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dnet-hadoop
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Code Issues 14 Pull Requests 12 Projects 2 Releases 2 Wiki Activity

Merge remote-tracking branch 'origin/master' into doiboost

This commit is contained in:
Sandro La Bruzzo 2020-05-26 09:15:50 +02:00
parent 25f52e19a4 d6aada4957
commit 79c26382da
31 changed files with 193 additions and 52 deletions
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2
dhp-build/dhp-build-assembly-resources/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-build</artifactId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<artifactId>dhp-build-assembly-resources</artifactId>

2
dhp-build/dhp-build-properties-maven-plugin/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-build</artifactId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<artifactId>dhp-build-properties-maven-plugin</artifactId>

2
dhp-build/dhp-code-style/pom.xml
View File

@ -5,7 +5,7 @@
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-code-style</artifactId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
<packaging>jar</packaging>

2
dhp-build/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<artifactId>dhp-build</artifactId>
<packaging>pom</packaging>

2
dhp-common/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>

2
dhp-schemas/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>

69
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java Normal file
View File

@ -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<Qualifier> {
@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);
}
}

2
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java
View File

@ -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;

3
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java
View File

@ -2,6 +2,7 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
import java.util.Objects;
public class Field<T> implements Serializable {
@ -39,6 +40,6 @@ public class Field<T> implements Serializable {
if (getClass() != obj.getClass())
return false;
Field<T> other = (Field<T>) obj;
return getValue().equals(other.getValue());
return Objects.equals(getValue(), other.getValue());
}
}

1
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java
View File

@ -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());
}

28
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
View File

@ -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 +312,14 @@ public class Result extends OafEntity implements Serializable {
}
return a.size() > b.size() ? a : b;
}
private StructuredProperty getMainTitle(List<StructuredProperty> 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;
}
}

2
dhp-workflows/dhp-actionmanager/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-workflows</artifactId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<artifactId>dhp-actionmanager</artifactId>

2
dhp-workflows/dhp-aggregation/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-workflows</artifactId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<artifactId>dhp-aggregation</artifactId>

6
dhp-workflows/dhp-blacklist/pom.xml
View File

@ -1,11 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

4
dhp-workflows/dhp-broker-events/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
@ -57,7 +57,7 @@
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-openaire-broker-common</artifactId>
<version>[1.0.0,2.0.0)</version>
<version>[2.0.0,3.0.0)</version>
</dependency>
</dependencies>

3
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java
View File

@ -53,8 +53,7 @@ public abstract class AbstractEnrichMissingPublication
return new UpdateInfo<>(
getTopic(),
highlightValue, source.getLeft(), target.getLeft(),
(p, rel) -> {
}, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common
(p, rel) -> p.getPublications().add(rel),
rel -> rel.getInstances().get(0).getUrl());
}

2
dhp-workflows/dhp-dedup-openaire/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-dedup-openaire</artifactId>

10
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java
View File

@ -90,10 +90,18 @@ 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, IOException {
public void publicationMergerTest2() throws InstantiationException, IllegalAccessException {
Publication pub_merged = DedupRecordFactory
.entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class);

2
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json
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File diff suppressed because one or more lines are too long

2
dhp-workflows/dhp-dedup-scholexplorer/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

2
dhp-workflows/dhp-distcp/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

6
dhp-workflows/dhp-enrichment/pom.xml
View File

@ -1,11 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

2
dhp-workflows/dhp-graph-mapper/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

52
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -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<Instance> instances = prepareInstances(doc, info, collectedFrom, hostedBy);
r.setInstance(instances);
r.setBestaccessright(getBestAccessRights(instances));
}
private List<Context> prepareContexts(final Document doc, final DataInfo info) {
@ -368,6 +358,34 @@ public abstract class AbstractMdRecordToOafMapper {
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
protected static Qualifier getBestAccessRights(List<Instance> instanceList) {
if (instanceList != null) {
final Optional<Qualifier> 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) {

23
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -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());

2
dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

2
dhp-workflows/dhp-graph-provision/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

2
dhp-workflows/dhp-stats-update/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-stats-update</artifactId>

2
dhp-workflows/dhp-worfklow-profiles/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

2
dhp-workflows/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>

2
pom.xml
View File

@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.2.1-SNAPSHOT</version>
<version>1.2.2-SNAPSHOT</version>
<packaging>pom</packaging>
<licenses>