miriam.baglioni
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dnet-hadoop
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merge branch with fork master

This commit is contained in:
Miriam Baglioni 2020-06-15 11:23:26 +02:00
parent 68cf0fd03f 0d52816244
commit 9dd3ef22c5
107 changed files with 5320 additions and 803 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>1.2.2-SNAPSHOT</version>
<version>1.2.3-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>1.2.2-SNAPSHOT</version>
<version>1.2.3-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>1.2.2-SNAPSHOT</version>
<version>1.2.3-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>1.2.2-SNAPSHOT</version>
<version>1.2.3-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>1.2.2-SNAPSHOT</version>
<version>1.2.3-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>

11
dhp-common/src/main/java/eu/dnetlib/dhp/common/FunctionalInterfaceSupport.java
View File

@ -2,6 +2,7 @@
package eu.dnetlib.dhp.common;
import java.io.Serializable;
import java.util.function.Consumer;
import java.util.function.Supplier;
/** Provides serializable and throwing extensions to standard functional interfaces. */
@ -10,6 +11,16 @@ public class FunctionalInterfaceSupport {
private FunctionalInterfaceSupport() {
}
/**
* Serializable consumer of any kind of objects. To be used withing spark processing pipelines when supplying
* functions externally.
*
* @param <T>
*/
@FunctionalInterface
public interface SerializableConsumer<T> extends Consumer<T>, Serializable {
}
/**
* Serializable supplier of any kind of objects. To be used withing spark processing pipelines when supplying
* functions externally.

30
dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java
View File

@ -16,6 +16,12 @@ import com.google.common.collect.Iterables;
import com.google.common.collect.Lists;
import com.google.common.hash.Hashing;
/**
* PacePerson tries to derive information from the fullname string of an author. Such informations are Names, Surnames
* an Fullname split into terms. It provides also an additional field for the original data. The calculation of the
* names and the surnames is not always possible. When it is impossible to assert which are the names and the surnames,
* the lists are empty.
*/
public class PacePerson {
private static final String UTF8 = "UTF-8";
@ -26,10 +32,19 @@ public class PacePerson {
private static Set<String> particles = null;
/**
* Capitalizes a string
*
* @param s the string to capitalize
* @return the input string with capital letter
*/
public static final String capitalize(final String s) {
return WordUtils.capitalize(s.toLowerCase(), ' ', '-');
}
/**
* Adds a dot to a string with length equals to 1
*/
public static final String dotAbbreviations(final String s) {
return s.length() == 1 ? s + "." : s;
}
@ -46,6 +61,12 @@ public class PacePerson {
return h;
}
/**
* The constructor of the class. It fills the fields of the class basing on the input fullname.
*
* @param s the input string (fullname of the author)
* @param aggressive set the string normalization type
*/
public PacePerson(String s, final boolean aggressive) {
original = s;
s = Normalizer.normalize(s, Normalizer.Form.NFD);
@ -64,6 +85,7 @@ public class PacePerson {
// s = s.replaceAll("[\\W&&[^,-]]", "");
}
// if the string contains a comma, it can derive surname and name by splitting on it
if (s.contains(",")) {
final String[] arr = s.split(",");
if (arr.length == 1) {
@ -74,21 +96,23 @@ public class PacePerson {
fullname.addAll(surname);
fullname.addAll(name);
}
} else {
} else { // otherwise, it should rely on CAPS terms and short terms
fullname = splitTerms(s);
int lastInitialPosition = fullname.size();
boolean hasSurnameInUpperCase = false;
// computes lastInitialPosition and hasSurnameInUpperCase
for (int i = 0; i < fullname.size(); i++) {
final String term = fullname.get(i);
if (term.length() == 1) {
lastInitialPosition = i;
lastInitialPosition = i; // first word in the name longer than 1 (to avoid name with dots)
} else if (term.equals(term.toUpperCase())) {
hasSurnameInUpperCase = true;
hasSurnameInUpperCase = true; // if one of the words is CAPS
}
}
// manages particular cases of fullnames
if (lastInitialPosition < fullname.size() - 1) { // Case: Michele G. Artini
name = fullname.subList(0, lastInitialPosition + 1);
surname = fullname.subList(lastInitialPosition + 1, fullname.size());

