 100644 index 0000000..7bee51b --- /dev/null +++ b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpGrantTest.java @@ -0,0 +1,118 @@ +package eu.dnetlib.dhp.oa.graph.dump.skgif; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.skgif.model.Datasource; +import eu.dnetlib.dhp.skgif.model.Grant; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.io.Serializable; +import java.nio.file.Files; +import java.nio.file.Path; + +/** + * @author miriam.baglioni + * @Date 22/02/24 + */ +public class DumpGrantTest implements Serializable { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(DumpGrantTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpGrantTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpGrantTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpGrantTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testDumpGrant() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph/") + .getPath(); + + + DumpGrant.main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-outputPath", workingDir.toString() + "/" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD grant = sc + .textFile(workingDir.toString() + "/Grant") + .map(item -> OBJECT_MAPPER.readValue(item, Grant.class)); + + Dataset grantDataset = spark.createDataset(grant.rdd(), Encoders.bean(Grant.class)); +Assertions.assertEquals(12,grantDataset.count()); + grantDataset.show(false); +// Assertions.assertEquals(7, relationDataset.count()); +// RelationPerProduct temp = relationDataset.filter((FilterFunction) r -> r.getResultId().equalsIgnoreCase("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).first(); +// Assertions.assertEquals(3, temp.getFunding().size()+temp.getRelatedProduct().size()+temp.getOrganizations().size()); +// Assertions.assertEquals(1, temp.getFunding().size()); +// Assertions.assertEquals(2, temp.getRelatedProduct().size()); +// Assertions.assertEquals(1, temp.getRelatedProduct().stream().filter(rp -> rp.getRelation_type().equalsIgnoreCase("issupplementedby")).count()); +// Assertions.assertEquals(1, temp.getRelatedProduct().stream().filter(rp -> rp.getRelation_type().equalsIgnoreCase("isdocumentedby")).count()); +// +// JavaRDD researchProduct = sc +// .textFile(workingDir.toString() + "/publication/researchproduct") +// .map(item -> OBJECT_MAPPER.readValue(item, ResearchProduct.class)); +// +// org.apache.spark.sql.Dataset researchProductDataset = spark +// .createDataset(researchProduct.rdd(), Encoders.bean(ResearchProduct.class)); +// +// Assertions.assertEquals(1, researchProductDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, "50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))).count()); +// ResearchProduct product = researchProductDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, "50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))).first(); +// Assertions.assertEquals(2, product.getRelevant_organizations().size()); +// Assertions.assertEquals(1, product.getFunding().size()); +// Assertions.assertEquals(0, product.getRelated_products().size()); +// Assertions.assertEquals(1, product.getContributions().size()); +// Assertions.assertEquals(2, product.getManifestations().size()); +// +// researchProductDataset.show(false); +// +// + + } +} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpOrganizationTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpOrganizationTest.java new file mode 100644 index 0000000..4abcb66 --- /dev/null +++ b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpOrganizationTest.java @@ -0,0 +1,122 @@ +package eu.dnetlib.dhp.oa.graph.dump.skgif; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.RelationPerProduct; +import eu.dnetlib.dhp.skgif.model.Organization; +import eu.dnetlib.dhp.skgif.model.Prefixes; +import eu.dnetlib.dhp.skgif.model.ResearchProduct; +import org.apache.commons.io.FileUtils; +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.FilterFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.io.Serializable; +import java.nio.file.Files; +import java.nio.file.Path; + +/** + * @author miriam.baglioni + * @Date 22/02/24 + */ +public class DumpOrganizationTest implements Serializable { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(DumpOrganizationTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpOrganizationTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpOrganizationTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpOrganizationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testDumpOrganization() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph/") + .getPath(); + + + DumpOrganization + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-outputPath", workingDir.toString() + "/" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD organization = sc + .textFile(workingDir.toString() + "/Organization") + .map(item -> OBJECT_MAPPER.readValue(item, Organization.class)); + + Dataset organizationDataset = spark.createDataset(organization.rdd(), Encoders.bean(Organization.class)); +Assertions.assertEquals(34-19,organizationDataset.count()); + organizationDataset.show(false); +// Assertions.assertEquals(7, relationDataset.count()); +// RelationPerProduct temp = relationDataset.filter((FilterFunction) r -> r.getResultId().equalsIgnoreCase("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).first(); +// Assertions.assertEquals(3, temp.getFunding().size()+temp.getRelatedProduct().size()+temp.getOrganizations().size()); +// Assertions.assertEquals(1, temp.getFunding().size()); +// Assertions.assertEquals(2, temp.getRelatedProduct().size()); +// Assertions.assertEquals(1, temp.getRelatedProduct().stream().filter(rp -> rp.getRelation_type().equalsIgnoreCase("issupplementedby")).count()); +// Assertions.assertEquals(1, temp.getRelatedProduct().stream().filter(rp -> rp.getRelation_type().equalsIgnoreCase("isdocumentedby")).count()); +// +// JavaRDD researchProduct = sc +// .textFile(workingDir.toString() + "/publication/researchproduct") +// .map(item -> OBJECT_MAPPER.readValue(item, ResearchProduct.class)); +// +// org.apache.spark.sql.Dataset researchProductDataset = spark +// .createDataset(researchProduct.rdd(), Encoders.bean(ResearchProduct.class)); +// +// Assertions.assertEquals(1, researchProductDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, "50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))).count()); +// ResearchProduct product = researchProductDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, "50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))).first(); +// Assertions.assertEquals(2, product.getRelevant_organizations().size()); +// Assertions.assertEquals(1, product.getFunding().size()); +// Assertions.assertEquals(0, product.getRelated_products().size()); +// Assertions.assertEquals(1, product.getContributions().size()); +// Assertions.assertEquals(2, product.getManifestations().size()); +// +// researchProductDataset.show(false); +// +// + + } +} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpResultTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpResultTest.java new file mode 100644 index 0000000..e64dd33 --- /dev/null +++ b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpResultTest.java @@ -0,0 +1,281 @@ +package eu.dnetlib.dhp.oa.graph.dump.skgif; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.EmitPerManifestation; +import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.RelationPerProduct; +import eu.dnetlib.dhp.skgif.model.