diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 327c33d6f2..8bae191d38 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 873046e080..ad8cd57b4a 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 8099a72e4e..08f5de9ee8 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index a700a29187..369e25b24b 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index c7cb11b085..60e66f45a2 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT ../ diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java similarity index 99% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java rename to dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java index 6e474f2f38..1909ddcca6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.oa.graph.raw.common; +package eu.dnetlib.dhp.common; import java.nio.charset.StandardCharsets; import java.text.Normalizer; diff --git a/dhp-schemas/pom.xml b/dhp-schemas/pom.xml index fe5d0c431a..5e864cf940 100644 --- a/dhp-schemas/pom.xml +++ b/dhp-schemas/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT ../ diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java new file mode 100644 index 0000000000..db523ad1ac --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java @@ -0,0 +1,69 @@ + +package eu.dnetlib.dhp.schema.common; + +import java.util.Comparator; + +import eu.dnetlib.dhp.schema.oaf.Qualifier; + +public class LicenseComparator implements Comparator { + + @Override + public int compare(Qualifier left, Qualifier right) { + + if (left == null && right == null) + return 0; + if (left == null) + return 1; + if (right == null) + return -1; + + String lClass = left.getClassid(); + String rClass = right.getClassid(); + + if (lClass.equals(rClass)) + return 0; + + if (lClass.equals("OPEN SOURCE")) + return -1; + if (rClass.equals("OPEN SOURCE")) + return 1; + + if (lClass.equals("OPEN")) + return -1; + if (rClass.equals("OPEN")) + return 1; + + if (lClass.equals("6MONTHS")) + return -1; + if (rClass.equals("6MONTHS")) + return 1; + + if (lClass.equals("12MONTHS")) + return -1; + if (rClass.equals("12MONTHS")) + return 1; + + if (lClass.equals("EMBARGO")) + return -1; + if (rClass.equals("EMBARGO")) + return 1; + + if (lClass.equals("RESTRICTED")) + return -1; + if (rClass.equals("RESTRICTED")) + return 1; + + if (lClass.equals("CLOSED")) + return -1; + if (rClass.equals("CLOSED")) + return 1; + + if (lClass.equals("UNKNOWN")) + return -1; + if (rClass.equals("UNKNOWN")) + return 1; + + // Else (but unlikely), lexicographical ordering will do. + return lClass.compareTo(rClass); + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java index cc77e1ea0c..9d572ee30a 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java @@ -8,7 +8,7 @@ public class DataInfo implements Serializable { private Boolean invisible = false; private Boolean inferred; - private Boolean deletedbyinference; + private Boolean deletedbyinference = false; private String trust; private String inferenceprovenance; private Qualifier provenanceaction; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java index 1a85c6842d..8358bc4b37 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Objects; public class Field implements Serializable { @@ -39,6 +40,6 @@ public class Field implements Serializable { if (getClass() != obj.getClass()) return false; Field other = (Field) obj; - return getValue().equals(other.getValue()); + return Objects.equals(getValue(), other.getValue()); } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java index 09742748d7..2823ee49dd 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java @@ -106,6 +106,7 @@ public abstract class OafEntity extends Oaf implements Serializable { .stream(lists) .filter(Objects::nonNull) .flatMap(List::stream) + .filter(Objects::nonNull) .distinct() .collect(Collectors.toList()); } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index 711b1ca681..11fdaa4f92 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -244,7 +244,25 @@ public class Result extends OafEntity implements Serializable { subject = mergeLists(subject, r.getSubject()); + // merge title lists: main title with higher trust and distinct between the others + StructuredProperty baseMainTitle = null; + if (title != null) { + baseMainTitle = getMainTitle(title); + title.remove(baseMainTitle); + } + + StructuredProperty newMainTitle = null; + if (r.getTitle() != null) { + newMainTitle = getMainTitle(r.getTitle()); + r.getTitle().remove(newMainTitle); + } + + if (newMainTitle != null && compareTrust(this, r) < 0) + baseMainTitle = newMainTitle; + title = mergeLists(title, r.getTitle()); + if (title != null && baseMainTitle != null) + title.add(baseMainTitle); relevantdate = mergeLists(relevantdate, r.getRelevantdate()); @@ -294,4 +312,15 @@ public class Result extends OafEntity implements Serializable { } return a.size() > b.size() ? a : b; } + + private StructuredProperty getMainTitle(List titles) { + // need to check if the list of titles contains more than 1 main title? (in that case, we should chose which + // main title select in the list) + for (StructuredProperty title : titles) { + if (title.getQualifier() != null && title.getQualifier().getClassid() != null) + if (title.getQualifier().getClassid().equals("main title")) + return title; + } + return null; + } } diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index 22a81f7da8..ec6247102e 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 1c5465c14a..9f082df70a 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 37abc22f61..a3cc15b744 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -1,11 +1,9 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java b/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java index bbfd15674e..585848589c 100644 --- a/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java +++ b/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java @@ -61,12 +61,6 @@ public class BlackListTest { spark.stop(); } - /* - * String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); final String outputPath = - * parser.get("outputPath"); log.info("outputPath {}: ", outputPath); final String blacklistPath = - * parser.get("hdfsPath"); log.info("blacklistPath {}: ", blacklistPath); final String mergesPath = - * parser.get("mergesPath"); log.info("mergesPath {}: ", mergesPath); - */ @Test public void noRemoveTest() throws Exception { SparkRemoveBlacklistedRelationJob diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 8b7ec38511..0e84d99a45 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT 4.0.0 @@ -57,7 +57,7 @@ eu.dnetlib dnet-openaire-broker-common - [1.0.0,2.0.0) + [2.0.0,3.0.0) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index fa425a1819..d5e577972d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -30,30 +30,30 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.model.Event; import eu.dnetlib.dhp.broker.model.EventFactory; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAbstract; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAuthorOrcid; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsReferencedBy; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsRelatedTo; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsSupplementedBy; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsSupplementedTo; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetReferences; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingOpenAccess; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPid; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingProject; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationDate; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsReferencedBy; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsRelatedTo; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsSupplementedBy; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsSupplementedTo; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationReferences; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingSoftware; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingSubject; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreOpenAccess; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMorePid; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreProject; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreSoftware; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreSubject; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; +import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsReferencedBy; +import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsRelatedTo; +import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsSupplementedBy; +import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsSupplementedTo; +import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetReferences; +import eu.dnetlib.dhp.broker.oa.matchers.relatedProjects.EnrichMissingProject; +import eu.dnetlib.dhp.broker.oa.matchers.relatedProjects.EnrichMoreProject; +import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsReferencedBy; +import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsRelatedTo; +import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsSupplementedBy; +import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsSupplementedTo; +import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationReferences; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingAbstract; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingAuthorOrcid; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingOpenAccess; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPid; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPublicationDate; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingSoftware; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingSubject; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreOpenAccess; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMorePid; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSoftware; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSubject; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.common.HdfsSupport; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsReferencedBy.java deleted file mode 100644 index 3b9326fef2..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsReferencedBy.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingDatasetIsReferencedBy - extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { - - public EnrichMissingDatasetIsReferencedBy() { - super(true); - } - - @Override - protected List> findUpdates(final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return null; - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Dataset highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_DATASET_IS_REFERENCED_BY, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> p.getDatasets().add(rel), - rel -> rel.getInstances().get(0).getUrl()); - } -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsRelatedTo.java deleted file mode 100644 index 35f7c52b42..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsRelatedTo.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingDatasetIsRelatedTo - extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { - - public EnrichMissingDatasetIsRelatedTo() { - super(true); - } - - @Override - protected List> findUpdates(final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return null; - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Dataset highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_DATASET_IS_RELATED_TO, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> p.getDatasets().add(rel), - rel -> rel.getInstances().get(0).getUrl()); - } -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedBy.java deleted file mode 100644 index 1faa305b52..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedBy.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingDatasetIsSupplementedBy - extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { - - public EnrichMissingDatasetIsSupplementedBy() { - super(true); - } - - @Override - protected List> findUpdates(final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return null; - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Dataset highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_BY, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> p.getDatasets().add(rel), - rel -> rel.getInstances().get(0).getUrl()); - } -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedTo.java deleted file mode 100644 index d1b067272d..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedTo.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingDatasetIsSupplementedTo - extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { - - public EnrichMissingDatasetIsSupplementedTo() { - super(true); - } - - @Override - protected List> findUpdates(final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return null; - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Dataset highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_TO, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> p.getDatasets().add(rel), - rel -> rel.getInstances().get(0).getUrl()); - } -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetReferences.java deleted file mode 100644 index ce6adeba27..