From 554551682d0501fa7664fab0a9bee8be6b0309d3 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 11 Oct 2023 16:09:19 +0200 Subject: [PATCH 1/7] [raw graph] adopting the new COAR based vocabularies for the resource typing --- .../common/vocabulary/VocabularyGroup.java | 21 ++++++++++++ .../dhp/schema/oaf/utils/OafMapperUtils.java | 10 +++++- .../raw/AbstractMdRecordToOafMapper.java | 31 ++++++++++++++++++ .../dhp/oa/graph/raw/OafToOafMapper.java | 32 ++++++++++++++++--- .../dhp/oa/graph/raw/OdfToOafMapper.java | 27 ++++++++++++++++ .../oa/graph/raw/OriginalTypeComparator.java | 32 +++++++++++++++++++ .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 21 ++++++++++++ .../dnetlib/dhp/oa/graph/clean/synonyms.txt | 7 +++- .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 4 ++- .../dnetlib/dhp/oa/graph/raw/oaf_record.xml | 4 ++- pom.xml | 2 +- 11 files changed, 182 insertions(+), 9 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java index fc7175270..4c1feac45 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java @@ -135,6 +135,27 @@ public class VocabularyGroup implements Serializable { return vocs.get(vocId.toLowerCase()).getSynonymAsQualifier(syn); } + public Qualifier lookupTermBySynonym(final String vocId, final String syn) { + if (StringUtils.isBlank(vocId)) { + return OafMapperUtils.unknown("", ""); + } + + final Vocabulary vocabulary = vocs.get(vocId.toLowerCase()); + + return Optional + .ofNullable(vocabulary.getTerm(syn)) + .map( + term -> OafMapperUtils + .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) + .orElse( + Optional + .ofNullable(vocabulary.getTermBySynonym(syn)) + .map( + term -> OafMapperUtils + .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) + .orElse(null)); + } + /** * getSynonymAsQualifierCaseSensitive * diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index c58096d35..1c557c805 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -14,7 +14,6 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.schema.common.AccessRightComparator; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; @@ -141,6 +140,15 @@ public class OafMapperUtils { .collect(Collectors.toList()); } + public static InstanceTypeMapping instanceTypeMapping(String originalType, Qualifier term) { + final InstanceTypeMapping m = new InstanceTypeMapping(); + m.setVocabularyName(term.getSchemeid()); + m.setOriginalType(originalType); + m.setTypeCode(term.getClassid()); + m.setTypeLabel(term.getClassname()); + return m; + } + public static Qualifier unknown(final String schemeid, final String schemename) { return qualifier(UNKNOWN, "Unknown", schemeid, schemename); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index b37e6a755..2fed7d627 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -41,6 +41,11 @@ public abstract class AbstractMdRecordToOafMapper { protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; + + protected static final String OPENAIRE_COAR_RESOURCE_TYPES_3_1 = "openaire::coar_resource_types_3_1"; + + public static final String OPENAIRE_USER_RESOURCE_TYPES = "openaire::user_resource_types"; + protected static final Qualifier ORCID_PID_TYPE = qualifier( ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, @@ -516,6 +521,32 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); + protected abstract String findOriginalType(Document doc); + + protected List prepareInstanceTypeMapping(Document doc) { + return Optional.ofNullable(findOriginalType(doc)) + .map(originalType -> { + final List mappings = Lists.newArrayList(); + + if (vocs.vocabularyExists(OPENAIRE_COAR_RESOURCE_TYPES_3_1)) { + + // TODO verify what the vocabs return when a synonym is not defined + Qualifier coarTerm = vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType); + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); + + if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { + + // TODO verify what the vocabs return when a synonym is not defined + Qualifier userTerm = vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid()); + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, userTerm)); + } + } + + return mappings; + }) + .orElse(new ArrayList<>()); + } + private Journal prepareJournal(final Document doc, final DataInfo info) { final Node n = doc.selectSingleNode("//oaf:journal"); if (n != null) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index a9f9367af..5cdb434f1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -5,12 +5,10 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import java.net.URLDecoder; -import java.util.ArrayList; -import java.util.HashSet; -import java.util.List; -import java.util.Set; +import java.util.*; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Element; @@ -25,6 +23,8 @@ import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; +import static org.apache.commons.lang3.StringUtils.contains; + public class OafToOafMapper extends AbstractMdRecordToOafMapper { public OafToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, @@ -139,6 +139,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final List alternateIdentifier = prepareResultPids(doc, info); final List pid = IdentifierFactory.getPids(alternateIdentifier, collectedfrom); + instance.setInstanceTypeMapping(prepareInstanceTypeMapping(doc)); + final Set pids = new HashSet<>(pid); instance @@ -187,6 +189,28 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { return Lists.newArrayList(instance); } + /** + * The Dublin Core element dc:type can be repeated, but we need to base our mapping on a single value + * So this method tries to give precedence to the COAR resource type, when available. Otherwise, it looks for the + * openaire's info:eu-repo type, and as last resort picks the 1st type text available + * + * http://purl.org/coar/resource_type/c_5794 + * info:eu-repo/semantics/article + * Conference article + * + * @param doc the input document + * @return the chosen resource type + */ + @Override + protected String findOriginalType(Document doc) { + return (String) doc.selectNodes("//dc:type") + .stream() + .map(o -> "" + ((Node) o).getText().trim()) + .sorted(new OriginalTypeComparator()) + .findFirst() + .orElse(null); + } + @Override protected List> prepareSources(final Document doc, final DataInfo info) { return prepareListFields(doc, "//dc:source", info); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index bbd1e7ab1..c01775327 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -9,6 +9,7 @@ import java.net.URLDecoder; import java.util.*; import java.util.stream.Collectors; +import org.apache.commons.lang3.ObjectUtils; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Element; @@ -139,6 +140,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final List alternateIdentifier = prepareResultPids(doc, info); final List pid = IdentifierFactory.getPids(alternateIdentifier, collectedfrom); + instance.setInstanceTypeMapping(prepareInstanceTypeMapping(doc)); + final Set pids = new HashSet<>(pid); instance @@ -217,6 +220,30 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { } } + @Override + protected List prepareInstanceTypeMapping(Document doc) { + return null; + } + + /** + * The Datacite element + * + * journal article + * + * @param doc the input document + * @return the chosen resource type + */ + @Override + protected String findOriginalType(Document doc) { + final Element resourceType = (Element) doc.selectSingleNode( + "//metadata/*[local-name() = 'resource']/*[local-name() = 'resourceType']"); + + final String resourceTypeURI = resourceType.attributeValue("anyURI"); + final String resourceTypeTxt = resourceType.getText(); + + return ObjectUtils.firstNonNull(resourceTypeURI, resourceTypeTxt); + } + @Override protected List> prepareSources(final Document doc, final DataInfo info) { return new ArrayList<>(); // Not present in ODF ??? diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java new file mode 100644 index 000000000..2eeead32e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java @@ -0,0 +1,32 @@ +package eu.dnetlib.dhp.oa.graph.raw; + +import java.util.Comparator; + +import static org.apache.commons.lang3.StringUtils.contains; +import static org.apache.commons.lang3.StringUtils.startsWith; + +public class OriginalTypeComparator implements Comparator { + + @Override + public int compare(String t1, String t2) { + + if (t1.equals(t2)) { + return 0; + } + if (startsWith(t1, "http") && contains(t1, "coar") && contains(t1, "resource_type")) { + return -1; + } + if (startsWith(t2, "http") && contains(t2, "coar") && contains(t2, "resource_type")) { + return 1; + } + if (startsWith(t1, "info:eu-repo/semantics")) { + return -1; + } + if (startsWith(t2, "info:eu-repo/semantics")) { + return 1; + } + + return t1.compareTo(t2); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index b506d3a62..5df2b7a3b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -116,6 +116,27 @@ class MappersTest { assertNotNull(instance.getPid()); assertTrue(instance.getPid().isEmpty()); + assertNotNull(instance.getInstanceTypeMapping()); + assertEquals(2, instance.getInstanceTypeMapping().size()); + + Optional coarType = instance.getInstanceTypeMapping() + .stream() + .filter(itm -> AbstractMdRecordToOafMapper.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .findFirst(); + + assertTrue(coarType.isPresent()); + assertEquals("http://purl.org/coar/resource_type/c_5794", coarType.get().getTypeCode()); + assertEquals("conference paper", coarType.get().getTypeLabel()); + + Optional userType = instance.getInstanceTypeMapping() + .stream() + .filter(itm -> AbstractMdRecordToOafMapper.