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 fc71752706..64b6f91af2 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 +135,24 @@ public class VocabularyGroup implements Serializable { return vocs.get(vocId.toLowerCase()).getSynonymAsQualifier(syn); } + public Qualifier lookupTermBySynonym(final String vocId, final String syn) { + return find(vocId) + .map( + vocabulary -> 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))) + .orElse(null); + } + /** * getSynonymAsQualifierCaseSensitive * 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 f5c8eea19e..0225a50635 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 7a8acbd36c..7cb32eab58 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.net.MalformedURLException; @@ -870,4 +872,97 @@ 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 c58096d353..4cecd08954 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 +140,28 @@ public class OafMapperUtils { .collect(Collectors.toList()); } + public static InstanceTypeMapping instanceTypeMapping(String originalType, String code, String label, + String vocabularyName) { + final InstanceTypeMapping m = new InstanceTypeMapping(); + m.setVocabularyName(vocabularyName); + m.setOriginalType(originalType); + 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 58e3ca7113..5128784576 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-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 45f5f9729d..ee36609189 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 +216,19 @@ 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) + 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 c079f7537c..89bc8d948b 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 +185,11 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) - else + 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( OafMapperUtils.qualifier( "0046", @@ -194,6 +198,11 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + i.setInstanceTypeMapping(List(itm).asJava) + } if (input.datasource == null || input.datasource.isEmpty) return null @@ -265,6 +274,10 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + 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")) d.setInstance(List(i).asJava) @@ -471,6 +484,10 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + 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")) d.setInstance(List(i).asJava) @@ -571,6 +588,11 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + 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 410686f972..f3f8b4f020 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 +188,24 @@ 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) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) + 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) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_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 565d34e622..65e3953570 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 +283,11 @@ case object Crossref2Oaf { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + //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( cobjCategory.substring(0, 4), @@ -367,7 +372,7 @@ 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() 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 bca6a2aae6..6d995fb4c7 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 +41,7 @@ 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 Qualifier ORCID_PID_TYPE = qualifier( ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, @@ -169,7 +170,8 @@ public abstract class AbstractMdRecordToOafMapper { final DataInfo info, final long lastUpdateTimestamp) { - final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + final OafEntity entity = createEntity( + doc, type, instances, collectedFrom, info, lastUpdateTimestamp); final Set originalId = Sets.newHashSet(entity.getOriginalId()); originalId.add(entity.getId()); @@ -516,6 +518,19 @@ 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(); + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, OPENAIRE_COAR_RESOURCE_TYPES_3_1)); + 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 a9f9367af5..a63296d189 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 @@ -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 +189,29 @@ 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 bbd1e7ab19..e63b01a002 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 { } } + /** + * The Datacite element + * + * journal article + * + * @param doc the input document + * @return the chosen resource type + */ + @Override + protected String findOriginalType(Document doc) { + 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(null); + } + @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 0000000000..c3d8b47895 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java @@ -0,0 +1,33 @@ + +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) { + + 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/group/GroupEntitiesSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java index 0887adf45e..242aed88e0 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 53b3f8432d..6d6b2ffbdf 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 da7a890ee0..ac0435ce21 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; @@ -74,7 +79,7 @@ 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 +102,14 @@ 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 -> { @@ -116,6 +121,27 @@ class MappersTest { assertNotNull(instance.getPid()); assertTrue(instance.getPid().isEmpty()); + assertNotNull(instance.getInstanceTypeMapping()); + assertEquals(1, instance.getInstanceTypeMapping().size()); + + Optional coarType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .findFirst(); + + assertTrue(coarType.isPresent()); + assertNull(coarType.get().getTypeCode()); + assertNull(coarType.get().getTypeLabel()); + + Optional userType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) + .findFirst(); + + assertFalse(userType.isPresent()); + assertFalse(instance.getAlternateIdentifier().isEmpty()); assertEquals("doi", instance.getAlternateIdentifier().get(0).getQualifier().getClassid()); assertEquals("10.3897/oneeco.2.e13718", instance.getAlternateIdentifier().get(0).getValue()); @@ -207,7 +233,7 @@ 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() @@ -230,13 +256,13 @@ 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 -> { @@ -245,8 +271,8 @@ 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()); @@ -266,7 +292,7 @@ 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); @@ -322,7 +348,7 @@ 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() @@ -356,13 +382,13 @@ 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 -> { @@ -436,7 +462,7 @@ 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() @@ -448,14 +474,14 @@ 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 -> { @@ -464,8 +490,8 @@ 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 @@ -583,8 +609,129 @@ 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()); + + assertNull(p_cleaned.getMetaResourceType()); + + assertNotNull(p_cleaned.getInstance().get(0).getInstanceTypeMapping()); + assertEquals(1, 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()) && + Objects.isNull(t.getTypeCode()) && Objects.isNull(t.getTypeLabel()))); + + assertTrue( + p_cleaned + .getInstance() + .get(0) + .getInstanceTypeMapping() + .stream() + .noneMatch( + t -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(t.getVocabularyName()))); } @Test @@ -603,9 +750,9 @@ 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); @@ -875,7 +1022,7 @@ 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() @@ -885,14 +1032,14 @@ 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 -> { @@ -901,8 +1048,8 @@ 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 @@ -932,10 +1079,10 @@ 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("&")); } } @@ -952,7 +1099,7 @@ 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 409dfd5dcd..a17a3949a0 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 +1245,858 @@ 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_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 @=@ 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image-plot +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ecc8 @=@ image +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12ce @=@ film +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12ce @=@ Film, vidéo / Motion picture, video +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12ce @=@ http://purl.org/coar/resource_type/c_12ce +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12ce @=@ Video +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12ce @=@ vídeo +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/C53B-JCY5 @=@ H1 Myönnetty patentti +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/C53B-JCY5 @=@ http://purl.org/coar/resource_type/C53B-JCY5 +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_15cd @=@ brevet +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_15cd @=@ http://purl.org/coar/resource_type/c_15cd +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_15cd @=@ Patent +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_15cd @=@ Patente +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_15cd @=@ Registered Copyright +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_15cd @=@ Traducción de patente +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/SB3Y-W4EH @=@ Solicitud de patente +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_e9a0 @=@ http://purl.org/coar/resource_type/c_e9a0 +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_e9a0 @=@ interactiveResource +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_e059 @=@ http://purl.org/coar/resource_type/c_e059 +openaire::coar_resource_types_3_1 @=@ 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http://purl.org/coar/resource_type/c_1843 @=@ corpus +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_1843 @=@ event +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_1843 @=@ http://purl.org/coar/resource_type/c_1843 +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_1843 @=@ http://purl.org/coar/resource_type/c_26e4 +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_1843 @=@ info:eu-repo/semantics/other +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_1843 @=@ misc +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_1843 @=@ model +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_1843 @=@ other research product +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_1843 @=@ other +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_1843 @=@ otro 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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 0000000000..182820a088 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml @@ -0,0 +1,68 @@ + + +
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