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetReferences.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingDatasetReferences - extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { - - public EnrichMissingDatasetReferences() { - super(true); - } - - @Override - protected List> findUpdates(final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return null; - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Dataset highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_DATASET_REFERENCES, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> p.getDatasets().add(rel), - rel -> rel.getInstances().get(0).getUrl()); - } -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsReferencedBy.java deleted file mode 100644 index 8bcee5a1fc..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsReferencedBy.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingPublicationIsReferencedBy - extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { - - public EnrichMissingPublicationIsReferencedBy() { - super(true); - } - - @Override - protected List> findUpdates( - final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return Arrays.asList(); - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Publication highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_PUBLICATION_IS_REFERENCED_BY, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> { - }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common - rel -> rel.getOriginalId()); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsRelatedTo.java deleted file mode 100644 index 0c16f9f564..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsRelatedTo.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingPublicationIsRelatedTo - extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { - - public EnrichMissingPublicationIsRelatedTo() { - super(true); - } - - @Override - protected List> findUpdates( - final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return Arrays.asList(); - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Publication highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_PUBLICATION_IS_RELATED_TO, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> { - }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common - rel -> rel.getOriginalId()); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedBy.java deleted file mode 100644 index 0b3c332708..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedBy.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingPublicationIsSupplementedBy - extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { - - public EnrichMissingPublicationIsSupplementedBy() { - super(true); - } - - @Override - protected List> findUpdates( - final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return Arrays.asList(); - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Publication highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_BY, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> { - }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common - rel -> rel.getOriginalId()); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedTo.java deleted file mode 100644 index 0e72a84239..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedTo.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingPublicationIsSupplementedTo - extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { - - public EnrichMissingPublicationIsSupplementedTo() { - super(true); - } - - @Override - protected List> findUpdates( - final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return Arrays.asList(); - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Publication highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_TO, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> { - }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common - rel -> rel.getOriginalId()); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationReferences.java deleted file mode 100644 index 6d1124974e..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationReferences.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingPublicationReferences - extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { - - public EnrichMissingPublicationReferences() { - super(true); - } - - @Override - protected List> findUpdates( - final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return Arrays.asList(); - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Publication highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_PUBLICATION_REFERENCES, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> { - }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common - rel -> rel.getOriginalId()); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java new file mode 100644 index 0000000000..321fd43184 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java @@ -0,0 +1,63 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Result; + +public abstract class AbstractEnrichMissingDataset + extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { + + private final Topic topic; + + public AbstractEnrichMissingDataset(final Topic topic) { + super(true); + this.topic = topic; + } + + @Override + protected final List> findUpdates( + final Pair> source, + final Pair> target) { + + final Set existingDatasets = target + .getRight() + .stream() + .map(Dataset::getId) + .collect(Collectors.toSet()); + + return source + .getRight() + .stream() + .filter(d -> !existingDatasets.contains(d.getId())) + .map(ConversionUtils::oafDatasetToBrokerDataset) + .map(i -> generateUpdateInfo(i, source, target)) + .collect(Collectors.toList()); + + } + + @Override + protected final UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Dataset highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + getTopic(), + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> p.getDatasets().add(rel), + rel -> rel.getInstances().get(0).getUrl()); + } + + public Topic getTopic() { + return topic; + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java new file mode 100644 index 0000000000..74ce761f48 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingDatasetIsReferencedBy extends AbstractEnrichMissingDataset { + + public EnrichMissingDatasetIsReferencedBy() { + super(Topic.ENRICH_MISSING_DATASET_IS_REFERENCED_BY); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java new file mode 100644 index 0000000000..05a8910591 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingDatasetIsRelatedTo extends AbstractEnrichMissingDataset { + + public