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) + .findFirst(); + + assertTrue(userType.isPresent()); + assertEquals("Article", userType.get().getTypeCode()); + assertEquals("Article", userType.get().getTypeLabel()); + assertFalse(instance.getAlternateIdentifier().isEmpty()); assertEquals("doi", instance.getAlternateIdentifier().get(0).getQualifier().getClassid()); assertEquals("10.3897/oneeco.2.e13718", instance.getAlternateIdentifier().get(0).getValue()); 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 409dfd5dc..b3fa94b20 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 @@ -1245,4 +1245,9 @@ dnet:relation_relClass @=@ IsRelatedTo @=@ isRelatedTo dnet:relation_subRelType @=@ relationship @=@ publicationDataset dnet:provenanceActions @=@ iis @=@ erroneous label to be cleaned FOS @=@ 0101 mathematics @=@ FOS: Mathematics -FOS @=@ 0102 computer and information sciences @=@ FOS: Computer and information sciences \ No newline at end of file +FOS @=@ 0102 computer and information sciences @=@ FOS: Computer and information sciences +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_5794 @=@ Proceedings paper +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_5794 @=@ Conference article +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_5794 @=@ http://purl.org/eprint/type/ConferencePaper +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_5794 @=@ Conference article +openaire::user_resource_types @=@ Article @=@ http://purl.org/coar/resource_type/c_5794 \ No newline at end of file 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 24ce42fc2..a38c0e987 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 @@ -1121,4 +1121,6 @@ dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ supplement @=@ supplem dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ version @=@ version FOS @=@ Fields of Science and Technology classification @=@ 0101 mathematics @=@ 0101 mathematics FOS @=@ Fields of Science and Technology classification @=@ 0102 computer and information sciences @=@ 0102 computer and information sciences -FOS @=@ Fields of Science and Technology classification @=@ 0103 physical sciences @=@ 0103 physical sciences \ No newline at end of file +FOS @=@ Fields of Science and Technology classification @=@ 0103 physical sciences @=@ 0103 physical sciences +openaire::coar_resource_types_3_1 @=@ openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_5794 @=@ conference paper +openaire::user_resource_types @=@ openaire::user_resource_types @=@ Article @=@ Article \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml index 277578185..492fc9a7a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml @@ -47,7 +47,9 @@ provisioning services regulating services supporting services - Research Article + conference paper + http://purl.org/coar/resource_type/c_5794 + info:eu-repo/semantics/article 0001 2017-01-01 diff --git a/pom.xml b/pom.xml index 9cd82a343..0f1ec78af 100644 --- a/pom.xml +++ b/pom.xml @@ -888,7 +888,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [3.17.1] + [4.17.2-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 54fbf09ac63d1076a51ab791f093b33d9c4520bb Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 Oct 2023 08:57:47 +0200 Subject: [PATCH 2/7] [raw graph] WIP: mapping original resource types --- .../raw/AbstractMdRecordToOafMapper.java | 64 +- .../dhp/oa/graph/raw/OafToOafMapper.java | 28 +- .../dhp/oa/graph/raw/OdfToOafMapper.java | 22 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 60 +- .../dnetlib/dhp/oa/graph/clean/synonyms.txt | 855 +++++++++++++++++- .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 292 +++++- 6 files changed, 1244 insertions(+), 77 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 2fed7d627..5f0acbab7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -42,10 +42,6 @@ public abstract class AbstractMdRecordToOafMapper { protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; - protected static final String OPENAIRE_COAR_RESOURCE_TYPES_3_1 = "openaire::coar_resource_types_3_1"; - - public static final String OPENAIRE_USER_RESOURCE_TYPES = "openaire::user_resource_types"; - protected static final Qualifier ORCID_PID_TYPE = qualifier( ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, @@ -129,7 +125,9 @@ public abstract class AbstractMdRecordToOafMapper { final String type = getResultType(doc, instances); - return createOafs(doc, type, instances, collectedFrom, entityInfo, lastUpdateTimestamp); + final Qualifier metaResourceType = getMetaResourceType(instances); + + return createOafs(doc, type, metaResourceType, instances, collectedFrom, entityInfo, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); return Lists.newArrayList(); @@ -155,6 +153,30 @@ public abstract class AbstractMdRecordToOafMapper { return type; } + protected Qualifier getMetaResourceType(final List instances) { + + if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) { + Optional instanceTypeMapping = instances + .stream() + .flatMap(i -> i.getInstanceTypeMapping().stream()) + .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) + .findFirst(); + + if (!instanceTypeMapping.isPresent()) { + throw new IllegalStateException("unable to find an instance from " + OPENAIRE_COAR_RESOURCE_TYPES_3_1); + } else { + final String typeCode = instanceTypeMapping.get().getTypeCode(); + return Optional + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) + .orElseThrow(() -> + new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + + OPENAIRE_META_RESOURCE_TYPE)); + } + } else { + throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available"); + } + } + private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) { final String dsId = doc.valueOf(xpathId); final String dsName = doc.valueOf(xpathName); @@ -169,12 +191,13 @@ public abstract class AbstractMdRecordToOafMapper { protected List createOafs( final Document doc, final String type, + final Qualifier metaResourceType, final List instances, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { - final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + final OafEntity entity = createEntity(doc, type, metaResourceType, instances, collectedFrom, info, lastUpdateTimestamp); final Set originalId = Sets.newHashSet(entity.getOriginalId()); originalId.add(entity.getId()); @@ -207,6 +230,7 @@ public abstract class AbstractMdRecordToOafMapper { private OafEntity createEntity(final Document doc, final String type, + final Qualifier metaResourceType, final List instances, final KeyValue collectedFrom, final DataInfo info, @@ -214,12 +238,12 @@ public abstract class AbstractMdRecordToOafMapper { switch (type.toLowerCase()) { case "publication": final Publication p = new Publication(); - populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(p, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); p.setJournal(prepareJournal(doc, info)); return p; case "dataset": final Dataset d = new Dataset(); - populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(d, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); d.setStoragedate(prepareDatasetStorageDate(doc, info)); d.setDevice(prepareDatasetDevice(doc, info)); d.setSize(prepareDatasetSize(doc, info)); @@ -230,7 +254,7 @@ public abstract class AbstractMdRecordToOafMapper { return d; case "software": final Software s = new Software(); - populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(s, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); s.setLicense(prepareSoftwareLicenses(doc, info)); s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); @@ -240,7 +264,7 @@ public abstract class AbstractMdRecordToOafMapper { case "otherresearchproducts": default: final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(o, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); o.setTool(prepareOtherResearchProductTools(doc, info)); @@ -377,11 +401,13 @@ public abstract class AbstractMdRecordToOafMapper { private void populateResultFields( final Result r, + final Qualifier metaResourceType, final Document doc, final List instances, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { + r.setMetaResourceType(metaResourceType); r.setDataInfo(info); r.setLastupdatetimestamp(lastUpdateTimestamp); r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); @@ -531,15 +557,17 @@ public abstract class AbstractMdRecordToOafMapper { if (vocs.vocabularyExists(OPENAIRE_COAR_RESOURCE_TYPES_3_1)) { // TODO verify what the vocabs return when a synonym is not defined - Qualifier coarTerm = vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType); - mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); + Optional.ofNullable(vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType)) + .ifPresent(coarTerm -> { + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); + if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { - if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { - - // TODO verify what the vocabs return when a synonym is not defined - Qualifier userTerm = vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid()); - mappings.add(OafMapperUtils.instanceTypeMapping(originalType, userTerm)); - } + // TODO verify what the vocabs return when a synonym is not defined + Optional + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid())) + .ifPresent(type -> mappings.add(OafMapperUtils.instanceTypeMapping(originalType, type))); + } + }); } return mappings; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 5cdb434f1..6bcc8ec44 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -1,29 +1,27 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.schema.common.ModelConstants.*; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; - -import java.net.URLDecoder; -import java.util.