*; +import eu.dnetlib.dhp.utils.DHPUtils; +import org.apache.commons.io.FileUtils; +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.FilterFunction; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import javax.validation.constraints.AssertTrue; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.stream.Collectors; + +/** + * @author miriam.baglioni + * @Date 20/02/24 + */ +public class DumpResultTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(DumpResultTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpResultTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpResultTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpResultTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testEmitFromResult() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph/") + .getPath(); + + final String workingDir = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/workingDir/") + .getPath(); + + DumpResult + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-workingDir", workingDir + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD relation = sc + .textFile(workingDir + "/aggrelation") + .map(item -> OBJECT_MAPPER.readValue(item, RelationPerProduct.class)); + + Dataset relationDataset = spark.createDataset(relation.rdd(), Encoders.bean(RelationPerProduct.class)); + + relationDataset.show(false); + Assertions.assertEquals(7, relationDataset.count()); + RelationPerProduct temp = relationDataset.filter((FilterFunction) r -> r.getResultId().equalsIgnoreCase("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).first(); + Assertions.assertEquals(3, temp.getFunding().size()+temp.getRelatedProduct().size()+temp.getOrganizations().size()); + Assertions.assertEquals(1, temp.getFunding().size()); + Assertions.assertEquals(2, temp.getRelatedProduct().size()); + Assertions.assertEquals(1, temp.getRelatedProduct().stream().filter(rp -> rp.getRelation_type().equalsIgnoreCase("issupplementedby")).count()); + Assertions.assertEquals(1, temp.getRelatedProduct().stream().filter(rp -> rp.getRelation_type().equalsIgnoreCase("isdocumentedby")).count()); + + JavaRDD researchProduct = sc + .textFile(workingDir.toString() + "/publication/researchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, ResearchProduct.class)); + + org.apache.spark.sql.Dataset researchProductDataset = spark + .createDataset(researchProduct.rdd(), Encoders.bean(ResearchProduct.class)); + + Assertions.assertEquals(1, researchProductDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, "50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))).count()); + ResearchProduct product = researchProductDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, "50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))).first(); + Assertions.assertEquals(2, product.getRelevant_organizations().size()); + Assertions.assertEquals(1, product.getFunding().size()); + Assertions.assertEquals(0, product.getRelated_products().size()); + Assertions.assertEquals(1, product.getContributions().size()); + Assertions.assertEquals(2, product.getManifestations().size()); + + researchProductDataset.show(false); + + + + } + + @Test + public void testEmitFromDedupedResult() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph_complete_entities/") + .getPath(); + + final String workingDir = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/workingDir_complete_entities/") + .getPath(); + + DumpResult + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-workingDir", workingDir, + "-outputPath", workingDir + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD researchProduct = sc + .textFile(workingDir.toString() + "ResearchProduct") + .map(item -> OBJECT_MAPPER.readValue(item, ResearchProduct.class)); + + org.apache.spark.sql.Dataset researchProductDataset = spark + .createDataset(researchProduct.rdd(), Encoders.bean(ResearchProduct.class)); + + Assertions.assertEquals(1, researchProductDataset.count()); + + ResearchProduct rp = researchProductDataset.first(); + + //check the local identifier + Assertions.assertEquals("product_____::e22a152ab43b9215d14ece613f76ec84", rp.getLocal_identifier()); + + //check the pids of the result + Assertions.assertEquals(3,rp.getIdentifiers().size()); + Assertions.assertEquals(1, rp.getIdentifiers().stream().filter(p->p.getScheme().equalsIgnoreCase("doi")).count()); + Assertions.assertEquals("10.1007/s40199-021-00403-x", rp.getIdentifiers().stream().filter(p->p.getScheme().equalsIgnoreCase("doi")).collect(Collectors.toList()).get(0).getValue()); + Assertions.assertEquals(1, rp.getIdentifiers().stream().filter(p->p.getScheme().equalsIgnoreCase("pmid")).count()); + Assertions.assertEquals("34327650", rp.getIdentifiers().stream().filter(p->p.getScheme().equalsIgnoreCase("pmid")).collect(Collectors.toList()).get(0).getValue()); + Assertions.assertEquals(1, rp.getIdentifiers().stream().filter(p->p.getScheme().equalsIgnoreCase("pmc")).count()); + Assertions.assertEquals("PMC8602609", rp.getIdentifiers().stream().filter(p->p.getScheme().equalsIgnoreCase("pmc")).collect(Collectors.toList()).get(0).getValue()); + + //check the title + Assertions.assertEquals(1, rp.getTitles().keySet().size()); + Assertions.assertTrue(rp.getTitles().keySet().contains("none")); + Assertions.assertEquals(1, rp.getTitles().get("none").size()); + + //check abstract + Assertions.assertEquals(1, rp.getAbstracts().keySet().size()); + Assertions.assertTrue(rp.getAbstracts().keySet().contains("none")); + Assertions.assertEquals(1, rp.getAbstracts().get("none").size()); + + //check type + Assertions.assertEquals("literature", rp.getProduct_type()); + + //check topics + Assertions.assertEquals(3, rp.getTopics().size()); + Assertions.assertTrue(rp.getTopics().stream().anyMatch(t -> t.getTopic().equalsIgnoreCase(Prefixes.TOPIC.label + DHPUtils.md5("FOSSustained delivery")))); + + //check contributions + Assertions.assertEquals(4, rp.getContributions().size()); + Assertions.assertEquals(3, rp.getContributions().stream().filter(c -> c.getPerson().startsWith("person")).count()); + Assertions.assertEquals(1, rp.getContributions().stream().filter(c -> c.getPerson().startsWith("temp")).count()); + rp.getContributions().forEach(c -> Assertions.assertTrue(c.getDeclared_affiliation()==null)); + Assertions.assertEquals(1, rp.getContributions().stream().filter(c -> c.getPerson().equals(Utils.getIdentifier(Prefixes.PERSON, "0000-0001-8284-6269true"))) + .collect(Collectors.toList()).get(0).getRank()); + Assertions.assertEquals(2, rp.getContributions().stream().filter(c -> c.getPerson().equals(Utils.getIdentifier(Prefixes.PERSON, "0000-0002-0940-893xtrue"))) + .collect(Collectors.toList()).get(0).getRank()); + Assertions.assertEquals(3, rp.getContributions().stream().filter(c -> c.getPerson().equals(Utils.getIdentifier(Prefixes.PERSON, "0000-0001-5291-577xtrue"))) + .collect(Collectors.toList()).get(0).getRank()); + Assertions.assertEquals(4, rp.getContributions().stream().filter(c -> c.getPerson().equals(Utils.getIdentifier(Prefixes.TEMPORARY_PERSON, "50|doi_dedup___::0000661be7c602727bae9690778b16514"))) + .collect(Collectors.toList()).get(0).getRank()); + researchProductDataset.show(10,100,true); + + //check manifestation 1 + Assertions.assertEquals(3, rp.getManifestations().size()); + Manifestation manifestation = rp.getManifestations().stream().filter(m -> m.getHosting_datasource().equals(Utils.getIdentifier(Prefixes.DATASOURCE , "10|doajarticles::6107489403b31fc7cf37cb7fda35f7f1"))) + .collect(Collectors.toList()).get(0); + Assertions.assertEquals("Article" , manifestation.getProduct_local_type()); + Assertions.assertEquals("dnet:publication_resource", manifestation.getProduct_local_type_schema()); + Assertions.assertEquals(1, manifestation.getDates().size()); + Assertions.assertEquals("2021-07-29", manifestation.getDates().get(0).getValue()); + Assertions.assertEquals("publishing", manifestation.getDates().get(0).getType()); + Assertions.assertEquals(PeerReview.PEER_REVIEWED.label, manifestation.getPeer_review()); + Assertions.assertEquals("unavailable", manifestation.getMetadata_curation()); + Assertions.assertEquals(AccessRight.CLOSED.label, manifestation.getAccess_right()); + Assertions.assertEquals("Springer Nature TDM", manifestation.getLicence()); + Assertions.assertEquals("https://doi.org/10.1007/s40199-021-00403-x", manifestation.getUrl()); + Assertions.assertEquals("10.1007/s40199-021-00403-x", manifestation.getPid()); + Assertions.assertTrue(manifestation.getBiblio() != null); + Biblio biblio = manifestation.getBiblio(); + Assertions.assertTrue(biblio.getEdition() == null); + Assertions.assertTrue(biblio.getIssue() == null); + Assertions.assertEquals("Springer Science and Business Media LLC",biblio.getPublisher() ); + Assertions.assertEquals("29", biblio.getVolume()); + Assertions.assertEquals("415", biblio.getStart_page()); + Assertions.assertEquals("438", biblio.getEnd_page()); + + //check manifestation 2 + manifestation = rp.getManifestations().stream().filter(m -> m.getHosting_datasource().equals(Utils.getIdentifier(Prefixes.DATASOURCE , "10|openaire____::55045bd2a65019fd8e6741a755395c8c"))) + .collect(Collectors.toList()).get(0); + Assertions.assertEquals("Article" , manifestation.getProduct_local_type()); + Assertions.assertEquals("dnet:publication_resource", manifestation.getProduct_local_type_schema()); + Assertions.assertEquals(1, manifestation.getDates().size()); + Assertions.assertEquals("2020-01-03", manifestation.getDates().get(0).getValue()); + Assertions.assertEquals("publishing", manifestation.getDates().get(0).getType()); + Assertions.assertEquals(PeerReview.NON_PEER_REVIEWED.label, manifestation.getPeer_review()); + Assertions.assertEquals("unavailable", manifestation.getMetadata_curation()); + Assertions.assertEquals(AccessRight.UNAVAILABLE.label, manifestation.getAccess_right()); + Assertions.assertEquals(null, manifestation.getLicence()); + Assertions.assertEquals("https://pubmed.ncbi.nlm.nih.gov/34327650", manifestation.getUrl()); + Assertions.assertEquals("34327650", manifestation.getPid()); + Assertions.assertTrue(manifestation.getBiblio() == null); + + //check manifestation 3 + manifestation = rp.getManifestations().stream().filter(m -> m.getHosting_datasource().equals(Utils.getIdentifier(Prefixes.DATASOURCE , "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c"))) + .collect(Collectors.toList()).get(0); + Assertions.assertEquals("Other literature type" , manifestation.getProduct_local_type()); + Assertions.assertEquals("dnet:publication_resource", manifestation.getProduct_local_type_schema()); + Assertions.assertEquals(1, manifestation.getDates().size()); + Assertions.assertEquals("2021-07-29", manifestation.getDates().get(0).getValue()); + Assertions.assertEquals("publishing", manifestation.getDates().get(0).getType()); + Assertions.assertEquals(PeerReview.NON_PEER_REVIEWED.label, manifestation.getPeer_review()); + Assertions.assertEquals("unavailable", manifestation.getMetadata_curation()); + Assertions.assertEquals(AccessRight.OPEN.label, manifestation.getAccess_right()); + Assertions.assertEquals(null, manifestation.getLicence()); + Assertions.assertEquals("https://europepmc.org/articles/PMC8602609/", manifestation.getUrl()); + Assertions.assertEquals("PMC8602609", manifestation.getPid()); + Assertions.assertTrue(manifestation.getBiblio() == null); + + //check relevant organization + Assertions.assertEquals(1,rp.getRelevant_organizations().size()); + Assertions.assertEquals(Prefixes.ORGANIZATION.label + "601e510b1fda7cc6cb03329531502171", rp.getRelevant_organizations().get(0)); + + + //check funding + Assertions.assertEquals(1,rp.getFunding().size()); + Assertions.assertEquals(Prefixes.GRANT.label + "a7795022763d413f5de59036ebbd0c52", rp.getFunding().get(0)); + + //check related products + Assertions.assertEquals(5, rp.getRelated_products().size()); + Assertions.assertEquals(4, rp.getRelated_products().stream().filter(r -> r.getRelation_type().equalsIgnoreCase(RelationType.CITATION.label)).collect(Collectors.toList()).get(0).getProduct_list().size()); + Assertions.assertEquals(1, rp.getRelated_products().stream().filter(r -> r.getRelation_type().equalsIgnoreCase(RelationType.DOCUMENTS.label)).collect(Collectors.toList()).get(0).getProduct_list().size()); + Assertions.assertEquals(1, rp.getRelated_products().stream().filter(r -> r.getRelation_type().equalsIgnoreCase(RelationType.PART.label)).collect(Collectors.toList()).get(0).getProduct_list().size()); + Assertions.assertEquals(1, rp.getRelated_products().stream().filter(r -> r.getRelation_type().equalsIgnoreCase(RelationType.SUPPLEMENT.label)).collect(Collectors.toList()).get(0).getProduct_list().size()); + Assertions.assertEquals(1, rp.getRelated_products().stream().filter(r -> r.getRelation_type().equalsIgnoreCase(RelationType.VERSION.label)).collect(Collectors.toList()).get(0).getProduct_list().size()); + + + } + +} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/EmitFromResultJobTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/EmitFromResultJobTest.java index 2e2855c..006cbe5 100644 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/EmitFromResultJobTest.java +++ b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/skgif/EmitFromResultJobTest.java @@ -4,15 +4,16 @@ package eu.dnetlib.dhp.oa.graph.dump.skgif; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; -import java.util.List; -import java.util.Optional; +import eu.dnetlib.dhp.skgif.model.Topic; import org.apache.commons.io.FileUtils; 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.FilterFunction; +import org.apache.spark.api.java.function.ForeachFunction; +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.AfterAll; import org.junit.jupiter.api.Assertions; @@ -22,23 +23,10 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts; -import eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob; -import eu.dnetlib.dhp.oa.model.Instance; -import eu.dnetlib.dhp.oa.model.OpenAccessRoute; -import eu.dnetlib.dhp.oa.model.Score; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; -import eu.dnetlib.dhp.oa.model.graph.GraphResult; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.skgif.EmitFromResults; -import eu.dnetlib.dhp.skgif.beans.EmitPerManifestation; -import eu.dnetlib.dhp.skgif.model.Manifestation; + +import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.EmitPerManifestation; import eu.dnetlib.dhp.skgif.model.Persons; -import eu.dnetlib.dhp.skgif.model.ResultTopic; //@Disabled public class EmitFromResultJobTest { @@ -82,7 +70,7 @@ public class EmitFromResultJobTest { @Test public void testEmitFromResult() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") + .getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph/") .getPath(); EmitFromResults @@ -101,683 +89,111 @@ public class EmitFromResultJobTest { .textFile(workingDir.toString() + "/result/Persons") .map(item -> OBJECT_MAPPER.readValue(item, Persons.class)); - JavaRDD topics = sc + JavaRDD topics = sc .textFile(workingDir.toString() + "/result/Topic") - .map(item -> OBJECT_MAPPER.readValue(item, ResultTopic.class)); + .map(item -> OBJECT_MAPPER.readValue(item, Topic.class)); JavaRDD manifestation = sc - .textFile(workingDir.toString() + "/result/Persons") + .textFile(workingDir.toString() + "/publication/manifestation") .map(item -> OBJECT_MAPPER.readValue(item, EmitPerManifestation.class)); org.apache.spark.sql.Dataset personsDataset = spark .createDataset(persons.rdd(), Encoders.bean(Persons.class)); personsDataset.show(false); + Persons claudiaBorer = personsDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase("tmp_person__::2c1eea261f7d9a97ab7ca8c4200781db")) + .first(); + + Assertions.assertEquals(2, personsDataset.filter((FilterFunction) p -> p.getGiven_name().equalsIgnoreCase("claudia") && p.getFamily_name().equalsIgnoreCase("borer")).count()); + Assertions.assertEquals(1, personsDataset.filter((FilterFunction) p -> p.getGiven_name().equalsIgnoreCase("claudia") && p.getFamily_name().equalsIgnoreCase("borer") && !p.getLocal_identifier().equalsIgnoreCase("tmp_person__::2c1eea261f7d9a97ab7ca8c4200781db")).count()); + Assertions.assertEquals("claudia", claudiaBorer.getGiven_name().toLowerCase()); + Assertions.assertEquals("borer", claudiaBorer.getFamily_name().toLowerCase()); + + Assertions.assertEquals(2, personsDataset.filter((FilterFunction) p -> p.getLocal_identifier().startsWith("person")).count()); + Assertions.assertEquals(1, personsDataset.filter((FilterFunction) p -> p.getLocal_identifier().startsWith("person") && p.getIdentifiers().get(0).getValue().equals("0000-0002-5597-4916")).count()); + Persons orcidPerson = personsDataset.filter((FilterFunction) p -> p.getLocal_identifier().startsWith("person") && p.getIdentifiers().get(0).getValue().equals("0000-0002-5597-4916")).first(); + Assertions.assertEquals("M.", orcidPerson.getGiven_name()); + Assertions.assertEquals("Kooi", orcidPerson.getFamily_name()); + Assertions.assertEquals(1, orcidPerson.getIdentifiers().size()); + Assertions.assertEquals("orcid", orcidPerson.getIdentifiers().get(0).getScheme()); + Assertions.assertEquals("0000-0002-5597-4916", orcidPerson.getIdentifiers().get(0).getValue()); + + Dataset manifestationDataset = spark + .createDataset(manifestation.rdd(), Encoders.bean(EmitPerManifestation.class)); + manifestationDataset.show(false); + Assertions.assertEquals(4, manifestationDataset.count()); + + Dataset topicDataset = spark + .createDataset(topics.rdd(), Encoders.bean(Topic.class)); + Assertions.assertEquals(0, topicDataset.count()); } + @Test - public void testDatasetDump() throws Exception { + public void testEmitFromResultComplete() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph_complete_entities/") + .getPath(); - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); + EmitFromResults + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-outputPath", workingDir.toString() + "/result/", + "-workingDir", workingDir.toString() + "/" - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); + }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + JavaRDD persons = sc + .textFile(workingDir.toString() + "/result/Persons") + .map(item -> OBJECT_MAPPER.readValue(item, Persons.class)); + org.apache.spark.sql.Dataset personsDataset = spark + .createDataset(persons.rdd(), Encoders.bean(Persons.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + personsDataset.foreach((ForeachFunction) p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p))); - Assertions.assertEquals(1, verificationDataset.count()); + JavaRDD topics = sc + .textFile(workingDir.toString() + "/result/Topic") + .map(item -> OBJECT_MAPPER.readValue(item, Topic.class)); + Dataset topicDataset = spark + .createDataset(topics.rdd(), Encoders.bean(Topic.class)); + Assertions.assertEquals(3, topicDataset.count()); - Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count()); + topicDataset.foreach((ForeachFunction) t -> System.out.println(OBJECT_MAPPER.writeValueAsString(t))); - // the common fields in the result have been already checked. Now checking only - // community specific fields + JavaRDD manifestation = sc + .textFile(workingDir.toString() + "/publication/manifestation") + .map(item -> OBJECT_MAPPER.readValue(item, EmitPerManifestation.class)); - GraphResult gr = verificationDataset.first(); + Dataset manifestationDataset = spark + .createDataset(manifestation.rdd(), Encoders.bean(EmitPerManifestation.class)); + manifestationDataset.show(false); - Assertions.assertEquals(2, gr.getGeolocation().size()); - Assertions.assertEquals(2, gr.getGeolocation().stream().filter(gl -> gl.getBox().equals("")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("")).count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> gl.getPlace().equals("18 York St, Ottawa, ON K1N 5S6; Ottawa; Ontario; Canada")) - .count()); - Assertions - .assertEquals( - 1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("45.427242 -75.693904")).count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> gl.getPoint().equals("") && !gl.getPlace().equals("")) - .count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> !gl.getPoint().equals("") && gl.getPlace().equals("")) - .count()); +// Persons claudiaBorer = personsDataset.filter((FilterFunction) p -> p.getLocal_identifier().equalsIgnoreCase("tmp_person__::2c1eea261f7d9a97ab7ca8c4200781db")) +// .first(); +// +// Assertions.assertEquals(2, personsDataset.filter((FilterFunction) p -> p.getGiven_name().equalsIgnoreCase("claudia") && p.getFamily_name().equalsIgnoreCase("borer")).count()); +// Assertions.assertEquals(1, personsDataset.filter((FilterFunction) p -> p.getGiven_name().equalsIgnoreCase("claudia") && p.getFamily_name().equalsIgnoreCase("borer") && !p.getLocal_identifier().equalsIgnoreCase("tmp_person__::2c1eea261f7d9a97ab7ca8c4200781db")).count()); +// Assertions.assertEquals("claudia", claudiaBorer.getGiven_name().toLowerCase()); +// Assertions.assertEquals("borer", claudiaBorer.getFamily_name().toLowerCase()); +// +// Assertions.assertEquals(2, personsDataset.filter((FilterFunction) p -> p.getLocal_identifier().startsWith("person")).count()); +// Assertions.assertEquals(1, personsDataset.filter((FilterFunction) p -> p.getLocal_identifier().startsWith("person") && p.getIdentifiers().get(0).getValue().equals("0000-0002-5597-4916")).count()); +// Persons orcidPerson = personsDataset.filter((FilterFunction) p -> p.getLocal_identifier().startsWith("person") && p.getIdentifiers().get(0).getValue().equals("0000-0002-5597-4916")).first(); +// Assertions.assertEquals("M.", orcidPerson.getGiven_name()); +// Assertions.assertEquals("Kooi", orcidPerson.getFamily_name()); +// Assertions.assertEquals(1, orcidPerson.getIdentifiers().size()); +// Assertions.assertEquals("orcid", orcidPerson.getIdentifiers().get(0).getScheme()); +// Assertions.assertEquals("0000-0002-5597-4916", orcidPerson.getIdentifiers().get(0).getValue()); +// - Assertions.assertEquals("1024Gb", gr.getSize()); +// Assertions.assertEquals(4, manifestationDataset.count()); +// - Assertions.assertEquals("1.01", gr.getVersion()); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); - Assertions.assertEquals(null, gr.getProgrammingLanguage()); - Assertions.assertEquals(null, gr.getDocumentationUrl()); - Assertions.assertEquals(null, gr.getContactperson()); - Assertions.assertEquals(null, gr.getContactgroup()); - Assertions.assertEquals(null, gr.getTool()); } - - @Test - public void testSoftwareDump() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'software'").count()); - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(2, gr.getDocumentationUrl().size()); - Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_1")); - Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_2")); - - Assertions.assertEquals("code_repo", gr.getCodeRepositoryUrl()); - - Assertions.assertEquals("perl", gr.getProgrammingLanguage()); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getContactperson()); - Assertions.assertEquals(null, gr.getContactgroup()); - Assertions.assertEquals(null, gr.getTool()); - Assertions.assertEquals(null, gr.getGeolocation()); - Assertions.assertEquals(null, gr.getSize()); - Assertions.assertEquals(null, gr.getVersion()); - - } - - @Test - public void testOrpDump() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'other'").count()); - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(2, gr.getContactperson().size()); - Assertions.assertTrue(gr.getContactperson().contains(("contact_person1"))); - Assertions.assertTrue(gr.getContactperson().contains(("contact_person2"))); - - Assertions.assertEquals(1, gr.getContactgroup().size()); - Assertions.assertTrue(gr.getContactgroup().contains(("contact_group"))); - - Assertions.assertEquals(2, gr.getTool().size()); - Assertions.assertTrue(gr.getTool().contains("tool1")); - Assertions.assertTrue(gr.getTool().contains("tool2")); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getDocumentationUrl()); - Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); - Assertions.assertEquals(null, gr.getProgrammingLanguage()); - Assertions.assertEquals(null, gr.getGeolocation()); - Assertions.assertEquals(null, gr.getSize()); - Assertions.assertEquals(null, gr.getVersion()); - - } - - @Test - public void testPublicationDumpCommunity() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count()); - - // the common fields in the result have been already checked. Now checking only - // community specific fields - - CommunityResult cr = verificationDataset.first(); - - Assertions.assertEquals(1, cr.getContext().size()); - Assertions.assertEquals("dh-ch", cr.getContext().get(0).getCode()); - Assertions.assertEquals("Digital Humanities and Cultural Heritage", cr.getContext().get(0).getLabel()); - Assertions.assertEquals(1, cr.getContext().get(0).getProvenance().size()); - Assertions.assertEquals("Inferred by OpenAIRE", cr.getContext().get(0).getProvenance().get(0).getProvenance()); - Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust()); - - Assertions.assertEquals(1, cr.getCollectedfrom().size()); - Assertions - .assertEquals("openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey()); - Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue()); - - Assertions.assertEquals(1, cr.getInstance().size()); - Assertions - .assertEquals( - "openaire____::fdc7e0400d8c1634cdaf8051dbae23db", - cr.getInstance().get(0).getCollectedfrom().getKey()); - Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue()); - Assertions - .assertEquals( - "openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey()); - Assertions.assertEquals("One Ecosystem", cr.getInstance().get(0).getHostedby().getValue()); - - } - - @Test - public void testDataset() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(90, verificationDataset.count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset - .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_16ec'").count() == verificationDataset - .filter("bestAccessright.code = 'c_16ec' and bestAccessright.label = 'RESTRICTED'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_14cb'").count() == verificationDataset - .filter("bestAccessright.code = 'c_14cb' and bestAccessright.label = 'CLOSED'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_f1cf'").count() == verificationDataset - .filter("bestAccessright.code = 'c_f1cf' and bestAccessright.label = 'EMBARGO'") - .count()); - - Assertions.assertTrue(verificationDataset.filter("size(context) > 0").count() == 90); - - Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); - - } - - @Test - public void testDataset2All() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(5, verificationDataset.count()); - - } - - @Test - public void testDataset2Communities() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(0, verificationDataset.count()); - - } - - @Test - public void