EnrichMissingDatasetIsRelatedTo() { + super(Topic.ENRICH_MISSING_DATASET_IS_RELATED_TO); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java new file mode 100644 index 0000000000..23bd68fa1b --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingDatasetIsSupplementedBy extends AbstractEnrichMissingDataset { + + public EnrichMissingDatasetIsSupplementedBy() { + super(Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_BY); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java new file mode 100644 index 0000000000..03160b6f00 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingDatasetIsSupplementedTo extends AbstractEnrichMissingDataset { + + public EnrichMissingDatasetIsSupplementedTo() { + super(Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_TO); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java new file mode 100644 index 0000000000..bf1df053d6 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingDatasetReferences extends AbstractEnrichMissingDataset { + + public EnrichMissingDatasetReferences() { + super(Topic.ENRICH_MISSING_DATASET_REFERENCES); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java similarity index 90% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java index 0197c99b1b..461266d567 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.relatedProjects; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.List; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java similarity index 90% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreProject.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java index 4bf45d9437..d9bfb62d59 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.relatedProjects; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.List; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java new file mode 100644 index 0000000000..75e77b3c6f --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java @@ -0,0 +1,63 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; + +public abstract class AbstractEnrichMissingPublication + extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { + + private final Topic topic; + + public AbstractEnrichMissingPublication(final Topic topic) { + super(true); + this.topic = topic; + } + + @Override + protected final List> findUpdates( + final Pair> source, + final Pair> target) { + + final Set existingPublications = target + .getRight() + .stream() + .map(Publication::getId) + .collect(Collectors.toSet()); + + return source + .getRight() + .stream() + .filter(d -> !existingPublications.contains(d.getId())) + .map(ConversionUtils::oafPublicationToBrokerPublication) + .map(i -> generateUpdateInfo(i, source, target)) + .collect(Collectors.toList()); + + } + + @Override + protected final UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Publication highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + getTopic(), + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> p.getPublications().add(rel), + rel -> rel.getInstances().get(0).getUrl()); + } + + public Topic getTopic() { + return topic; + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java new file mode 100644 index 0000000000..73fa8a45f6 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingPublicationIsReferencedBy extends AbstractEnrichMissingPublication { + + public EnrichMissingPublicationIsReferencedBy() { + super(Topic.ENRICH_MISSING_PUBLICATION_IS_REFERENCED_BY); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java new file mode 100644 index 0000000000..361ea3b342 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingPublicationIsRelatedTo extends AbstractEnrichMissingPublication { + + public EnrichMissingPublicationIsRelatedTo() { + super(Topic.ENRICH_MISSING_PUBLICATION_IS_RELATED_TO); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java new file mode 100644 index 0000000000..7e8863b1ed --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingPublicationIsSupplementedBy extends AbstractEnrichMissingPublication { + + public EnrichMissingPublicationIsSupplementedBy() { + super(Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_BY); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java new file mode 100644 index 0000000000..dc4e513777 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingPublicationIsSupplementedTo extends AbstractEnrichMissingPublication { + + public EnrichMissingPublicationIsSupplementedTo() { + super(Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_TO); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java new file mode 100644 index 0000000000..5198098bcf --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingPublicationReferences extends AbstractEnrichMissingPublication { + + public EnrichMissingPublicationReferences() { + super(Topic.ENRICH_MISSING_PUBLICATION_REFERENCES); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java similarity index 90% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java index 6dab6355fd..a418b633ed 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java @@ -1,11 +1,12 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java similarity index 90% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java index c7146ad79a..b5c2f7e723 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.List; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java similarity index 93% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java index 81263c6c3f..c7e9dcbc11 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Instance; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java similarity index 91% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java index 5f10bb4d9e..522d46d402 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Pid; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java similarity index 90% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java index 19ef2bab7e..197ace97c8 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java @@ -1,11 +1,12 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSoftware.java similarity index 91% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSoftware.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSoftware.java index 954ee48be7..4fcba43a40 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSoftware.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.List; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java similarity index 93% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java index a7c72f6ea3..290bad48b3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.List; import java.util.Set; @@ -8,6 +8,7 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Qualifier; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java similarity index 93% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java index 2cd2775c9e..c376da44d2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.List; import java.util.Set; @@ -7,6 +7,7 @@ import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Instance; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java similarity index 92% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java index 048d19747d..2ee327c831 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.List; import java.util.Set; @@ -7,6 +7,7 @@ import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Pid; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSoftware.java similarity index 91% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSoftware.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSoftware.java index 9760504f64..a1affff623 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSoftware.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.List; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java similarity index 93% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java index 67c2f01161..b38445e885 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.List; import java.util.Set; @@ -8,6 +8,7 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index 2e2ce202ad..2f87d0ee76 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -7,6 +7,8 @@ import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.broker.objects.Instance; import eu.dnetlib.broker.objects.Pid; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class ConversionUtils { @@ -33,4 +35,15 @@ public class ConversionUtils { return Pair.of(sp.getQualifier().getClassid(), sp.getValue()); } + public static final eu.dnetlib.broker.objects.Dataset oafDatasetToBrokerDataset(final Dataset d) { + final eu.dnetlib.broker.objects.Dataset res = new eu.dnetlib.broker.objects.Dataset(); + // TODO + return res; + } + + public static final eu.dnetlib.broker.objects.Publication oafPublicationToBrokerPublication(final Publication d) { + final eu.dnetlib.broker.objects.Publication res = new eu.dnetlib.broker.objects.Publication(); + // TODO + return res; + } } diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index fcc356ac08..44cf9e67cc 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java index 43df19f8a4..ee5fd51656 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java @@ -20,12 +20,7 @@ public class AuthorMerger { public static List merge(List> authors) { - authors.sort(new Comparator>() { - @Override - public int compare(List o1, List o2) { - return -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2)); - } - }); + authors.sort((o1, o2) -> -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2))); List author = new ArrayList<>(); @@ -86,12 +81,21 @@ public class AuthorMerger { .stream() .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) .max(Comparator.comparing(Tuple2::_1)); - if (simAuthor.isPresent() && simAuthor.get()._1() > THRESHOLD) { - Author r = simAuthor.get()._2(); - if (r.getPid() == null) { - r.setPid(new ArrayList<>()); + + if (simAuthor.isPresent()) { + double th = THRESHOLD; + // increase the threshold if the surname is too short + if (simAuthor.get()._2().getSurname() != null + && simAuthor.get()._2().getSurname().length() <= 3) + th = 0.99; + + if (simAuthor.get()._1() > th) { + Author r = simAuthor.get()._2(); + if (r.getPid() == null) { + r.setPid(new ArrayList<>()); + } + r.getPid().add(a._1()); } - r.getPid().add(a._1()); } }); } @@ -99,7 +103,8 @@ public class AuthorMerger { public static String pidToComparableString(StructuredProperty pid) { return (pid.getQualifier() != null ? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : "" - : "") + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); + : "") + + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); } public static int countAuthorsPids(List authors) { @@ -120,9 +125,10 @@ public class AuthorMerger { final Person pa = parse(a); final Person pb = parse(b); + // if both are accurate (e.g. they have name and surname) if (pa.isAccurate() & pb.isAccurate()) { - return new JaroWinkler() - .score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())); + return new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())) * 0.5 + + new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString())) * 0.5; } else { return new JaroWinkler() .score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index 0a3bf62ea8..b8ccb038d7 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -21,6 +21,7 @@ import scala.Tuple2; public class EntityMergerTest implements Serializable { List> publications; + List> publications2; String testEntityBasePath; DataInfo dataInfo; @@ -36,6 +37,7 @@ public class EntityMergerTest implements Serializable { .getAbsolutePath(); publications = readSample(testEntityBasePath + "/publication_merge.json", Publication.class); + publications2 = readSample(testEntityBasePath + "/publication_merge2.json", Publication.class); pub_top = getTopPub(publications); @@ -88,6 +90,25 @@ public class EntityMergerTest implements Serializable { // verify authors assertEquals(pub_merged.getAuthor().size(), 9); assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4); + + // verify title + int count = 0; + for (StructuredProperty title : pub_merged.getTitle()) { + if (title.getQualifier().getClassid().equals("main title")) + count++; + } + assertEquals(count, 1); + } + + @Test + public void publicationMergerTest2() throws InstantiationException, IllegalAccessException { + + Publication pub_merged = DedupRecordFactory + .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); + + assertEquals(pub_merged.getAuthor().size(), 27); + // insert assertions here + } public DataInfo setDI() { diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json index 015f9294a3..28548c5322 100644 --- 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Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. 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Neoplasms"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Herpesviridae"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Prostate Hyperplasia"}],"description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Purpose: Previously, we reported the presence of virus-encoded microRNAs (miRNAs) in the urine of prostate cancer (CaP) patients. In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. Further studies will be required to elucidate the role of these miRNAs with respect to CaP and herpes viral infections."