*; -import java.util.stream.Collectors; - -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import org.apache.commons.lang3.StringUtils; -import org.dom4j.Document; -import org.dom4j.Element; -import org.dom4j.Node; - import com.google.common.collect.Lists; - import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; +import org.apache.commons.lang3.StringUtils; +import org.dom4j.Document; +import org.dom4j.Element; +import org.dom4j.Node; -import static org.apache.commons.lang3.StringUtils.contains; +import java.net.URLDecoder; +import java.util.ArrayList; +import java.util.HashSet; +import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; public class OafToOafMapper extends AbstractMdRecordToOafMapper { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index c01775327..c383e9300 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -220,11 +220,6 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { } } - @Override - protected List prepareInstanceTypeMapping(Document doc) { - return null; - } - /** * The Datacite element * @@ -235,13 +230,20 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { */ @Override protected String findOriginalType(Document doc) { - final Element resourceType = (Element) doc.selectSingleNode( - "//metadata/*[local-name() = 'resource']/*[local-name() = 'resourceType']"); + String resourceType = Optional.ofNullable((Element) doc.selectSingleNode( + "//*[local-name()='metadata']/*[local-name() = 'resource']/*[local-name() = 'resourceType']")) + .map(element -> { + final String resourceTypeURI = element.attributeValue("anyURI"); + final String resourceTypeTxt = element.getText(); - final String resourceTypeURI = resourceType.attributeValue("anyURI"); - final String resourceTypeTxt = resourceType.getText(); + return ObjectUtils.firstNonNull(resourceTypeURI, resourceTypeTxt); + }) + .orElse(doc.valueOf( + "//*[local-name()='metadata']/*[local-name() = 'resource']/*[local-name() = 'CobjCategory']/text()") + ); + + return resourceType; - return ObjectUtils.firstNonNull(resourceTypeURI, resourceTypeTxt); } @Override diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 5df2b7a3b..4d30a3fa8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -74,7 +74,7 @@ class MappersTest { assertTrue(StringUtils.isNotBlank(p.getDateofcollection())); assertTrue(StringUtils.isNotBlank(p.getDateoftransformation())); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() .stream() @@ -97,14 +97,14 @@ class MappersTest { assertEquals("Votsi", author.get().getSurname()); assertEquals("Nefta", author.get().getName()); - assertTrue(p.getSubject().size() > 0); + assertFalse(p.getSubject().isEmpty()); assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); assertTrue(p.getPid().isEmpty()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -121,7 +121,7 @@ class MappersTest { Optional coarType = instance.getInstanceTypeMapping() .stream() - .filter(itm -> AbstractMdRecordToOafMapper.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .filter(itm -> ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) .findFirst(); assertTrue(coarType.isPresent()); @@ -130,7 +130,7 @@ class MappersTest { Optional userType = instance.getInstanceTypeMapping() .stream() - .filter(itm -> AbstractMdRecordToOafMapper.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) + .filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) .findFirst(); assertTrue(userType.isPresent()); @@ -228,7 +228,7 @@ class MappersTest { assertTrue(StringUtils.isNotBlank(p.getDateofcollection())); assertTrue(StringUtils.isNotBlank(p.getDateoftransformation())); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() .stream() @@ -251,13 +251,13 @@ class MappersTest { assertEquals("Votsi", author.get().getSurname()); assertEquals("Nefta", author.get().getName()); - assertTrue(p.getSubject().size() > 0); - assertTrue(p.getPid().size() > 0); + assertFalse(p.getSubject().isEmpty()); + assertFalse(p.getPid().isEmpty()); assertEquals("PMC1517292", p.getPid().get(0).getValue()); assertEquals("pmc", p.getPid().get(0).getQualifier().getClassid()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -287,7 +287,7 @@ class MappersTest { final List list = new OafToOafMapper(vocs, true, true).processMdRecord(xml); - assertTrue(list.size() > 0); + assertFalse(list.isEmpty()); assertTrue(list.get(0) instanceof Publication); final Publication p = (Publication) list.get(0); @@ -343,7 +343,7 @@ class MappersTest { assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526"))); assertValidId(d.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); - assertTrue(d.getAuthor().size() > 0); + assertFalse(d.getAuthor().isEmpty()); final Optional author = d .getAuthor() @@ -377,13 +377,13 @@ class MappersTest { final Field affiliation = opAff.get(); assertEquals("ISTI-CNR", affiliation.getValue()); - assertTrue(d.getSubject().size() > 0); - assertTrue(d.getInstance().size() > 0); - assertTrue(d.getContext().size() > 0); - assertTrue(d.getContext().get(0).getId().length() > 0); + assertFalse(d.getSubject().isEmpty()); + assertFalse(d.getInstance().isEmpty()); + assertFalse(d.getContext().isEmpty()); + assertFalse(d.getContext().get(0).getId().isEmpty()); assertNotNull(d.getInstance()); - assertTrue(d.getInstance().size() > 0); + assertFalse(d.getInstance().isEmpty()); d .getInstance() .forEach(i -> { @@ -457,7 +457,7 @@ class MappersTest { // assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); assertValidId(p.getCollectedfrom().get(0).getKey()); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() @@ -469,14 +469,14 @@ class MappersTest { assertEquals("Potwarka", author.get().getSurname()); assertEquals("Luke R.", author.get().getName()); - assertTrue(p.getSubject().size() > 0); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getSubject().isEmpty()); + assertFalse(p.getInstance().isEmpty()); assertNotNull(p.getTitle()); assertFalse(p.getTitle().isEmpty()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -624,9 +624,9 @@ class MappersTest { assertValidId(s.getId()); assertValidId(s.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); - assertTrue(s.getAuthor().size() > 0); - assertTrue(s.getSubject().size() > 0); - assertTrue(s.getInstance().size() > 0); + assertFalse(s.getAuthor().isEmpty()); + assertFalse(s.getSubject().isEmpty()); + assertFalse(s.getInstance().isEmpty()); final Relation r1 = (Relation) list.get(1); final Relation r2 = (Relation) list.get(2); @@ -882,7 +882,7 @@ class MappersTest { assertEquals(2, p.getOriginalId().size()); assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("df76e73f-0483-49a4-a9bb-63f2f985574a"))); assertValidId(p.getCollectedfrom().get(0).getKey()); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() @@ -892,14 +892,14 @@ class MappersTest { assertEquals("Museum Sønderjylland", author.get().getFullname()); - assertTrue(p.getSubject().size() > 0); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getSubject().isEmpty()); + assertFalse(p.getInstance().isEmpty()); assertNotNull(p.getTitle()); assertFalse(p.getTitle().isEmpty()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -939,10 +939,10 @@ class MappersTest { System.out.println("***************"); final Dataset p = (Dataset) list.get(0); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); for (String url : p.getInstance().get(0).getUrl()) { System.out.println(url); - assertTrue(!url.contains("&")); + assertFalse(url.contains("&")); } } @@ -959,7 +959,7 @@ class MappersTest { assertTrue(o.isPresent()); Publication p = (Publication) o.get(); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); assertEquals("https://doi.org/10.1155/2015/439379", p.getInstance().get(0).getUrl().get(0)); 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 b3fa94b20..a17a3949a 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 @@ -1246,8 +1246,857 @@ dnet:relation_subRelType @=@ relationship @=@ publicationDataset dnet:provenanceActions @=@ iis @=@ erroneous label to be cleaned FOS @=@ 0101 mathematics @=@ FOS: Mathematics FOS @=@ 0102 computer and information sciences @=@ FOS: Computer and information sciences +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ Chemical Structures +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ Data Cube +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ Dataset/Dataset +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ Ensemble de données / Dataset +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ Research Data +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ dataset +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ http://purl.org/coar/resource_type/c_ddb1 +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/ACF7-8YT9 @=@ collection +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/ACF7-8YT9 @=@ Collection of Datasets +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/ACF7-8YT9 @=@ RO-crate +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/ACF7-8YT9 @=@ Supplementary Collection of Datasets +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/ACF7-8YT9 @=@ Supplementary Dataset +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cc @=@ http://purl.org/coar/resource_type/c_12cc +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cc @=@ Planimetría +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_cb28 @=@ clinicalTrial +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_cb28 @=@ http://purl.org/coar/resource_type/c_cb28 +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cd @=@ Carte géographique / Map +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cd @=@ http://purl.org/coar/resource_type/c_12cd +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cd @=@ map +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cd @=@ Mapa +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_18cc @=@ Audio +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_18cc @=@ http://purl.org/coar/resource_type/c_18cc +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_18cc @=@ sound +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ Book Prospectus +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ Dictionary Entry +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ Disclosure +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ Literature review +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ Reseña bibliográfica +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ bibliography +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ http://purl.org/coar/resource_type/c_86bc +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_8a7e @=@ AUDIOVISUAL_DOCUMENT +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_8a7e @=@ Audiovisual/Audiovisual +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_8a7e @=@ http://purl.org/coar/resource_type/c_8a7e +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ Diagram +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ Drawing +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ Figure +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ Image/Image +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ Imagen - Image +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ Imagen 3-D +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ Imagen +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ Photo +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ Plot +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ StillImage|PRESERVED_SPECIMEN +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ fotó +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ grafika +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ http://purl.org/coar/resource_type/c_ecc8 +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ image-diagram +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ image-drawing +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ image-figure +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ image-other +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ image-photo +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ image-plot +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ image 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Research Software @=@ software:research_software +openaire::meta_resource_types @=@ Research Software @=@ http://purl.org/coar/resource_type/c_c950 +openaire::meta_resource_types @=@ Research Software @=@ software +openaire::meta_resource_types @=@ Research Software @=@ http://purl.org/coar/resource_type/c_5ce6 +openaire::meta_resource_types @=@ Research Software @=@ software:source_code +openaire::meta_resource_types @=@ Research Software @=@ http://purl.org/coar/resource_type/QH80-2R4E +openaire::meta_resource_types @=@ Other Research Products @=@ learning_object +openaire::meta_resource_types @=@ Other Research Products @=@ http://purl.org/coar/resource_type/c_e059 +openaire::meta_resource_types @=@ Other Research Products @=@ other +openaire::meta_resource_types @=@ Other Research Products @=@ http://purl.org/coar/resource_type/c_1843 +openaire::meta_resource_types @=@ Other Research Products @=@ trademark +openaire::meta_resource_types @=@ Other Research Products @=@ http://purl.org/coar/resource_type/H6QP-SC1X +openaire::meta_resource_types @=@ Other Research Products @=@ workflow +openaire::meta_resource_types @=@ Other Research Products @=@ http://purl.org/coar/resource_type/c_393c \ No newline at end of file From 6dfcd0c9a2072c589709a97769185a966def58b4 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 Oct 2023 12:57:18 +0200 Subject: [PATCH 3/7] [raw graph] mapping original resource types --- .../raw/AbstractMdRecordToOafMapper.java | 63 ++++--- .../dhp/oa/graph/raw/OafToOafMapper.java | 41 +++-- .../dhp/oa/graph/raw/OdfToOafMapper.java | 22 ++- .../oa/graph/raw/OriginalTypeComparator.java | 43 ++--- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 168 ++++++++++++++++-- .../dnetlib/dhp/oa/graph/raw/oaf_crossref.xml | 68 +++++++ 6 files changed, 308 insertions(+), 97 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 5f0acbab7..49133cedb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -157,20 +157,20 @@ public abstract class AbstractMdRecordToOafMapper { if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) { Optional instanceTypeMapping = instances - .stream() - .flatMap(i -> i.getInstanceTypeMapping().stream()) - .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) - .findFirst(); + .stream() + .flatMap(i -> i.getInstanceTypeMapping().stream()) + .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) + .findFirst(); if (!instanceTypeMapping.isPresent()) { - throw new IllegalStateException("unable to find an instance from " + OPENAIRE_COAR_RESOURCE_TYPES_3_1); + return null; } else { final String typeCode = instanceTypeMapping.get().getTypeCode(); return Optional - .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) - .orElseThrow(() -> - new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + - OPENAIRE_META_RESOURCE_TYPE)); + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) + .orElseThrow( + () -> new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + + OPENAIRE_META_RESOURCE_TYPE)); } } else { throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available"); @@ -197,7 +197,8 @@ public abstract class AbstractMdRecordToOafMapper { final DataInfo info, final long lastUpdateTimestamp) { - final OafEntity entity = createEntity(doc, type, metaResourceType, instances, collectedFrom, info, lastUpdateTimestamp); + final OafEntity entity = createEntity( + doc, type, metaResourceType, instances, collectedFrom, info, lastUpdateTimestamp); final Set originalId = Sets.newHashSet(entity.getOriginalId()); originalId.add(entity.getId()); @@ -550,29 +551,33 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract String findOriginalType(Document doc); protected List prepareInstanceTypeMapping(Document doc) { - return Optional.ofNullable(findOriginalType(doc)) - .map(originalType -> { - final List mappings = Lists.newArrayList(); + return Optional + .ofNullable(findOriginalType(doc)) + .map(originalType -> { + final List mappings = Lists.newArrayList(); - if (vocs.vocabularyExists(OPENAIRE_COAR_RESOURCE_TYPES_3_1)) { + if (vocs.vocabularyExists(OPENAIRE_COAR_RESOURCE_TYPES_3_1)) { - // TODO verify what the vocabs return when a synonym is not defined - Optional.ofNullable(vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType)) - .ifPresent(coarTerm -> { - mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); - if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { + // TODO verify what the vocabs return when a synonym is not defined + Optional + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType)) + .ifPresent(coarTerm -> { + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); + if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { - // TODO verify what the vocabs return when a synonym is not defined - Optional - .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid())) - .ifPresent(type -> mappings.add(OafMapperUtils.instanceTypeMapping(originalType, type))); - } - }); - } + // TODO verify what the vocabs return when a synonym is not defined + Optional + .ofNullable( + vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid())) + .ifPresent( + type -> mappings.add(OafMapperUtils.instanceTypeMapping(originalType, type))); + } + }); + } - return mappings; - }) - .orElse(new ArrayList<>()); + return mappings; + }) + .orElse(new ArrayList<>()); } private Journal prepareJournal(final Document doc, final DataInfo info) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 6bcc8ec44..a63296d18 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -1,17 +1,8 @@ package eu.dnetlib.dhp.oa.graph.raw; -import com.google.common.collect.Lists; -import eu.dnetlib.dhp.common.PacePerson; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; -import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; -import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; -import org.apache.commons.lang3.StringUtils; -import org.dom4j.Document; -import org.dom4j.Element; -import org.dom4j.Node; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import java.net.URLDecoder; import java.util.ArrayList; @@ -20,8 +11,19 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import static eu.dnetlib.dhp.schema.common.ModelConstants.*; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; +import org.apache.commons.lang3.StringUtils; +import org.dom4j.Document; +import org.dom4j.Element; +import org.dom4j.Node; + +import com.google.common.collect.Lists; + +import eu.dnetlib.dhp.common.PacePerson; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; public class OafToOafMapper extends AbstractMdRecordToOafMapper { @@ -201,12 +203,13 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { */ @Override protected String findOriginalType(Document doc) { - return (String) doc.selectNodes("//dc:type") - .stream() - .map(o -> "" + ((Node) o).getText().trim()) - .sorted(new OriginalTypeComparator()) - .findFirst() - .orElse(null); + return (String) doc + .selectNodes("//dc:type") + .stream() + .map(o -> "" + ((Node) o).getText().trim()) + .sorted(new OriginalTypeComparator()) + .findFirst() + .orElse(null); } @Override diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index c383e9300..e63b01a00 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -230,20 +230,18 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { */ @Override protected String findOriginalType(Document doc) { - String resourceType = Optional.ofNullable((Element) doc.selectSingleNode( + return Optional + .ofNullable( + (Element) doc + .selectSingleNode( "//*[local-name()='metadata']/*[local-name() = 'resource']/*[local-name() = 'resourceType']")) - .map(element -> { - final String resourceTypeURI = element.attributeValue("anyURI"); - final String resourceTypeTxt = element.getText(); - - return ObjectUtils.firstNonNull(resourceTypeURI, resourceTypeTxt); - }) - .orElse(doc.valueOf( - "//*[local-name()='metadata']/*[local-name() = 'resource']/*[local-name() = 'CobjCategory']/text()") - ); - - return resourceType; + .map(element -> { + final String resourceTypeURI = element.attributeValue("anyURI"); + final String resourceTypeTxt = element.getText(); + return ObjectUtils.firstNonNull(resourceTypeURI, resourceTypeTxt); + }) + .orElse(null); } @Override diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java index 2eeead32e..c3d8b4789 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java @@ -1,32 +1,33 @@ -package eu.dnetlib.dhp.oa.graph.raw; -import java.util.Comparator; +package eu.dnetlib.dhp.oa.graph.raw; import static org.apache.commons.lang3.StringUtils.contains; import static org.apache.commons.lang3.StringUtils.startsWith; +import java.util.Comparator; + public class OriginalTypeComparator implements Comparator { - @Override - public int compare(String t1, String t2) { + @Override + public int compare(String t1, String t2) { - if (t1.equals(t2)) { - return 0; - } - if (startsWith(t1, "http") && contains(t1, "coar") && contains(t1, "resource_type")) { - return -1; - } - if (startsWith(t2, "http") && contains(t2, "coar") && contains(t2, "resource_type")) { - return 1; - } - if (startsWith(t1, "info:eu-repo/semantics")) { - return -1; - } - if (startsWith(t2, "info:eu-repo/semantics")) { - return 1; - } + if (t1.equals(t2)) { + return 0; + } + if (startsWith(t1, "http") && contains(t1, "coar") && contains(t1, "resource_type")) { + return -1; + } + if (startsWith(t2, "http") && contains(t2, "coar") && contains(t2, "resource_type")) { + return 1; + } + if (startsWith(t1, "info:eu-repo/semantics")) { + return -1; + } + if (startsWith(t2, "info:eu-repo/semantics")) { + return 1; + } - return t1.compareTo(t2); - } + return t1.compareTo(t2); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 4d30a3fa8..e6997ac1d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -14,6 +14,8 @@ import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; import org.dom4j.DocumentException; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @@ -25,8 +27,11 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.Constants; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.clean.CleaningRuleMap; +import eu.dnetlib.dhp.oa.graph.clean.OafCleaner; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.PidType; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -119,19 +124,21 @@ class MappersTest { assertNotNull(instance.getInstanceTypeMapping()); assertEquals(2, instance.getInstanceTypeMapping().size()); - Optional coarType = instance.getInstanceTypeMapping() - .stream() - .filter(itm -> ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) - .findFirst(); + Optional coarType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .findFirst(); assertTrue(coarType.isPresent()); assertEquals("http://purl.org/coar/resource_type/c_5794", coarType.get().getTypeCode()); assertEquals("conference paper", coarType.get().getTypeLabel()); - Optional userType = instance.getInstanceTypeMapping() - .stream() - .filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) - .findFirst(); + Optional userType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) + .findFirst(); assertTrue(userType.isPresent()); assertEquals("Article", userType.get().getTypeCode()); @@ -266,8 +273,8 @@ class MappersTest { }); Publication p_cleaned = cleanup(p, vocs); - assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); assertNotNull(p.getInstance().get(0).getPid()); assertEquals(2, p.getInstance().get(0).getPid().size()); @@ -485,8 +492,8 @@ class MappersTest { }); Publication p_cleaned = cleanup(p, vocs); - assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); } @Test @@ -604,8 +611,137 @@ class MappersTest { assertTrue(i.getUrl().contains("https://clinicaltrials.gov/ct2/show/NCT02321059")); Dataset d_cleaned = cleanup(d, vocs); - assertEquals("0000", d_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", d_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", d_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", d_cleaned.getInstance().get(0).getRefereed().getClassname()); + } + + @Test + void test_record_from_Crossref() throws IOException { + + final CleaningRuleMap mapping = CleaningRuleMap.create(vocs); + + final String xml = IOUtils + .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_crossref.xml"))); + final List list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); + + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Publication); + + final Publication p = OafCleaner.apply(fixVocabularyNames((Publication) list.get(0)), mapping); + + assertNotNull(p.getDateofcollection()); + assertEquals("2020-08-06T07:04:09.62Z", p.getDateofcollection()); + + assertNotNull(p.getDateoftransformation()); + assertEquals("2020-08-06T07:20:57.911Z", p.getDateoftransformation()); + + assertNotNull(p.getDataInfo()); + assertFalse(p.getDataInfo().getInvisible()); + assertFalse(p.getDataInfo().getDeletedbyinference()); + assertEquals("0.9", p.getDataInfo().getTrust()); + + assertValidId(p.getId()); + assertEquals(2, p.getOriginalId().size()); + + assertEquals("50|doi_________::7f0f7807f17db50e5c2b5c452ccaf06d", p.getOriginalId().get(0)); + assertValidId(p.getCollectedfrom().get(0).getKey()); + + assertNotNull(p.getTitle()); + assertEquals(1, p.getTitle().size()); + assertEquals( + "A case report of serious haemolysis in a glucose-6-phosphate dehydrogenase-deficient COVID-19 patient receiving hydroxychloroquine", + p + .getTitle() + .get(0) + .getValue()); + + assertNotNull(p.getDescription()); + assertEquals(0, p.getDescription().size()); + + assertEquals(8, p.getAuthor().size()); + + assertNotNull(p.getInstance()); + assertEquals(1, p.getInstance().size()); + + final Instance i = p.getInstance().get(0); + + assertNotNull(i.getAccessright()); + assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemeid()); + assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemename()); + assertEquals("OPEN", i.getAccessright().getClassid()); + assertEquals("Open Access", i.getAccessright().getClassname()); + + assertNotNull(i.getCollectedfrom()); + assertEquals("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", i.getCollectedfrom().getKey()); + assertEquals("Crossref", i.getCollectedfrom().getValue()); + + assertNotNull(i.getHostedby()); + assertEquals("10|openaire____::55045bd2a65019fd8e6741a755395c8c", i.getHostedby().getKey()); + assertEquals("Unknown Repository", i.getHostedby().getValue()); + + assertNotNull(i.getInstancetype()); + assertEquals("0001", i.getInstancetype().getClassid()); + assertEquals("Article", i.getInstancetype().getClassname()); + assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemeid()); + assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemename()); + + assertNull(i.getLicense()); + assertNotNull(i.getDateofacceptance()); + assertEquals("2020-06-04", i.getDateofacceptance().getValue()); + + assertNull(i.getProcessingchargeamount()); + assertNull(i.getProcessingchargecurrency()); + + assertNotNull(i.getPid()); + assertEquals(1, i.getPid().size()); + + assertNotNull(i.getAlternateIdentifier()); + assertEquals(0, i.getAlternateIdentifier().size()); + + assertNotNull(i.getUrl()); + assertEquals(1, i.getUrl().size()); + assertTrue(i.getUrl().contains("http://dx.doi.org/10.1080/23744235.2020.1774644")); + + assertEquals("", p.getInstance().get(0).getRefereed().getClassid()); + assertEquals("", p.getInstance().get(0).getRefereed().getClassname()); + + Publication p_cleaned = cleanup(p, vocs); + + assertEquals("0001", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("peerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + + assertNotNull(p_cleaned.getMetaResourceType()); + assertEquals("Research Literature", p_cleaned.getMetaResourceType().getClassid()); + assertEquals("Research Literature", p_cleaned.getMetaResourceType().getClassname()); + assertEquals(ModelConstants.OPENAIRE_META_RESOURCE_TYPE, p_cleaned.getMetaResourceType().getSchemeid()); + assertEquals(ModelConstants.OPENAIRE_META_RESOURCE_TYPE, p_cleaned.getMetaResourceType().getSchemename()); + + assertNotNull(p_cleaned.getInstance().get(0).getInstanceTypeMapping()); + assertEquals(2, p_cleaned.getInstance().get(0).getInstanceTypeMapping().size()); + + assertTrue( + p_cleaned + .getInstance() + .get(0) + .getInstanceTypeMapping() + .stream() + .anyMatch( + t -> "journal-article".equals(t.getOriginalType()) && + ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName()) && + "http://purl.org/coar/resource_type/c_2df8fbb1".equals(t.getTypeCode()) && + "research article".equals(t.getTypeLabel()))); + + assertTrue( + p_cleaned + .getInstance() + .get(0) + .getInstanceTypeMapping() + .stream() + .anyMatch( + t -> "journal-article".equals(t.getOriginalType()) && + ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(t.getVocabularyName()) && + "Article".equals(t.getTypeCode()) && + "Article".equals(t.getTypeLabel()))); } @Test @@ -908,8 +1044,8 @@ class MappersTest { }); Dataset p_cleaned = cleanup(p, vocs); - assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml new file mode 100644 index 000000000..182820a08 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml @@ -0,0 +1,68 @@ + + +
+ doi_________::7f0f7807f17db50e5c2b5c452ccaf06d + doi_________::7f0f7807f17db50e5c2b5c452ccaf06d + 2020-08-06T07:04:09.62Z + + + + + + 2020-08-06T07:20:57.911Z + openaire____ +
+ + A case report of serious haemolysis in a glucose-6-phosphate dehydrogenase-deficient COVID-19 patient receiving hydroxychloroquine + Maillart, E. + Leemans, S. + Van Noten, H. + Vandergraesen, T. + Mahadeb, B. + Salaouatchi, M. T. + De Bels, D. + Clevenbergh, P. + + http://dx.doi.org/10.1080/23744235.2020.1774644 + + Informa UK Limited + Crossref + Infectious Diseases + Microbiology (medical) + General Immunology and Microbiology + Infectious Diseases + General Medicine + journal-article + 0001 + 2020-06-04 + + OPEN + + + 10.1080/23744235.2020.1774644 + Infectious Diseases + + + + + file%3A%2F%2F%2Fsrv%2Fclaims%2Frecords%2Fpublication%2Fcrossref + + + + + + + false + false + 0.9 + + + + + \ No newline at end of file From d28b7085f6f13a644926302e47da314dcb22de5d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 17 Oct 2023 11:09:31 +0200 Subject: [PATCH 4/7] more NPE checks --- .../common/vocabulary/VocabularyGroup.java | 25 ++++++++----------- 1 file changed, 11 insertions(+), 14 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java index 4c1feac45..64b6f91af 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java @@ -136,24 +136,21 @@ public class VocabularyGroup implements Serializable { } public Qualifier lookupTermBySynonym(final String vocId, final String syn) { - if (StringUtils.isBlank(vocId)) { - return OafMapperUtils.unknown("", ""); - } - - final Vocabulary vocabulary = vocs.get(vocId.toLowerCase()); - - return Optional - .ofNullable(vocabulary.getTerm(syn)) + return find(vocId) .map( - term -> OafMapperUtils - .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) - .orElse( - Optional - .ofNullable(vocabulary.getTermBySynonym(syn)) + vocabulary -> Optional + .ofNullable(vocabulary.getTerm(syn)) .map( term -> OafMapperUtils .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) - .orElse(null)); + .orElse( + Optional + .ofNullable(vocabulary.getTermBySynonym(syn)) + .map( + term -> OafMapperUtils + .