testPublication() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(74, verificationDataset.count()); - verificationDataset.show(false); - - Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count()); - - } - - @Test - public void testSoftware() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(6, verificationDataset.count()); - - Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count()); - - } - - @Test - public void testORP() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(3, verificationDataset.count()); - - Assertions.assertEquals(3, verificationDataset.filter("type = 'other'").count()); - - } - - @Test - public void testRecord() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpCommunityProducts - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(2, verificationDataset.count()); - verificationDataset.show(false); - - Assertions.assertEquals(2, verificationDataset.filter("type = 'publication'").count()); - - } - - @Test - public void testArticlePCA() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(23, verificationDataset.count()); - - Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count()); - - verificationDataset.createOrReplaceTempView("check"); - - org.apache.spark.sql.Dataset temp = spark - .sql( - "select id " + - "from check " + - "lateral view explode (instance) i as inst " + - "where inst.articleprocessingcharge is not null"); - - Assertions.assertTrue(temp.count() == 2); - - Assertions.assertTrue(temp.filter("id = 'datacite____::05c611fdfc93d7a2a703d1324e28104a'").count() == 1); - - Assertions.assertTrue(temp.filter("id = 'dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); - - temp = spark - .sql( - "select id, inst.articleprocessingcharge.amount, inst.articleprocessingcharge.currency " + - "from check " + - "lateral view explode (instance) i as inst " + - "where inst.articleprocessingcharge is not null"); - - Assertions - .assertEquals( - "3131.64", - temp - .filter("id = 'datacite____::05c611fdfc93d7a2a703d1324e28104a'") - .collectAsList() - .get(0) - .getString(1)); - Assertions - .assertEquals( - "EUR", - temp - .filter("id = 'datacite____::05c611fdfc93d7a2a703d1324e28104a'") - .collectAsList() - .get(0) - .getString(2)); - - Assertions - .assertEquals( - "2578.35", - temp - .filter("id = 'dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'") - .collectAsList() - .get(0) - .getString(1)); - Assertions - .assertEquals( - "EUR", - temp - .filter("id = 'dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'") - .collectAsList() - .get(0) - .getString(2)); - } - - @Test - public void testresultNotDumped() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/resultNotDumped.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpEntitiesJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/result", - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - Assertions.assertEquals(0, tmp.count()); - - } - } diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/subset/DumpSubsetTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/subset/DumpSubsetTest.java deleted file mode 100644 index cdfa2f3..0000000 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/subset/DumpSubsetTest.java +++ /dev/null @@ -1,522 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.subset; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -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.FilterFunction; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.complete.Extractor; -import eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; -import eu.dnetlib.dhp.oa.model.graph.GraphResult; -import eu.dnetlib.dhp.oa.model.graph.ResearchCommunity; -import eu.dnetlib.dhp.schema.oaf.*; - -/** - * @author miriam.baglioni - * @Date 16/11/22 - */ -public class DumpSubsetTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(DumpSubsetTest.class); - - private static final CommunityMap map = new CommunityMap(); - - static { - map.put("egi", "EGI Federation"); - map.put("fet-fp7", "FET FP7"); - map.put("fet-h2020", "FET H2020"); - map.put("clarin", "CLARIN"); - map.put("fam", "Fisheries and Aquaculture Management"); - map.put("ni", "Neuroinformatics"); - map.put("mes", "European Marine Scinece"); - map.put("instruct", "Instruct-Eric"); - map.put("rda", "Research Data Alliance"); - map.put("elixir-gr", "ELIXIR GR"); - map.put("aginfra", "Agricultural and Food Sciences"); - map.put("dariah", "DARIAH EU"); - map.put("risis", "RISI"); - map.put("ee", "SDSN - Greece"); - map.put("oa-pg", "EC Post-Grant Open Access Pilot"); - map.put("beopen", "Transport Research"); - map.put("euromarine", "Euromarine"); - map.put("ifremer", "Ifremer"); - map.put("dh-ch", "Digital Humanities and Cultural Heritage"); - map.put("science-innovation-policy", "Science and Innovation Policy Studies"); - map.put("covid-19", "COVID-19"); - map.put("enrmaps", "Energy Research"); - map.put("epos", "EPOS"); - - } - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DumpSubsetTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(DumpSubsetTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(DumpSubsetTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test // Step 1 - void testSelectionConstraints() throws Exception { - final String pathMap = "{\"author\" : \"$['author'][*]['fullname']\", " + - "\"title\" : \"$['title'][*]['value']\", \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\", " - + - "\"contributor\" : \"$['contributor'][*]['value']\", \"description\" : \"$['description'][*]['value']\", " - + - "\"dateofacceptance\" : \"$['dateofacceptance']['value']\", " + - "\"context\": \"['context'][*]['id']\"}"; - final String constraint = "{\"criteria\":[{\"constraint\":[{\"verb\":\"lesser_than\",\"field\":\"dateofacceptance\",\"value\":\"2023-01-01\"},{\"verb\":\"greater_than\",\"field\":\"dateofacceptance\",\"value\":\"2006-12-31\"}]}]}"; - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/input/publication") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpResult - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString(), - "-communityMapPath", communityMapPath, - "-pathMap", pathMap, - "-selectionCriteria", constraint, - "-resultType", "publication", - "-masterDuplicatePath", getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/masterDuplicate/correspondence") - .getPath() - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump/publication") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - Assertions.assertEquals(16, tmp.count()); - - JavaRDD tmp_pubs = sc - .textFile(workingDir.toString() + "/original/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - - JavaRDD input = sc - .textFile(sourcePath) - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - - Assertions - .assertTrue( - input - .filter(r -> r.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) - .first() - .getCollectedfrom() - .stream() - .anyMatch( - cf -> cf.getKey().equals("10|openaire____::806360c771262b4d6770e7cdf04b5c5a") - && cf.getValue().equals("ZENODO"))); - Assertions.assertEquals(16, tmp_pubs.count()); - Assertions - .assertTrue( - tmp_pubs - .filter(r -> r.