27
dhp-common/src/test/java/eu/dnetlib/dhp/common/PacePersonTest.java Normal file
View File

@ -0,0 +1,27 @@
package eu.dnetlib.dhp.common;
import static org.junit.jupiter.api.Assertions.*;
import org.junit.jupiter.api.Test;
public class PacePersonTest {
@Test
public void pacePersonTest1() {
PacePerson p = new PacePerson("Artini, Michele", false);
assertEquals("Artini", p.getSurnameString());
assertEquals("Michele", p.getNameString());
assertEquals("Artini, Michele", p.getNormalisedFullname());
}
@Test
public void pacePersonTest2() {
PacePerson p = new PacePerson("Michele G. Artini", false);
assertEquals("Artini, Michele G.", p.getNormalisedFullname());
assertEquals("Michele G", p.getNameString());
assertEquals("Artini", p.getSurnameString());
}
}

2
dhp-schemas/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.2.2-SNAPSHOT</version>
<version>1.2.3-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>

11
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
View File

@ -14,6 +14,7 @@ public class ModelConstants {
public static final String DNET_DATA_CITE_RESOURCE = "dnet:dataCite_resource";
public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
public static final String DNET_COUNTRY_TYPE = "dnet:countries";
public static final String DNET_REVIEW_LEVELS = "dnet:review_levels";
public static final String SYSIMPORT_CROSSWALK_REPOSITORY = "sysimport:crosswalk:repository";
public static final String SYSIMPORT_CROSSWALK_ENTITYREGISTRY = "sysimport:crosswalk:entityregistry";
@ -25,6 +26,10 @@ public class ModelConstants {
public static final String ORP_RESULTTYPE_CLASSID = "other";
public static final String RESULT_RESULT = "resultResult";
/**
* @deprecated Use {@link ModelConstants#RELATIONSHIP} instead.
*/
@Deprecated
public static final String PUBLICATION_DATASET = "publicationDataset";
public static final String IS_RELATED_TO = "isRelatedTo";
public static final String SUPPLEMENT = "supplement";
@ -34,6 +39,12 @@ public class ModelConstants {
public static final String IS_PART_OF = "IsPartOf";
public static final String HAS_PARTS = "HasParts";
public static final String RELATIONSHIP = "relationship";
public static final String CITATION = "citation";
public static final String CITES = "cites";
public static final String IS_CITED_BY = "IsCitedBy";
public static final String REVIEW = "review";
public static final String REVIEWS = "reviews";
public static final String IS_REVIEWED_BY = "IsReviewedBy";
public static final String RESULT_PROJECT = "resultProject";
public static final String OUTCOME = "outcome";

6
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java
View File

@ -31,7 +31,7 @@ public class Instance implements Serializable {
// typed results
private Field<String> processingchargecurrency;
private Field<String> refereed; // peer-review status
private Qualifier refereed; // peer-review status
public Field<String> getLicense() {
return license;
@ -113,11 +113,11 @@ public class Instance implements Serializable {
this.processingchargecurrency = processingchargecurrency;
}
public Field<String> getRefereed() {
public Qualifier getRefereed() {
return refereed;
}
public void setRefereed(Field<String> refereed) {
public void setRefereed(Qualifier refereed) {
this.refereed = refereed;
}

