From 2a4f65795f981faeac358875f89ce450e905b88f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 15 Jun 2020 18:32:24 +0200 Subject: [PATCH] WIP: graph cleaner implementation --- .../dhp/oa/graph/raw/common/Vocabulary.java | 2 +- .../oa/graph/raw/common/VocabularyGroup.java | 9 +- .../oa/graph/clean/CleaningFunctionTest.java | 4 +- .../eu/dnetlib/dhp/oa/graph/clean/result.json | 8 +- .../dnetlib/dhp/oa/graph/clean/synonyms.txt | 1592 ++++++++--------- .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 1197 +++++++------ 6 files changed, 1400 insertions(+), 1412 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java index ffa64861c..9bf198c8b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java @@ -61,7 +61,7 @@ public class Vocabulary implements Serializable { } public VocabularyTerm getTermBySynonym(final String syn) { - return getTerm(synonyms.get(syn)); + return getTerm(synonyms.get(syn.toLowerCase())); } public Qualifier getTermAsQualifier(final String termId) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java index 447228bf9..d9ff62596 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java @@ -3,7 +3,6 @@ package eu.dnetlib.dhp.oa.graph.raw.common; import java.io.Serializable; import java.util.*; -import java.util.function.Supplier; import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; @@ -14,7 +13,7 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class VocabularyGroup implements Serializable { - public static final String VOCABULARIES_XQUERY = "for $x in collection(' /db/DRIVER/VocabularyDSResources/VocabularyDSResourceType') \n" + public static final String VOCABULARIES_XQUERY = "for $x in collection('/db/DRIVER/VocabularyDSResources/VocabularyDSResourceType') \n" + "let $vocid := $x//VOCABULARY_NAME/@code\n" + "let $vocname := $x//VOCABULARY_NAME/text()\n" + @@ -46,7 +45,7 @@ public class VocabularyGroup implements Serializable { } vocs.addTerm(vocId, termId, termName); - vocs.addSynonyms(vocId, termId, termId); + // vocs.addSynonyms(vocId, termId, termId); } } @@ -58,7 +57,7 @@ public class VocabularyGroup implements Serializable { final String syn = arr[2].trim(); vocs.addSynonyms(vocId, termId, syn); - vocs.addSynonyms(vocId, termId, termId); + // vocs.addSynonyms(vocId, termId, termId); } } @@ -135,7 +134,7 @@ public class VocabularyGroup implements Serializable { Optional .ofNullable(vocs.get(id)) .orElseThrow(() -> new IllegalArgumentException("missing vocabulary id: " + vocId)) - .addSynonym(syn, termId); + .addSynonym(syn.toLowerCase(), termId); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java index d1f152342..1b21ce2d3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java @@ -60,8 +60,8 @@ public class CleaningFunctionTest { assertNotNull(p_out); - assertEquals("eng", p_out.getLanguage().getClassid()); - assertEquals("English", p_out.getLanguage().getClassname()); + assertEquals("und", p_out.getLanguage().getClassid()); + assertEquals("Undetermined", p_out.getLanguage().getClassname()); assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid()); assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index 89ebe5af5..b63a12f61 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -281,8 +281,8 @@ "value": "VIRTA" }, "instancetype": { - "classid": "Comentario", - "classname": "Comentario", + "classid": "Comment/debate", + "classname": "Comment/debate", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource" }, @@ -317,8 +317,8 @@ "vol": "" }, "language": { - "classid": "en", - "classname": "en", + "classid": "UNKNOWN", + "classname": "UNKNOWN", "schemeid": "dnet:languages", "schemename": "dnet:languages" }, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt index 10eba3e86..05484c8e5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt @@ -1,223 +1,9 @@ -dnet:countries @=@ AF @=@ AFG -dnet:countries @=@ AF @=@ Afghanistan -dnet:countries @=@ AD @=@ Andorra -dnet:countries @=@ AO @=@ Angola -dnet:countries @=@ AR @=@ ARG -dnet:countries @=@ AR @=@ Argentina -dnet:countries @=@ AU @=@ AUS -dnet:countries @=@ AU @=@ Australia -dnet:countries @=@ AT @=@ AUT -dnet:countries @=@ AT @=@ Austria -dnet:countries @=@ AZ @=@ AZE -dnet:countries @=@ BD @=@ Bangladesh -dnet:countries @=@ BY @=@ Belarus -dnet:countries @=@ BE @=@ BEL -dnet:countries @=@ BE @=@ Belgium -dnet:countries @=@ BJ @=@ BEN -dnet:countries @=@ BO @=@ Bolivia, Plurinational State of -dnet:countries @=@ BA @=@ BIH -dnet:countries @=@ BA @=@ Bosnia-Hercegovina -dnet:countries @=@ BR @=@ BRA -dnet:countries @=@ BR @=@ Brazil -dnet:countries @=@ BG @=@ Bulgaria -dnet:countries @=@ BF @=@ BFA -dnet:countries @=@ KH @=@ Campuchea -dnet:countries @=@ CM @=@ CMR -dnet:countries @=@ CA @=@ CAN -dnet:countries @=@ CA @=@ Canada -dnet:countries @=@ CV @=@ Cape Verde -dnet:countries @=@ CL @=@ CHL -dnet:countries @=@ CL @=@ Chile -dnet:countries @=@ CN @=@ CHN -dnet:countries @=@ CN @=@ China -dnet:countries @=@ CO @=@ COL -dnet:countries @=@ CO @=@ Colombia -dnet:countries @=@ CG @=@ Congo, Republic -dnet:countries @=@ CD @=@ Congo, the Democratic Republic of the -dnet:countries @=@ CD @=@ Congo Democratic Republic (formerly Zaire) -dnet:countries 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PF @=@ French Polynesia -dnet:countries @=@ PF @=@ PYF -dnet:countries @=@ TF @=@ French Southern Territories -dnet:countries @=@ GE @=@ Georgia -dnet:countries @=@ DE @=@ DEU -dnet:countries @=@ DE @=@ Germany -dnet:countries @=@ DE @=@ Germany, Berlin -dnet:countries @=@ GH @=@ GHA -dnet:countries @=@ GR @=@ EL -dnet:countries @=@ GR @=@ GRC -dnet:countries @=@ GL @=@ GRL -dnet:countries @=@ GN @=@ Guinea -dnet:countries @=@ GW @=@ Guinea-Bissau -dnet:countries @=@ VA @=@ Vatican State -dnet:countries @=@ HK @=@ HKG -dnet:countries @=@ HK @=@ Hong Kong -dnet:countries @=@ HK @=@ Hongkong -dnet:countries @=@ HU @=@ HUN -dnet:countries @=@ HU @=@ Hungary -dnet:countries @=@ IS @=@ ISL -dnet:countries @=@ IN @=@ IND -dnet:countries @=@ IN @=@ India -dnet:countries @=@ ID @=@ IDN -dnet:countries @=@ ID @=@ Indonesia -dnet:countries @=@ IR @=@ Iran -dnet:countries @=@ IR @=@ Iran, Islamic Republic of -dnet:countries @=@ IE @=@ IRL -dnet:countries @=@ IE @=@ Ireland -dnet:countries @=@ IL 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dnet:review_levels @=@ 0002 @=@ Documento de trabajo dnet:review_levels @=@ 0002 @=@ Documento de trabajo de investigaci??n +dnet:review_levels @=@ 0002 @=@ Draft dnet:review_levels @=@ 0002 @=@ E-pub ahead of print dnet:review_levels @=@ 0002 @=@ Editorial de revista, no evaluado por pares dnet:review_levels @=@ 0002 @=@ Editorial de revista, não avaliado por pares @@ -1095,7 +1048,6 @@ dnet:review_levels @=@ 0002 @=@ communication_invitee dnet:review_levels @=@ 0002 @=@ doc-type:preprint dnet:review_levels @=@ 0002 @=@ doc-type:workingPaper dnet:review_levels @=@ 0002 @=@ draf -dnet:review_levels @=@ 0002 @=@ draft dnet:review_levels @=@ 0002 @=@ eu-repo/semantics/submittedVersion dnet:review_levels @=@ 0002 @=@ http://purl.org/coar/resource_type/c_8042 dnet:review_levels @=@ 0002 @=@ http://purl.org/coar/resource_type/c_816b @@ -1178,6 +1130,7 @@ dnet:review_levels @=@ 0001 @=@ Artículo de investigación, Investigaciones ori dnet:review_levels @=@ 0001 @=@ Artículo evaluado por pares dnet:review_levels @=@ 0001 @=@ Artículo evaluado por pares, Ensayos de investigación dnet:review_levels @=@ 0001 @=@ Artículo evaluado por pares, Investigaciones empíricas, Artículos de investigación +dnet:review_levels @=@ 0001 @=@ Artículo revisado dnet:review_levels @=@ 0001 @=@ Artículo revisado por pares dnet:review_levels @=@ 0001 @=@ Artículos de estudiantes, Artículo evaluado por pares, Artículos de investigación dnet:review_levels @=@ 0001 @=@ Artículos de investigación evaluados por doble ciego @@ -1185,7 +1138,7 @@ dnet:review_levels @=@ 0001 @=@ Artículos evaluadores por doble ciego dnet:review_levels @=@ 0001 @=@ Artículos evaluados por pares dnet:review_levels @=@ 0001 @=@ Artículos evaluados por pares académicos dnet:review_levels @=@ 0001 @=@ Artículos revisados por pares -dnet:review_levels @=@ 0001 @=@ avaliadas pelos pares +dnet:review_levels @=@ 0001 @=@ Avaliadas pelos pares dnet:review_levels @=@ 0001 @=@ Avaliado anonimamente por pares dnet:review_levels @=@ 0001 @=@ Avaliado em duplo cego por pares dnet:review_levels @=@ 0001 @=@ Avaliado pela Editoria @@ -1236,6 +1189,7 @@ dnet:review_levels @=@ 0001 @=@ Peer-reviewed Review dnet:review_levels @=@ 0001 @=@ Peer-reviewed Review Article dnet:review_levels @=@ 0001 @=@ Peer-reviewed Text dnet:review_levels @=@ 0001 @=@ Peer-reviewed communication +dnet:review_levels @=@ 0001 @=@ Peer-reviewed conference proceedings dnet:review_levels @=@ 0001 @=@ Peer-reviewed research article dnet:review_levels @=@ 0001 @=@ Peer-reviewed short communication dnet:review_levels @=@ 0001 @=@ PeerReviewed diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt index 1daca3ca9..59bed7c3a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt @@ -1,414 +1,39 @@ ModularUiLabels @=@ ModularUiLabels @=@ PendingRepositoryResources @=@ Pending datasource ModularUiLabels @=@ ModularUiLabels @=@ RepositoryServiceResources @=@ Valid datasource -dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/OPENACCESS_VERSION @=@ Another Open Access version of a publication -dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/PID @=@ Another persistent identifier associated to your publications -dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/MESHEUROPMC @=@ Another classification term from the Medical Subject Headings (MeSH) that can be associated to your publications -dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/DDC @=@ Another Dewey Decimal classification term (DDC) that can be associated to your publications -dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/ACM @=@ Another ACM classification term that 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0001 @=@ peerReviewed \ No newline at end of file