}],"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2016-06-01"},"embargoenddate":null,"resourcetype":null,"context":[],"instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"dataInfo":null,"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed 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import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.util.ArrayList; import java.util.Optional; import org.apache.commons.io.IOUtils; @@ -100,6 +101,7 @@ public class SparkBulkTagJob { ResultTagger resultTagger = new ResultTagger(); readPath(spark, inputPath, resultClazz) + .map(patchResult(), Encoders.bean(resultClazz)) .map( (MapFunction) value -> resultTagger .enrichContextCriteria( @@ -119,4 +121,17 @@ public class SparkBulkTagJob { .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); } + // TODO remove this hack as soon as the values fixed by this method will be provided as NON null + private static MapFunction patchResult() { + return (MapFunction) r -> { + if (r.getDataInfo().getDeletedbyinference() == null) { + r.getDataInfo().setDeletedbyinference(false); + } + if (r.getContext() == null) { + r.setContext(new ArrayList<>()); + } + return r; + }; + } + } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java index 29ddde15f8..844fe29621 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java @@ -131,7 +131,7 @@ public class CommunityConfiguration implements Serializable { p -> { if (p.getSnd() == null) return p.getFst(); - if (((SelectionConstraints) p.getSnd()).verifyCriteria(param)) + if (p.getSnd().verifyCriteria(param)) return p.getFst(); else return null; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbResolver.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbResolver.java index 3d0db20632..f54a1cebab 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbResolver.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbResolver.java @@ -34,7 +34,7 @@ public class VerbResolver implements Serializable { .collect( Collectors .toMap( - value -> (String) ((ClassInfo) value) + value -> (String) value .getAnnotationInfo() .get(0) .getParameterValues() diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java index 98b573102a..f28c5aa06d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java @@ -77,9 +77,15 @@ public class PrepareDatasourceCountryAssociation { List allowedtypes, String inputPath, String outputPath) { - String whitelisted = ""; - for (String i : whitelist) { - whitelisted += " OR id = '" + i + "'"; + String whitelisted = " d.id = '" + whitelist.get(0) + "'"; + for (int i = 1; i < whitelist.size(); i++) { + whitelisted += " OR d.id = '" + whitelist.get(i) + "'"; + } + + String allowed = "d.datasourcetype.classid = '" + allowedtypes.get(0) + "'"; + + for (int i = 1; i < allowedtypes.size(); i++) { + allowed += " OR d.datasourcetype.classid = '" + allowedtypes.get(i) + "'"; } Dataset datasource = readPath(spark, inputPath + "/datasource", Datasource.class); @@ -90,26 +96,39 @@ public class PrepareDatasourceCountryAssociation { relation.createOrReplaceTempView("relation"); organization.createOrReplaceTempView("organization"); - String query = "SELECT source dataSourceId, named_struct('classid', country.classid, 'classname', country.classname) country " - + "FROM ( SELECT id " - + " FROM datasource " - + " WHERE (datainfo.deletedbyinference = false " - + whitelisted - + ") " - + getConstraintList("datasourcetype.classid = '", allowedtypes) - + ") d " - + "JOIN ( SELECT source, target " - + " FROM relation " - + " WHERE relclass = '" - + ModelConstants.IS_PROVIDED_BY - + "' " - + " AND datainfo.deletedbyinference = false ) rel " - + "ON d.id = rel.source " - + "JOIN (SELECT id, country " - + " FROM organization " - + " WHERE datainfo.deletedbyinference = false " - + " AND length(country.classid) > 0) o " - + "ON o.id = rel.target"; +// String query = "SELECT source dataSourceId, named_struct('classid', country.classid, 'classname', country.classname) country " +// + "FROM ( SELECT id " +// + " FROM datasource " +// + " WHERE (datainfo.deletedbyinference = false " +// + whitelisted +// + ") " +// + getConstraintList("datasourcetype.classid = '", allowedtypes) +// + ") d " +// + "JOIN ( SELECT source, target " +// + " FROM relation " +// + " WHERE relclass = '" +// + ModelConstants.IS_PROVIDED_BY +// + "' " +// + " AND datainfo.deletedbyinference = false ) rel " +// + "ON d.id = rel.source " +// + "JOIN (SELECT id, country " +// + " FROM organization " +// + " WHERE datainfo.deletedbyinference = false " +// + " AND length(country.classid) > 0) o " +// + "ON o.id = rel.target"; + + String query = "SELECT source dataSourceId, " + + "named_struct('classid', country.classid, 'classname', country.classname) country " + + "FROM datasource d " + + "JOIN relation rel " + + "ON d.id = rel.source " + + "JOIN organization o " + + "ON o.id = rel.target " + + "WHERE rel.datainfo.deletedbyinference = false " + + "and rel.relclass = '" + ModelConstants.IS_PROVIDED_BY + "'" + + "and o.datainfo.deletedbyinference = false " + + "and length(o.country.classid) > 0 " + + "and (" + allowed + " or " + whitelisted + ")"; spark .sql(query) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java index 34b3764131..8d0d6c48b9 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java @@ -4,7 +4,12 @@ package eu.dnetlib.dhp.countrypropagation; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import java.util.ArrayList; +import java.util.Set; +import java.util.stream.Collectors; + import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.sql.*; import org.apache.spark.sql.Dataset; @@ -13,6 +18,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.*; +import scala.Tuple2; public class PrepareResultCountrySet { private static final Logger log = LoggerFactory.getLogger(PrepareResultCountrySet.class); @@ -60,6 +66,7 @@ public class PrepareResultCountrySet { conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, outputPath); getPotentialResultToUpdate( spark, inputPath, @@ -89,10 +96,33 @@ public class PrepareResultCountrySet { spark .sql(RESULT_COUNTRYSET_QUERY) .as(Encoders.bean(ResultCountrySet.