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) - .first() - .getCollectedfrom() - .stream() - .anyMatch( - cf -> cf.getKey().equals("10|fairsharing_::cd0f74b5955dc87fd0605745c4b49ee8") - && cf.getValue().equals("ZENODO"))); - - tmp_pubs.foreach(p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p))); - - } - - @Test // Step 1 - void testSelectionConstraintsCommunity() throws Exception { - final String pathMap = "{\"author\" : \"$['author'][*]['fullname']\", " + - "\"title\" : \"$['title'][*]['value']\", \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\", " - + - "\"contributor\" : \"$['contributor'][*]['value']\", \"description\" : \"$['description'][*]['value']\", " - + - "\"dateofacceptance\" : \"$['dateofacceptance']['value']\", " + - "\"context\": \"$['context'][*]['id']\"}"; - final String constraint = "{\"criteria\":[{\"constraint\":[{\"verb\":\"equals\",\"field\":\"context\",\"value\":\"dh-ch\"}]}]}"; - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/input/publication") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - SparkDumpResult - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString(), - "-communityMapPath", communityMapPath, - "-pathMap", pathMap, - "-selectionCriteria", constraint, - "-resultType", "publication", - "-masterDuplicatePath", getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/masterDuplicate/empty") - .getPath() - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump/publication") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - Assertions.assertEquals(17, tmp.count()); - - JavaRDD tmp_pubs = sc - .textFile(workingDir.toString() + "/original/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - - Assertions.assertEquals(17, tmp_pubs.count()); - - Assertions - .assertEquals( - 17, tmp_pubs.filter(p -> p.getContext().stream().anyMatch(c -> c.getId().equals("dh-ch"))).count()); - - } - - @Test // Step2 - void testSelectSubset() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/input/") - .getPath(); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/original/publication") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/original/publication"); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/original/software") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/original/software"); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/original/dataset") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/original/dataset"); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/original/otherresearchproduct") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/original/otherresearchproduct"); - - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/publication") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/publication"); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/software") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/software"); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/dataset") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/dataset"); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/otherresearchproduct") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/otherresearchproduct"); - - SparkSelectSubset - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-outputPath", workingDir.toString() - - }); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/original/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - Assertions.assertEquals(20, tmp.count()); - - Assertions - .assertEquals( - 6, tmp.filter(r -> r.getSource().startsWith("50|") && r.getTarget().startsWith("50|")).count()); - Assertions - .assertEquals( - 3, tmp.filter(r -> r.getSource().startsWith("50|") && r.getTarget().startsWith("20|")).count()); - Assertions - .assertEquals( - 3, tmp.filter(r -> r.getSource().startsWith("20|") && r.getTarget().startsWith("50|")).count()); - Assertions - .assertEquals( - 4, tmp.filter(r -> r.getSource().startsWith("40|") && r.getTarget().startsWith("50|")).count()); - Assertions - .assertEquals( - 1, tmp.filter(r -> r.getSource().startsWith("10|") && r.getTarget().startsWith("20|")).count()); - Assertions - .assertEquals( - 1, tmp.filter(r -> r.getSource().startsWith("20|") && r.getTarget().startsWith("10|")).count()); - Assertions - .assertEquals( - 1, tmp.filter(r -> r.getSource().startsWith("20|") && r.getTarget().startsWith("40|")).count()); - Assertions - .assertEquals( - 1, tmp.filter(r -> r.getSource().startsWith("40|") && r.getTarget().startsWith("20|")).count()); - - JavaRDD tmp_datasource = sc - .textFile(workingDir.toString() + "/original/datasource") - .map(item -> OBJECT_MAPPER.readValue(item, Datasource.class)); - Assertions.assertEquals(5, tmp_datasource.count()); - Assertions - .assertEquals( - 0, - tmp_datasource - .filter(d -> d.getId().equals("10|issn___print::0a79337eaf5145faa478785423273355")) - .count()); - - JavaRDD tmp_organization = sc - .textFile(workingDir.toString() + "/original/organization") - .map(item -> OBJECT_MAPPER.readValue(item, Organization.class)); - Assertions.assertEquals(3, tmp_organization.count()); - - JavaRDD tmp_project = sc - .textFile(workingDir.toString() + "/original/project") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(3, tmp_project.count()); - - } - - @Test - public void selectValidContextTest() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/original/") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/communityMap") - .getPath(); - - final String contextPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/context/community_infrastructure") - .getPath(); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - SparkSelectValidContext - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-outputPath", workingDir.toString() + "/dump/community_infrastructure", - "-communityMapPath", communityMapPath, - "-contextPath", contextPath - - }); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump/community_infrastructure") - .map(item -> OBJECT_MAPPER.readValue(item, ResearchCommunity.class)); - - Assertions.assertEquals(6, tmp.count()); - - Assertions.assertEquals(1, tmp.filter(cr -> cr.getAcronym().equals("enermaps")).count()); - Assertions.assertEquals(1, tmp.filter(cr -> cr.getAcronym().equals("eutopia")).count()); - Assertions.assertEquals(1, tmp.filter(cr -> cr.getAcronym().equals("dh-ch")).count()); - Assertions.assertEquals(1, tmp.filter(cr -> cr.getAcronym().equals("beopen")).count()); - Assertions.assertEquals(1, tmp.filter(cr -> cr.getAcronym().equals("neanias-underwater")).count()); - Assertions.assertEquals(1, tmp.filter(cr -> cr.getAcronym().equals("sdsn-gr")).count()); - - } - - @Test - public void selectValidRelationContextTest() throws Exception { - - final String contextRelationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/working/relation") - .getPath(); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/publication") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/publication"); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/software") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/software"); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/dataset") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/dataset"); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/otherresearchproduct") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/otherresearchproduct"); - - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/organization") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/organization"); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/datasource") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/datasource"); - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/project") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/project"); - - sc - .textFile( - getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/community_infrastructure") - .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/communities_infrastructures"); - - SparkSelectValidRelationContext - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", workingDir.toString() + "/dump", - - "-contextRelationPath", contextRelationPath - - }); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump/relation") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.oa.model.graph.Relation.class)); - - Assertions.assertEquals(10, tmp.count()); - - Assertions.assertEquals(5, tmp.filter(r -> r.getSourceType().equals("context")).count()); - Assertions.assertEquals(5, tmp.filter(r -> r.getTargetType().equals("context")).count()); - - Assertions.assertEquals(2, tmp.filter(r -> r.getSourceType().equals("datasource")).count()); - Assertions.assertEquals(2, tmp.filter(r -> r.getTargetType().equals("datasource")).count()); - - Assertions.assertEquals(1, tmp.filter(r -> r.getSourceType().equals("project")).count()); - Assertions.assertEquals(1, tmp.filter(r -> r.getTargetType().equals("project")).count()); - - Assertions.assertEquals(2, tmp.filter(r -> r.getSourceType().equals("organization")).count()); - Assertions.assertEquals(2, tmp.filter(r -> r.getTargetType().equals("organization")).count()); - - } - - @Test - public void extractRelationFromResultTest() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/original/publication") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/communityMap") - .getPath(); - - Extractor ex = new Extractor(); - ex - .run( - false, sourcePath, workingDir.toString() + "/relation", - // eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); - eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.oa.model.graph.Relation.class)); - - Assertions.assertEquals(102, tmp.count()); - - Assertions.assertEquals(51, tmp.filter(r -> r.getSourceType().equals("result")).count()); - Assertions.assertEquals(39, tmp.filter(r -> r.getSourceType().equals("datasource")).count()); - Assertions.assertEquals(12, tmp.filter(r -> r.getSourceType().equals("context")).count()); - } - -} diff --git a/dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/skgif/graph/dataset b/dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/skgif/graph/dataset new file mode 100644 index 0000000..e03a521 --- /dev/null +++ b/dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/skgif/graph/dataset @@ -0,0 +1,7 @@ +{"author":[{"affiliation":[],"fullname":"Kooi, 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De aanleiding voor het onderzoek vormt de aanleg van een nieuwe waterleiding en een beluchtingstoren op het pompstation Beerschoten. In het kader van deze ontwikkeling dient een omgevingsvergunning te worden aangevraagd. Het plangebied bestaat uit het deel van het leidingtracé waar op basis van het vigerend bestemmingsplan een dubbelbestemming ‘Waarde Archeologie’ geldt. Op basis van het bureauonderzoek werd in het plangebied een podzolgrond in de top van het dekzand verwacht, waar bovenop mogelijk een circa één-meter dikke laag stuifzand ligt. Het archeologisch niveau bevindt zich hierbij direct onder de bouwvoor c.q. humeuze bovengrond of in de top van een al dan niet begraven podzolbodem. De resten, die hierin te verwachten zijn, dateren naar verwachting in het Laat-Paleolithicum tot en met de Middeleeuwen en betreffen sporen van nederzetting en/of landgebruik uit die periode. De verwachting hierop is middelhoog. Voor wat betreft resten uit de Nieuwe tijd is de verwachting laag. 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explore and examine the effectiveness of currently developed novel techniques to resolve the issues which are associated with the herbal constituents/extract. METHODS: A systematic thorough search and collection of reviewed information from Science direct, PubMed and Google Scholar databases based on various sets of key phrases have been performed. All the findings from these data have been studied and briefed based on their relevant and irrelevant information. RESULT: Herbal drugs are gaining more popularity in the modern world due to their applications in curing various ailments with minimum toxic effects, side effect or adverse effect. However, various challenges exist with herbal extracts/plant actives such as poor solubility (water/lipid), poor permeation, lack of targeting specificity, instability in highly acidic pH, and liver metabolism, etc. Nowadays with the expansion in the technology, novel drug delivery system provides avenues and newer opportunity towards the delivery of herbal drugs with improved physical chemical properties, pharmacokinetic and pharmacodynamic. Developing nano-strategies like Polymeric nanoparticles, Liposomes, Niosomes, Microspheres, Phytosomes, Nanoemulsion and Self Nano Emulsifying Drug Delivery System, etc. imparts benefits for delivery of phyto formulation and herbal bioactives. Nano formulation of phytoconstituents/ herbal extract could lead to enhancement of aqueous solubility, dissolution, bioavailability, stability, reduce toxicity, permeation, sustained delivery, protection from enzymatic degradation, etc. CONCLUSION: Based on the above findings, the conclusion can be drawn that the nano sized novel drug delivery systems of herbal and herbal bioactives have a potential future for upgrading the pharmacological action and defeating or overcoming the issues related with these constituents. The aims of the present review was to summarize and critically analyze the recent development of nano sized strategies for promising phytochemicals delivery systems along with their therapeutic applications supported by experimental evidence and discussing the opportunities for further aspects. 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