13
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
View File

@ -254,28 +254,25 @@ public class Result extends OafEntity implements Serializable {
final StructuredProperty p = baseMainTitle;
title = title.stream().filter(t -> t != p).collect(Collectors.toList());
}
//
//
// title.remove(baseMainTitle);
}
StructuredProperty newMainTitle = null;
if (r.getTitle() != null) {
newMainTitle = getMainTitle(r.getTitle());
if (newMainTitle != null) {
if (newMainTitle != null && title != null) {
final StructuredProperty p = newMainTitle;
title = title.stream().filter(t -> t != p).collect(Collectors.toList());
}
// r.getTitle().remove(newMainTitle);
}
if (newMainTitle != null && compareTrust(this, r) < 0)
if (newMainTitle != null && compareTrust(this, r) < 0) {
baseMainTitle = newMainTitle;
}
title = mergeLists(title, r.getTitle());
if (title != null && baseMainTitle != null)
if (title != null && baseMainTitle != null) {
title.add(baseMainTitle);
}
relevantdate = mergeLists(relevantdate, r.getRelevantdate());

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

@ -4,7 +4,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-workflows</artifactId>
<version>1.2.2-SNAPSHOT</version>
<version>1.2.3-SNAPSHOT</version>
</parent>
<artifactId>dhp-actionmanager</artifactId>

11
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java
View File

@ -96,12 +96,21 @@ public class ProtoConverter implements Serializable {
.stream()
.distinct()
.collect(Collectors.toCollection(ArrayList::new)) : null);
i.setRefereed(mapStringField(ri.getRefereed()));
i.setRefereed(mapRefereed(ri.getRefereed()));
i.setProcessingchargeamount(mapStringField(ri.getProcessingchargeamount()));
i.setProcessingchargecurrency(mapStringField(ri.getProcessingchargecurrency()));
return i;
}
private static Qualifier mapRefereed(FieldTypeProtos.StringField refereed) {
Qualifier q = new Qualifier();
q.setClassid(refereed.getValue());
q.setSchemename(refereed.getValue());
q.setSchemeid("dnet:review_levels");
q.setSchemename("dnet:review_levels");
return q;
}
private static List<ExternalReference> convertExternalRefs(OafProtos.Oaf oaf) {
ResultProtos.Result r = oaf.getEntity().getResult();
if (r.getExternalReferenceCount() > 0) {

2
dhp-workflows/dhp-aggregation/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-workflows</artifactId>
<version>1.2.2-SNAPSHOT</version>
<version>1.2.3-SNAPSHOT</version>
</parent>
<artifactId>dhp-aggregation</artifactId>

2
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java
View File

@ -8,6 +8,7 @@ import java.io.File;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
@ -19,6 +20,7 @@ import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
import eu.dnetlib.message.Message;
import eu.dnetlib.message.MessageManager;
@Disabled
public class DnetCollectorWorkerApplicationTests {
private final ArgumentApplicationParser argumentParser = mock(ArgumentApplicationParser.class);

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

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.2-SNAPSHOT</version>
<version>1.2.3-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

6
dhp-workflows/dhp-broker-events/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.2-SNAPSHOT</version>
<version>1.2.3-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
@ -40,6 +40,10 @@
<artifactId>dhp-schemas</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-pace-core</artifactId>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>

6
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java
View File

@ -37,7 +37,7 @@ public class EventFactory {
final Map<String, Object> map = createMapFromResult(updateInfo);
final String eventId = calculateEventId(
updateInfo.getTopicPath(), updateInfo.getTarget().getOriginalId().get(0),
updateInfo.getTopicPath(), updateInfo.getTarget().getResult().getOriginalId().get(0),
updateInfo.getHighlightValueAsString());
res.setEventId(eventId);
@ -54,8 +54,8 @@ public class EventFactory {
private static Map<String, Object> createMapFromResult(final UpdateInfo<?> updateInfo) {
final Map<String, Object> map = new HashMap<>();
final Result source = updateInfo.getSource();
final Result target = updateInfo.getTarget();
final Result source = updateInfo.getSource().getResult();
final Result target = updateInfo.getTarget().getResult();
final List<KeyValue> collectedFrom = target.getCollectedfrom();
if (collectedFrom.size() == 1) {