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .json(outputPath); + .toJavaRDD() + .mapToPair(value -> new Tuple2<>(value.getResultId(), value)) + .reduceByKey((a, b) -> { + ArrayList countryList = a.getCountrySet(); + Set countryCodes = countryList + .stream() + .map(country -> country.getClassid()) + .collect(Collectors.toSet()); + b + .getCountrySet() + .stream() + .forEach(c -> { + if (!countryCodes.contains(c.getClassid())) { + countryList.add(c); + countryCodes.add(c.getClassid()); + } + + }); + a.setCountrySet(countryList); + return a; + }) + .map(couple -> OBJECT_MAPPER.writeValueAsString(couple._2())) + .saveAsTextFile(outputPath, GzipCodec.class); +// .write() +// .option("compression", "gzip") +// .mode(SaveMode.Append) +// .json(outputPath); } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index bea847ca76..3fc1270645 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -22,6 +22,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; @@ -121,30 +122,39 @@ public class SparkOrcidToResultFromSemRelJob { } private static void enrichAuthor(Author a, List au) { + PacePerson pp = new PacePerson(a.getFullname(), false); for (AutoritativeAuthor aa : au) { - if (enrichAuthor(aa, a)) { + if (enrichAuthor(aa, a, pp.getNormalisedFirstName(), pp.getNormalisedSurname())) { return; } } } - private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author) { + private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author, + String author_name, + String author_surname) { boolean toaddpid = false; if (StringUtils.isNotEmpty(autoritative_author.getSurname())) { if (StringUtils.isNotEmpty(author.getSurname())) { + author_surname = author.getSurname(); + } + if (StringUtils.isNotEmpty(author_surname)) { if (autoritative_author .getSurname() .trim() - .equalsIgnoreCase(author.getSurname().trim())) { + .equalsIgnoreCase(author_surname.trim())) { // have the same surname. Check the name if (StringUtils.isNotEmpty(autoritative_author.getName())) { if (StringUtils.isNotEmpty(author.getName())) { + author_name = author.getName(); + } + if (StringUtils.isNotEmpty(author_name)) { if (autoritative_author .getName() .trim() - .equalsIgnoreCase(author.getName().trim())) { + .equalsIgnoreCase(author_name.trim())) { toaddpid = true; } // they could be differently written (i.e. only the initials of the name @@ -154,7 +164,7 @@ public class SparkOrcidToResultFromSemRelJob { .getName() .trim() .substring(0, 0) - .equalsIgnoreCase(author.getName().trim().substring(0, 0))) { + .equalsIgnoreCase(author_name.trim().substring(0, 0))) { toaddpid = true; } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java index 1f6264c186..0791fd68ce 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java @@ -105,11 +105,7 @@ public class SparkResultToProjectThroughSemRelJob { .stream() .forEach( (p -> { - if (potential_update - .getProjectSet() - .contains(p)) { - potential_update.getProjectSet().remove(p); - } + potential_update.getProjectSet().remove(p); })); } String resId = potential_update.getResultId(); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index 5574aad753..750d333e53 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -7,6 +7,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.*; import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; @@ -19,6 +20,7 @@ import com.google.gson.Gson; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; +import scala.Tuple2; public class PrepareResultCommunitySet { @@ -93,10 +95,24 @@ public class PrepareResultCommunitySet { result_organizationset .map(mapResultCommunityFn(organizationMap), Encoders.bean(ResultCommunityList.class)) .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .toJavaRDD() + .mapToPair(value -> new Tuple2<>(value.getResultId(), value)) + .reduceByKey((a, b) -> { + ArrayList cl = a.getCommunityList(); + b.getCommunityList().stream().forEach(s -> { + if (!cl.contains(s)) { + cl.add(s); + } + }); + a.setCommunityList(cl); + return a; + }) + .map(value -> OBJECT_MAPPER.writeValueAsString(value._2())) + .saveAsTextFile(outputPath, GzipCodec.class); +// .write() +// .mode(SaveMode.Overwrite) +// .option("compression", "gzip") +// .json(outputPath); } private static MapFunction mapResultCommunityFn( diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java index 0c5e1d8be6..ff34bd42a7 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java @@ -136,9 +136,7 @@ public class SparkResultToOrganizationFromIstRepoJob { .stream() .forEach( rId -> { - if (organization_list.contains(rId)) { - organization_list.remove(rId); - } + organization_list.remove(rId); }); } String resultId = potential_update.getResultId(); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/ResultToOrganizationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/ResultToOrganizationJobTest.java index 435b766052..cfcccc5f0d 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/ResultToOrganizationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/ResultToOrganizationJobTest.java @@ -99,6 +99,7 @@ public class ResultToOrganizationJobTest { .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); Assertions.assertEquals(0, tmp.count()); + FileUtils.deleteDirectory(workingDir.toFile()); } /** @@ -171,6 +172,7 @@ public class ResultToOrganizationJobTest { + "(target = '20|opendoar____::124266ebc4ece2934eb80edfda3f2091' " + "or target = '20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2')") .count()); + FileUtils.deleteDirectory(workingDir.toFile()); } @Test @@ -266,5 +268,6 @@ public class ResultToOrganizationJobTest { "relclass = 'isAuthorInstitutionOf' and " + "substring(source, 1,2) = '20' and substring(target, 1, 2) = '50'") .count()); + FileUtils.deleteDirectory(workingDir.toFile()); } } diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 62968c4107..aee3d27c1d 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT 4.0.0 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 c4639eb44a..5c89d5096f 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 @@ -10,23 +10,10 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.REPOSITORY_PROVENANCE_ACTIONS; -import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Date; -import java.util.HashMap; -import java.util.List; -import java.util.Map; +import java.util.*; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; @@ -34,6 +21,7 @@ import org.dom4j.DocumentFactory; import org.dom4j.DocumentHelper; import org.dom4j.Node; +import eu.dnetlib.dhp.schema.common.LicenseComparator; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.DataInfo; @@ -285,7 +273,9 @@ public abstract class AbstractMdRecordToOafMapper { r.setCoverage(prepareCoverages(doc, info)); r.setContext(prepareContexts(doc, info)); r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy)); + final List instances = prepareInstances(doc, info, collectedFrom, hostedBy); + r.setInstance(instances); + r.setBestaccessright(getBestAccessRights(instances)); } private List prepareContexts(final Document doc, final DataInfo info) { @@ -368,6 +358,34 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); + protected static Qualifier getBestAccessRights(List instanceList) { + if (instanceList != null) { + final Optional min = instanceList + .stream() + .map(i -> i.getAccessright()) + .min(new LicenseComparator()); + + final Qualifier rights = min.isPresent() ? min.get() : new Qualifier(); + + if (StringUtils.isBlank(rights.getClassid())) { + rights.setClassid(UNKNOWN); + } + if (StringUtils.isBlank(rights.getClassname()) + || UNKNOWN.equalsIgnoreCase(rights.getClassname())) { + rights.setClassname(NOT_AVAILABLE); + } + if (StringUtils.isBlank(rights.getSchemeid())) { + rights.setSchemeid(DNET_ACCESS_MODES); + } + if (StringUtils.isBlank(rights.getSchemename())) { + rights.setSchemename(DNET_ACCESS_MODES); + } + + return rights; + } + return null; + } + 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 af9fe7197e..53c0913c23 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 @@ -23,7 +23,7 @@ import org.dom4j.Node; import com.google.common.collect.Lists; -import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; +import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Field; 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 9c74c4a938..b9a1599174 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 @@ -28,7 +28,7 @@ import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Node; -import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; +import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Field; 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 631e7235ec..b9da9fb297 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 @@ -85,8 +85,19 @@ public class MappersTest { assertTrue(p.getSubject().size() > 0); assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); - assertTrue(p.getInstance().size() > 0); + assertNotNull(p.getInstance()); + assertTrue(p.getInstance().size() > 0); + p + .getInstance() + .stream() + .forEach(i -> { + assertNotNull(i.getAccessright()); + assertEquals("OPEN", i.getAccessright().getClassid()); + }); + + assertNotNull(p.getBestaccessright()); + assertEquals("OPEN", p.getBestaccessright().getClassid()); assertValidId(r1.getSource()); assertValidId(r1.getTarget()); assertValidId(r2.getSource()); @@ -164,6 +175,16 @@ public class MappersTest { assertTrue(d.getContext().size() > 0); assertTrue(d.getContext().get(0).getId().length() > 0); + assertNotNull(d.getInstance()); + assertTrue(d.getInstance().size() > 0); + d + .getInstance() + .stream() + .forEach(i -> { + assertNotNull(i.getAccessright()); + assertEquals("OPEN", i.getAccessright().getClassid()); + }); + assertValidId(r1.getSource()); assertValidId(r1.getTarget()); assertValidId(r2.getSource()); diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml index e0ee03660b..e0ce739cfb 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index 39699b3b67..62bf7186ce 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 6f042b45cf..f99298130b 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -769,7 +769,7 @@ public class XmlRecordFactory implements Serializable { XmlSerializationUtils.asXmlElement("websiteurl", o.getWebsiteurl().getValue())); } if (o.getLogourl() != null) { - metadata.add(XmlSerializationUtils.asXmlElement("websiteurl", o.getLogourl().getValue())); + metadata.add(XmlSerializationUtils.asXmlElement("logourl", o.getLogourl().getValue())); } if (o.getEclegalbody() != null) { @@ -801,13 +801,13 @@ public class XmlRecordFactory implements Serializable { .asXmlElement( "echighereducation", o.getEchighereducation().getValue())); } - if (o.getEcinternationalorganization() != null) { + if (o.getEcinternationalorganizationeurinterests() != null) { metadata .add( XmlSerializationUtils .asXmlElement( "ecinternationalorganizationeurinterests", - o.getEcinternationalorganization().getValue())); + o.getEcinternationalorganizationeurinterests().getValue())); } if (o.getEcinternationalorganization() != null) { metadata diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st index 1d3cffea09..0af39f2306 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st @@ -1,3 +1,3 @@ <$name$$if(hasId)$ objidentifier="$id$"$else$$endif$> - $metadata:{$it$}$ + $metadata:{ it | $it$ }$ \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/joined_entity.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/joined_entity.json new file mode 100644 index 0000000000..c512646988 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/joined_entity.json @@ -0,0 +1,1551 @@ +{ + "links": [ + { + "relatedEntity": { + "code": null, + "codeRepositoryUrl": null, + "pid": [ + { + "dataInfo": { + "deletedbyinference": false, + "provenanceaction": { + "classid": "sysimport:crosswalk", + "classname": "sysimport:crosswalk", + "schemename": "dnet:provenanceActions", + "schemeid": "dnet:provenanceActions" + }, + "inferred": false, + "inferenceprovenance": "", + "invisible": false, + "trust": "0.9" + }, + "qualifier": { + "classid": "pmc", + "classname": "pmc", + "schemename": "dnet:pid_types", + "schemeid": "dnet:pid_types" + }, + "value": "PMC17177" + }, + { + "dataInfo": { + "deletedbyinference": false, + "provenanceaction": { + "classid": "sysimport:crosswalk", + "classname": "sysimport:crosswalk", + "schemename": "dnet:provenanceActions", + "schemeid": "dnet:provenanceActions" + }, + "inferred": false, + "inferenceprovenance": "", + "invisible": false, + "trust": "0.9" + }, + "qualifier": { + "classid": "pmid", + "classname": "pmid", + "schemename": "dnet:pid_types", + "schemeid": "dnet:pid_types" + }, + "value": "11005843" + } + ], + "projectTitle": null, + "websiteurl": null, + "resulttype": { + "classid": "publication", + "classname": "publication", + "schemename": "dnet:result_typologies", + "schemeid": "dnet:result_typologies" + }, + "legalname": null, + "collectedfrom": [ + { + "dataInfo": null, + "value": "PubMed Central", + "key": "10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357" + } + ], + "id": "50|od_______267::4d85ada0191a351f529d1e8ace1a7117", + "title": { + "dataInfo": { + "deletedbyinference": false, 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+ "type": "publication", + "id": "50|dedup_wf_001::00f53f19cfaf4dde8d316e9e71f16a10" + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 06408937bc..d6ec4e6ab2 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-worfklow-profiles/pom.xml b/dhp-workflows/dhp-worfklow-profiles/pom.xml index 5f99cdc8d3..cb20db57eb 100644 --- a/dhp-workflows/dhp-worfklow-profiles/pom.xml +++ b/dhp-workflows/dhp-worfklow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 271c669397..cf9753da40 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.1-SNAPSHOT + 1.2.2-SNAPSHOT ../ diff --git 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