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) + .orElse(null))) + .orElse(null); } /** From 11a1207f9c8476db4fc926f707915c3209720106 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 22 Nov 2023 12:22:14 +0100 Subject: [PATCH 5/7] [graph cleaning] applying coar based vocabularies in bulk --- .../dhp/oa/merge/GroupEntitiesSparkJob.java | 40 +++++- .../oaf/utils/GraphCleaningFunctions.java | 95 +++++++++++++ .../dhp/schema/oaf/utils/OafMapperUtils.java | 21 ++- .../group_graph_entities_parameters.json | 6 + .../raw/AbstractMdRecordToOafMapper.java | 63 +-------- .../group/GroupEntitiesSparkJobTest.java | 131 ++++++++++++++++-- .../raw/GenerateEntitiesApplicationTest.java | 5 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 28 ++-- .../dhp/oa/graph/group/dataset/dataset.json | 6 +- .../graph/group/publication/publication.json | 6 +- pom.xml | 2 +- 11 files changed, 294 insertions(+), 109 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java index f5c8eea19..0225a5063 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java @@ -21,10 +21,15 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import scala.Tuple2; /** @@ -35,6 +40,12 @@ public class GroupEntitiesSparkJob { private static final Encoder OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class); + private ArgumentApplicationParser parser; + + public GroupEntitiesSparkJob(ArgumentApplicationParser parser) { + this.parser = parser; + } + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -51,6 +62,17 @@ public class GroupEntitiesSparkJob { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + + new GroupEntitiesSparkJob(parser).run(isSparkSessionManaged, isLookupService); + } + + public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) + throws ISLookUpException { + String graphInputPath = parser.get("graphInputPath"); log.info("graphInputPath: {}", graphInputPath); @@ -60,19 +82,21 @@ public class GroupEntitiesSparkJob { String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - boolean filterInvisible = Boolean.valueOf(parser.get("filterInvisible")); + boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible")); log.info("filterInvisible: {}", filterInvisible); SparkConf conf = new SparkConf(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); + runWithSparkSession( conf, isSparkSessionManaged, spark -> { HdfsSupport.remove(checkpointPath, spark.sparkContext().hadoopConfiguration()); - groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible); + groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible, vocs); }); } @@ -81,7 +105,7 @@ public class GroupEntitiesSparkJob { String inputPath, String checkpointPath, String outputPath, - boolean filterInvisible) { + boolean filterInvisible, VocabularyGroup vocs) { Dataset allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC); @@ -106,10 +130,14 @@ public class GroupEntitiesSparkJob { } Dataset groupedEntities = allEntities - .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) - .reduceGroups((ReduceFunction) (b, a) -> OafMapperUtils.mergeEntities(b, a)) .map( - (MapFunction, Tuple2>) t -> new Tuple2( + (MapFunction) entity -> GraphCleaningFunctions + .applyCoarVocabularies(entity, vocs), + OAFENTITY_KRYO_ENC) + .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) + .reduceGroups((ReduceFunction) OafMapperUtils::mergeEntities) + .map( + (MapFunction, Tuple2>) t -> new Tuple2<>( t._2().getClass().getName(), t._2()), Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC)); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index 324e3dd58..b23dade98 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -1,6 +1,8 @@ package eu.dnetlib.dhp.schema.oaf.utils; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.common.ModelConstants.OPENAIRE_META_RESOURCE_TYPE; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance; import java.time.LocalDate; @@ -784,4 +786,97 @@ public class GraphCleaningFunctions extends CleaningFunctions { return s; } + public static OafEntity applyCoarVocabularies(OafEntity entity, VocabularyGroup vocs) { + + if (entity instanceof Result) { + final Result result = (Result) entity; + + Optional + .ofNullable(result.getInstance()) + .ifPresent( + instances -> instances + .forEach( + instance -> { + if (Objects.isNull(instance.getInstanceTypeMapping())) { + List mapping = Lists.newArrayList(); + mapping + .add( + OafMapperUtils + .instanceTypeMapping( + instance.getInstancetype().getClassname(), + OPENAIRE_COAR_RESOURCE_TYPES_3_1)); + instance.setInstanceTypeMapping(mapping); + } + Optional optionalItm = instance + .getInstanceTypeMapping() + .stream() + .filter(GraphCleaningFunctions::originalResourceType) + .findFirst(); + if (optionalItm.isPresent()) { + InstanceTypeMapping coarItm = optionalItm.get(); + Optional + .ofNullable( + vocs + .lookupTermBySynonym( + OPENAIRE_COAR_RESOURCE_TYPES_3_1, coarItm.getOriginalType())) + .ifPresent(type -> { + coarItm.setTypeCode(type.getClassid()); + coarItm.setTypeLabel(type.getClassname()); + }); + final List mappings = Lists.newArrayList(); + if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { + Optional + .ofNullable( + vocs + .lookupTermBySynonym( + OPENAIRE_USER_RESOURCE_TYPES, coarItm.getTypeCode())) + .ifPresent( + type -> mappings + .add( + OafMapperUtils + .instanceTypeMapping(coarItm.getTypeCode(), type))); + } + if (!mappings.isEmpty()) { + instance.getInstanceTypeMapping().addAll(mappings); + } + } + })); + result.setMetaResourceType(getMetaResourceType(result.getInstance(), vocs)); + } + + return entity; + } + + private static boolean originalResourceType(InstanceTypeMapping itm) { + return StringUtils.isNotBlank(itm.getOriginalType()) && + OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName()) && + StringUtils.isBlank(itm.getTypeCode()) && + StringUtils.isBlank(itm.getTypeLabel()); + } + + private static Qualifier getMetaResourceType(final List instances, final VocabularyGroup vocs) { + + if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) { + Optional instanceTypeMapping = instances + .stream() + .flatMap( + i -> Optional.ofNullable(i.getInstanceTypeMapping()).map(Collection::stream).orElse(Stream.empty())) + .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) + .findFirst(); + + if (!instanceTypeMapping.isPresent()) { + return null; + } else { + final String typeCode = instanceTypeMapping.get().getTypeCode(); + return Optional + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) + .orElseThrow( + () -> new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + + OPENAIRE_META_RESOURCE_TYPE)); + } + } else { + throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available"); + } + } + } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 1c557c805..4cecd0895 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -140,15 +140,28 @@ public class OafMapperUtils { .collect(Collectors.toList()); } - public static InstanceTypeMapping instanceTypeMapping(String originalType, Qualifier term) { + public static InstanceTypeMapping instanceTypeMapping(String originalType, String code, String label, + String vocabularyName) { final InstanceTypeMapping m = new InstanceTypeMapping(); - m.setVocabularyName(term.getSchemeid()); + m.setVocabularyName(vocabularyName); m.setOriginalType(originalType); - m.setTypeCode(term.getClassid()); - m.setTypeLabel(term.getClassname()); + m.setTypeCode(code); + m.setTypeLabel(label); return m; } + public static InstanceTypeMapping instanceTypeMapping(String originalType, Qualifier term) { + return instanceTypeMapping(originalType, term.getClassid(), term.getClassname(), term.getSchemeid()); + } + + public static InstanceTypeMapping instanceTypeMapping(String originalType) { + return instanceTypeMapping(originalType, null, null, null); + } + + public static InstanceTypeMapping instanceTypeMapping(String originalType, String vocabularyName) { + return instanceTypeMapping(originalType, null, null, vocabularyName); + } + public static Qualifier unknown(final String schemeid, final String schemename) { return qualifier(UNKNOWN, "Unknown", schemeid, schemename); } diff --git a/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json b/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json index 58e3ca711..512878457 100644 --- a/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json +++ b/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json @@ -28,5 +28,11 @@ "paramLongName": "filterInvisible", "paramDescription": "if true filters out invisible entities", "paramRequired": true + }, + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "url to the ISLookup Service", + "paramRequired": true } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 49133cedb..a71908b02 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -125,9 +125,7 @@ public abstract class AbstractMdRecordToOafMapper { final String type = getResultType(doc, instances); - final Qualifier metaResourceType = getMetaResourceType(instances); - - return createOafs(doc, type, metaResourceType, instances, collectedFrom, entityInfo, lastUpdateTimestamp); + return createOafs(doc, type, instances, collectedFrom, entityInfo, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); return Lists.newArrayList(); @@ -153,30 +151,6 @@ public abstract class AbstractMdRecordToOafMapper { return type; } - protected Qualifier getMetaResourceType(final List instances) { - - if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) { - Optional instanceTypeMapping = instances - .stream() - .flatMap(i -> i.getInstanceTypeMapping().stream()) - .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) - .findFirst(); - - if (!instanceTypeMapping.isPresent()) { - return null; - } else { - final String typeCode = instanceTypeMapping.get().getTypeCode(); - return Optional - .