320
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java
View File

@ -3,15 +3,9 @@ package eu.dnetlib.dhp.broker.oa;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
@ -26,94 +20,38 @@ 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.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.relatedSoftware.EnrichMissingSoftware;
import eu.dnetlib.dhp.broker.oa.matchers.relatedSoftware.EnrichMoreSoftware;
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.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.EnrichMoreSubject;
import eu.dnetlib.dhp.broker.oa.util.BrokerConstants;
import eu.dnetlib.dhp.broker.oa.util.EventFinder;
import eu.dnetlib.dhp.broker.oa.util.EventGroup;
import eu.dnetlib.dhp.broker.oa.util.ResultAggregator;
import eu.dnetlib.dhp.broker.oa.util.ResultGroup;
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultAggregator;
import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedEntityFactory;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelationsAggregator;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.config.DedupConfig;
import scala.Tuple2;
public class GenerateEventsApplication {
private static final Logger log = LoggerFactory.getLogger(GenerateEventsApplication.class);
// Simple Matchers
private static final UpdateMatcher<Result, ?> enrichMissingAbstract = new EnrichMissingAbstract();
private static final UpdateMatcher<Result, ?> enrichMissingAuthorOrcid = new EnrichMissingAuthorOrcid();
private static final UpdateMatcher<Result, ?> enrichMissingOpenAccess = new EnrichMissingOpenAccess();
private static final UpdateMatcher<Result, ?> enrichMissingPid = new EnrichMissingPid();
private static final UpdateMatcher<Result, ?> enrichMissingPublicationDate = new EnrichMissingPublicationDate();
private static final UpdateMatcher<Result, ?> enrichMissingSubject = new EnrichMissingSubject();
private static final UpdateMatcher<Result, ?> enrichMoreOpenAccess = new EnrichMoreOpenAccess();
private static final UpdateMatcher<Result, ?> enrichMorePid = new EnrichMorePid();
private static final UpdateMatcher<Result, ?> enrichMoreSubject = new EnrichMoreSubject();
// Advanced matchers
private static final UpdateMatcher<Pair<Result, List<Project>>, ?> enrichMissingProject = new EnrichMissingProject();
private static final UpdateMatcher<Pair<Result, List<Project>>, ?> enrichMoreProject = new EnrichMoreProject();
private static final UpdateMatcher<Pair<Result, List<Software>>, ?> enrichMissingSoftware = new EnrichMissingSoftware();
private static final UpdateMatcher<Pair<Result, List<Software>>, ?> enrichMoreSoftware = new EnrichMoreSoftware();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMisissingPublicationIsRelatedTo = new EnrichMissingPublicationIsRelatedTo();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsReferencedBy =
new EnrichMissingPublicationIsReferencedBy();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationReferences = new EnrichMissingPublicationReferences();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsSupplementedTo =
new EnrichMissingPublicationIsSupplementedTo();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsSupplementedBy =
new EnrichMissingPublicationIsSupplementedBy();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMisissingDatasetIsRelatedTo =
new EnrichMissingDatasetIsRelatedTo();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsReferencedBy =
new EnrichMissingDatasetIsReferencedBy();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetReferences =
new EnrichMissingDatasetReferences();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsSupplementedTo =
new EnrichMissingDatasetIsSupplementedTo();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsSupplementedBy =
new EnrichMissingDatasetIsSupplementedBy();
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(GenerateEventsApplication.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json")));
.toString(
GenerateEventsApplication.class
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_broker_events.json")));
parser.parseArgument(args);