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) - .orElseThrow( - () -> new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + - OPENAIRE_META_RESOURCE_TYPE)); - } - } else { - throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available"); - } - } - private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) { final String dsId = doc.valueOf(xpathId); final String dsName = doc.valueOf(xpathName); @@ -191,14 +165,13 @@ public abstract class AbstractMdRecordToOafMapper { protected List createOafs( final Document doc, final String type, - final Qualifier metaResourceType, final List instances, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { final OafEntity entity = createEntity( - doc, type, metaResourceType, instances, collectedFrom, info, lastUpdateTimestamp); + doc, type, instances, collectedFrom, info, lastUpdateTimestamp); final Set originalId = Sets.newHashSet(entity.getOriginalId()); originalId.add(entity.getId()); @@ -231,7 +204,6 @@ public abstract class AbstractMdRecordToOafMapper { private OafEntity createEntity(final Document doc, final String type, - final Qualifier metaResourceType, final List instances, final KeyValue collectedFrom, final DataInfo info, @@ -239,12 +211,12 @@ public abstract class AbstractMdRecordToOafMapper { switch (type.toLowerCase()) { case "publication": final Publication p = new Publication(); - populateResultFields(p, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); p.setJournal(prepareJournal(doc, info)); return p; case "dataset": final Dataset d = new Dataset(); - populateResultFields(d, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); d.setStoragedate(prepareDatasetStorageDate(doc, info)); d.setDevice(prepareDatasetDevice(doc, info)); d.setSize(prepareDatasetSize(doc, info)); @@ -255,7 +227,7 @@ public abstract class AbstractMdRecordToOafMapper { return d; case "software": final Software s = new Software(); - populateResultFields(s, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); s.setLicense(prepareSoftwareLicenses(doc, info)); s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); @@ -265,7 +237,7 @@ public abstract class AbstractMdRecordToOafMapper { case "otherresearchproducts": default: final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); o.setTool(prepareOtherResearchProductTools(doc, info)); @@ -402,13 +374,11 @@ public abstract class AbstractMdRecordToOafMapper { private void populateResultFields( final Result r, - final Qualifier metaResourceType, final Document doc, final List instances, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { - r.setMetaResourceType(metaResourceType); r.setDataInfo(info); r.setLastupdatetimestamp(lastUpdateTimestamp); r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); @@ -555,26 +525,7 @@ public abstract class AbstractMdRecordToOafMapper { .ofNullable(findOriginalType(doc)) .map(originalType -> { final List mappings = Lists.newArrayList(); - - if (vocs.vocabularyExists(OPENAIRE_COAR_RESOURCE_TYPES_3_1)) { - - // TODO verify what the vocabs return when a synonym is not defined - Optional - .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType)) - .ifPresent(coarTerm -> { - mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); - if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { - - // TODO verify what the vocabs return when a synonym is not defined - Optional - .ofNullable( - vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid())) - .ifPresent( - type -> mappings.add(OafMapperUtils.instanceTypeMapping(originalType, type))); - } - }); - } - + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, OPENAIRE_COAR_RESOURCE_TYPES_3_1)); return mappings; }) .orElse(new ArrayList<>()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java index 0887adf45..242aed88e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java @@ -1,15 +1,23 @@ package eu.dnetlib.dhp.oa.graph.group; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.Mockito.lenient; import java.io.IOException; import java.net.URISyntaxException; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import org.apache.commons.cli.ParseException; import org.apache.commons.io.FileUtils; +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; @@ -17,20 +25,36 @@ import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.InstanceTypeMapping; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +@ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class GroupEntitiesSparkJobTest { + @Mock + private ISLookUpService isLookUpService; + + private VocabularyGroup vocabularies; + private static SparkSession spark; private static ObjectMapper mapper = new ObjectMapper() @@ -45,10 +69,10 @@ public class GroupEntitiesSparkJobTest { @BeforeAll public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName()); + workingDir = Files.createTempDirectory(GroupEntitiesSparkJobTest.class.getSimpleName()); SparkConf conf = new SparkConf(); - conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName()); + conf.setAppName(GroupEntitiesSparkJobTest.class.getSimpleName()); conf.setMaster("local"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); @@ -56,10 +80,17 @@ public class GroupEntitiesSparkJobTest { } @BeforeEach - public void beforeEach() throws IOException, URISyntaxException { + public void beforeEach() throws IOException, URISyntaxException, ISLookUpException { dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI()); checkpointPath = workingDir.resolve("grouped_entity"); outputPath = workingDir.resolve("dispatched_entity"); + + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + + vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); } @AfterAll @@ -71,18 +102,17 @@ public class GroupEntitiesSparkJobTest { @Test @Order(1) void testGroupEntities() throws Exception { - GroupEntitiesSparkJob.main(new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-graphInputPath", - dataInputPath.toString(), - "-checkpointPath", - checkpointPath.toString(), - "-outputPath", - outputPath.toString(), - "-filterInvisible", - Boolean.FALSE.toString() - }); + new GroupEntitiesSparkJob( + args( + "/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json", + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--graphInputPath", dataInputPath.toString(), + "--checkpointPath", checkpointPath.toString(), + "--outputPath", outputPath.toString(), + "--filterInvisible", Boolean.FALSE.toString(), + "--isLookupUrl", "lookupurl" + })).run(false, isLookUpService); Dataset checkpointTable = spark .read() @@ -109,6 +139,14 @@ public class GroupEntitiesSparkJobTest { .map((MapFunction) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class)); assertEquals(3, output.count()); + + List resultTypes = output + .map((MapFunction) value -> value.getResulttype().getClassid(), Encoders.STRING()) + .distinct() + .collectAsList(); + + assertEquals(2, resultTypes.size()); + assertEquals( 2, output @@ -121,5 +159,68 @@ public class GroupEntitiesSparkJobTest { .map((MapFunction) r -> r.getResulttype().getClassid(), Encoders.STRING()) .filter((FilterFunction) s -> s.equals("dataset")) .count()); + + Result result = output + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'") + .first(); + + result.getInstance().forEach(instance -> { + Optional coarType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .filter(itm -> "journal-article".equals(itm.getOriginalType())) + .findFirst(); + + assertTrue(coarType.isPresent()); + assertEquals("http://purl.org/coar/resource_type/c_2df8fbb1", coarType.get().getTypeCode()); + assertEquals("research article", coarType.get().getTypeLabel()); + }); + + final Dataset filtered = output.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'"); + assertEquals(1, filtered.count()); + result = filtered.first(); + + result + .getInstance() + .stream() + .flatMap(instance -> instance.getInstanceTypeMapping().stream()) + .filter(itm -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .filter(itm -> "Patent".equals(itm.getOriginalType())) + .forEach(itm -> { + assertEquals("http://purl.org/coar/resource_type/c_15cd", itm.getTypeCode()); + assertEquals("patent", itm.getTypeLabel()); + }); } + + private List vocs() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"))); + } + + private List synonyms() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"))); + } + + private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { + ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); + parser.parseArgument(args); + return parser; + } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + Objects + .requireNonNull( + GroupEntitiesSparkJobTest.class.getResourceAsStream(path))); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java index 53b3f8432..6d6b2ffbd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java @@ -92,13 +92,14 @@ class GenerateEntitiesApplicationTest { private List vocs() throws IOException { return IOUtils .readLines( - GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); + GenerateEntitiesApplicationTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); } private List synonyms() throws IOException { return IOUtils .readLines( - GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); + GenerateEntitiesApplicationTest.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index e6997ac1d..1f2defa01 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -122,7 +122,7 @@ class MappersTest { assertTrue(instance.getPid().isEmpty()); assertNotNull(instance.getInstanceTypeMapping()); - assertEquals(2, instance.getInstanceTypeMapping().size()); + assertEquals(1, instance.getInstanceTypeMapping().size()); Optional coarType = instance .getInstanceTypeMapping() @@ -131,8 +131,8 @@ class MappersTest { .findFirst(); assertTrue(coarType.isPresent()); - assertEquals("http://purl.org/coar/resource_type/c_5794", coarType.get().getTypeCode()); - assertEquals("conference paper", coarType.get().getTypeLabel()); + assertNull(coarType.get().getTypeCode()); + assertNull(coarType.get().getTypeLabel()); Optional userType = instance .getInstanceTypeMapping() @@ -140,9 +140,7 @@ class MappersTest { .filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) .findFirst(); - assertTrue(userType.isPresent()); - assertEquals("Article", userType.get().getTypeCode()); - assertEquals("Article", userType.get().getTypeLabel()); + assertFalse(userType.isPresent()); assertFalse(instance.getAlternateIdentifier().isEmpty()); assertEquals("doi", instance.getAlternateIdentifier().get(0).getQualifier().getClassid()); @@ -710,14 +708,10 @@ class MappersTest { assertEquals("0001", p_cleaned.getInstance().get(0).getRefereed().getClassid()); assertEquals("peerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); - assertNotNull(p_cleaned.getMetaResourceType()); - assertEquals("Research Literature", p_cleaned.getMetaResourceType().getClassid()); - assertEquals("Research Literature", p_cleaned.getMetaResourceType().getClassname()); - assertEquals(ModelConstants.OPENAIRE_META_RESOURCE_TYPE, p_cleaned.getMetaResourceType().getSchemeid()); - assertEquals(ModelConstants.OPENAIRE_META_RESOURCE_TYPE, p_cleaned.getMetaResourceType().getSchemename()); + assertNull(p_cleaned.getMetaResourceType()); assertNotNull(p_cleaned.getInstance().get(0).getInstanceTypeMapping()); - assertEquals(2, p_cleaned.getInstance().get(0).getInstanceTypeMapping().size()); + assertEquals(1, p_cleaned.getInstance().get(0).getInstanceTypeMapping().size()); assertTrue( p_cleaned @@ -728,8 +722,7 @@ class MappersTest { .anyMatch( t -> "journal-article".equals(t.getOriginalType()) && ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName()) && - "http://purl.org/coar/resource_type/c_2df8fbb1".equals(t.getTypeCode()) && - "research article".equals(t.getTypeLabel()))); + Objects.isNull(t.getTypeCode()) && Objects.isNull(t.getTypeLabel()))); assertTrue( p_cleaned @@ -737,11 +730,8 @@ class MappersTest { .get(0) .getInstanceTypeMapping() .stream() - .anyMatch( - t -> "journal-article".equals(t.getOriginalType()) && - ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(t.getVocabularyName()) && - "Article".equals(t.getTypeCode()) && - "Article".equals(t.getTypeLabel()))); + .noneMatch( + t -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(t.getVocabularyName()))); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json index e30be47e9..efbabb3c8 100644 --- 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diff --git a/pom.xml b/pom.xml index 0f1ec78af..3fd351c1d 100644 --- a/pom.xml +++ b/pom.xml @@ -888,7 +888,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [4.17.2-SNAPSHOT] + [4.17.2] [4.0.3] [6.0.5] [3.1.6] From af1c2634b3fc61c208dfd8e57fff1b11459dba5f Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 29 Nov 2023 12:45:30 +0100 Subject: [PATCH 6/7] added instanceTypeMapping original field in the mapping of - DOIBoost - Datacite - PubMed - Scholexplorer Datasource --- .../DataciteToOAFTransformation.scala | 15 ++++++++----- .../eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala | 21 +++++++++++++++++-- .../dhp/sx/bio/pubmed/PubMedToOaf.scala | 18 ++++++++++++---- .../doiboost/crossref/Crossref2Oaf.scala | 8 +++++-- 4 files changed, 49 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index 45f5f9729..17f1b90b0 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -166,7 +166,7 @@ object DataciteToOAFTransformation { resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup - ): (Qualifier, Qualifier) = { + ): (Qualifier, Qualifier, String) = { if (resourceType != null && resourceType.nonEmpty) { val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType) @@ -176,7 +176,7 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ) + ), resourceType ) } if (schemaOrg != null && schemaOrg.nonEmpty) { @@ -188,7 +188,7 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ) + ), schemaOrg ) } @@ -203,7 +203,7 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ) + ), resourceTypeGeneral ) } @@ -216,12 +216,17 @@ object DataciteToOAFTransformation { schemaOrg: String, vocabularies: VocabularyGroup ): Result = { - val typeQualifiers: (Qualifier, Qualifier) = + val typeQualifiers: (Qualifier, Qualifier, String) = getTypeQualifier(resourceType, resourceTypeGeneral, schemaOrg, vocabularies) if (typeQualifiers == null) return null val i = new Instance i.setInstancetype(typeQualifiers._1) + // ADD ORIGINAL TYPE + val itm = new InstanceTypeMapping + itm.setOriginalType(typeQualifiers._3) + i.setInstanceTypeMapping(List(itm).asJava) + typeQualifiers._2.getClassname match { case "dataset" => val r = new OafDataset diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala index c079f7537..3624c5369 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -176,7 +176,7 @@ object BioDBToOAF { i.setUrl(List(s"${resolvedURL(input.pidType)}${input.pid}").asJava) } - if (input.pidType.equalsIgnoreCase("clinicaltrials.gov")) + if (input.pidType.equalsIgnoreCase("clinicaltrials.gov")) { i.setInstancetype( OafMapperUtils.qualifier( "0037", @@ -185,7 +185,10 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) - else + val itm = new InstanceTypeMapping + itm.setOriginalType(input.pidType) + i.setInstanceTypeMapping(List(itm).asJava) + } else { i.setInstancetype( OafMapperUtils.qualifier( "0046", @@ -194,6 +197,10 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + i.setInstanceTypeMapping(List(itm).asJava) + } if (input.datasource == null || input.datasource.isEmpty) return null @@ -265,6 +272,9 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + i.setInstanceTypeMapping(List(itm).asJava) i.setCollectedfrom(collectedFromMap("uniprot")) d.setInstance(List(i).asJava) @@ -471,6 +481,9 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + i.setInstanceTypeMapping(List(itm).asJava) i.setCollectedfrom(collectedFromMap("pdb")) d.setInstance(List(i).asJava) @@ -571,6 +584,10 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + i.setInstanceTypeMapping(List(itm).asJava) + i.setCollectedfrom(collectedFromMap("ebi")) d.setInstance(List(i).asJava) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 410686f97..40ac48a7a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -188,12 +188,22 @@ object PubMedToOaf { val cojbCategory = getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, ja.get.getValue) pubmedInstance.setInstancetype(cojbCategory) + // ADD ORIGINAL TYPE to the publication + val itm = new InstanceTypeMapping + itm.setOriginalType(ja.get.getValue) + pubmedInstance.setInstanceTypeMapping(List(itm).asJava) } else { val i_type = article.getPublicationTypes.asScala - .map(s => getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue)) - .find(q => q != null) - if (i_type.isDefined) - pubmedInstance.setInstancetype(i_type.get) + .map(s => (s.getValue,getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue))) + .find(q => q._2 != null) + + if (i_type.isDefined) { + pubmedInstance.setInstancetype(i_type.get._2) + // ADD ORIGINAL TYPE to the publication + val itm = new InstanceTypeMapping + itm.setOriginalType(i_type.get._1) + pubmedInstance.setInstanceTypeMapping(List(itm).asJava) + } else return null } diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 565d34e62..f45c303f0 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -107,7 +107,7 @@ case object Crossref2Oaf { .map(f => f.id) } - def mappingResult(result: Result, json: JValue, cobjCategory: String): Result = { + def mappingResult(result: Result, json: JValue, cobjCategory: String, originalType:String): Result = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats //MAPPING Crossref DOI into PID @@ -283,6 +283,10 @@ case object Crossref2Oaf { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + //ADD ORIGINAL TYPE to the mapping + val itm = new InstanceTypeMapping + itm.setOriginalType(originalType) + instance.setInstanceTypeMapping(List(itm).asJava) result.setResourcetype( OafMapperUtils.qualifier( cobjCategory.substring(0, 4), @@ -367,7 +371,7 @@ case object Crossref2Oaf { objectType, mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type") ) - mappingResult(result, json, cOBJCategory) + mappingResult(result, json, cOBJCategory, originalType) if (result == null || result.getId == null) return List() From 86b5775e0859233ececfbc7425afee5a5b2c2c6f Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 29 Nov 2023 13:15:43 +0100 Subject: [PATCH 7/7] added vocabulary in instanceTypeMapping for - DOIBoost - Datacite - PubMed - Scholexplorer Datasource --- .../dnetlib/dhp/datacite/DataciteToOAFTransformation.scala | 2 ++ .../src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala | 5 +++++ .../scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala | 2 ++ .../scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala | 1 + 4 files changed, 10 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index 17f1b90b0..ee3660918 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -225,8 +225,10 @@ object DataciteToOAFTransformation { // ADD ORIGINAL TYPE val itm = new InstanceTypeMapping itm.setOriginalType(typeQualifiers._3) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) + typeQualifiers._2.getClassname match { case "dataset" => val r = new OafDataset diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala index 3624c5369..89bc8d948 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -187,6 +187,7 @@ object BioDBToOAF { ) val itm = new InstanceTypeMapping itm.setOriginalType(input.pidType) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) } else { i.setInstancetype( @@ -199,6 +200,7 @@ object BioDBToOAF { ) val itm = new InstanceTypeMapping itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) } @@ -274,6 +276,7 @@ object BioDBToOAF { ) val itm = new InstanceTypeMapping itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) i.setCollectedfrom(collectedFromMap("uniprot")) @@ -483,6 +486,7 @@ object BioDBToOAF { ) val itm = new InstanceTypeMapping itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) i.setCollectedfrom(collectedFromMap("pdb")) @@ -586,6 +590,7 @@ object BioDBToOAF { ) val itm = new InstanceTypeMapping itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 40ac48a7a..f3f8b4f02 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -191,6 +191,7 @@ object PubMedToOaf { // ADD ORIGINAL TYPE to the publication val itm = new InstanceTypeMapping itm.setOriginalType(ja.get.getValue) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) pubmedInstance.setInstanceTypeMapping(List(itm).asJava) } else { val i_type = article.getPublicationTypes.asScala @@ -202,6 +203,7 @@ object PubMedToOaf { // ADD ORIGINAL TYPE to the publication val itm = new InstanceTypeMapping itm.setOriginalType(i_type.get._1) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) pubmedInstance.setInstanceTypeMapping(List(itm).asJava) } else diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index f45c303f0..65e395357 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -286,6 +286,7 @@ case object Crossref2Oaf { //ADD ORIGINAL TYPE to the mapping val itm = new InstanceTypeMapping itm.setOriginalType(originalType) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) instance.setInstanceTypeMapping(List(itm).asJava) result.setResourcetype( OafMapperUtils.qualifier(