final Boolean isSparkSessionManaged = Optional
@ -128,8 +66,16 @@ public class GenerateEventsApplication {
final String eventsPath = parser.get("eventsPath");
log.info("eventsPath: {}", eventsPath);
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final String dedupConfigProfileId = parser.get("dedupConfProfile");
log.info("dedupConfigProfileId: {}", dedupConfigProfileId);
final SparkConf conf = new SparkConf();
final DedupConfig dedupConfig = loadDedupConfig(isLookupUrl, dedupConfigProfileId);
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
removeOutputDir(spark, eventsPath);
@ -137,14 +83,10 @@ public class GenerateEventsApplication {
final Dataset<Event> all = spark.emptyDataset(Encoders.kryo(Event.class));
for (final Class<? extends Result> r1 : BrokerConstants.RESULT_CLASSES) {
all.union(generateSimpleEvents(spark, graphPath, r1));
for (final Class<? extends Result> r2 : BrokerConstants.RESULT_CLASSES) {
all.union(generateRelationEvents(spark, graphPath, r1, r2));
}
all.union(generateEvents(spark, graphPath, r1, dedupConfig));
}
all.write().mode(SaveMode.Overwrite).json(eventsPath);
all.write().mode(SaveMode.Overwrite).option("compression", "gzip").json(eventsPath);
});
}
@ -153,155 +95,84 @@ public class GenerateEventsApplication {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
private static <R extends Result> Dataset<Event> generateSimpleEvents(final SparkSession spark,
final String graphPath,
final Class<R> resultClazz) {
final Dataset<Result> results = readPath(spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), Result.class)
.filter(r -> r.getDataInfo().getDeletedbyinference());
final Dataset<Relation> rels = readPath(spark, graphPath + "/relation", Relation.class)
.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
final TypedColumn<Tuple2<Result, Relation>, ResultGroup> aggr = new ResultAggregator().toColumn();
return results.joinWith(rels, results.col("id").equalTo(rels.col("source")), "inner")
.groupByKey((MapFunction<Tuple2<Result, Relation>, String>) t -> t._2.getTarget(), Encoders.STRING())
.agg(aggr)
.map((MapFunction<Tuple2<String, ResultGroup>, ResultGroup>) t -> t._2, Encoders.kryo(ResultGroup.class))
.filter(ResultGroup::isValid)
.map((MapFunction<ResultGroup, EventGroup>) g -> GenerateEventsApplication.generateSimpleEvents(g), Encoders.kryo(EventGroup.class))
.flatMap(group -> group.getData().iterator(), Encoders.kryo(Event.class));
}
private static EventGroup generateSimpleEvents(final ResultGroup results) {
final List<UpdateInfo<?>> list = new ArrayList<>();
for (final Result target : results.getData()) {
list.addAll(enrichMissingAbstract.searchUpdatesForRecord(target, results.getData()));
list.addAll(enrichMissingAuthorOrcid.searchUpdatesForRecord(target, results.getData()));
list.addAll(enrichMissingOpenAccess.searchUpdatesForRecord(target, results.getData()));
list.addAll(enrichMissingPid.searchUpdatesForRecord(target, results.getData()));
list.addAll(enrichMissingPublicationDate.searchUpdatesForRecord(target, results.getData()));
list.addAll(enrichMissingSubject.searchUpdatesForRecord(target, results.getData()));
list.addAll(enrichMoreOpenAccess.searchUpdatesForRecord(target, results.getData()));
list.addAll(enrichMorePid.searchUpdatesForRecord(target, results.getData()));
list.addAll(enrichMoreSubject.searchUpdatesForRecord(target, results.getData()));
}
final EventGroup events = new EventGroup();
list.stream().map(EventFactory::newBrokerEvent).forEach(events::addElement);
return events;
}
private static <SRC extends Result, TRG extends OafEntity> Dataset<Event> generateRelationEvents(final SparkSession spark,
private static <SRC extends Result> Dataset<Event> generateEvents(
final SparkSession spark,
final String graphPath,
final Class<SRC> sourceClass,
final Class<TRG> targetClass) {
final DedupConfig dedupConfig) {
final Dataset<SRC> sources = readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass)
.filter(r -> r.getDataInfo().getDeletedbyinference());
final Dataset<TRG> targets = readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), targetClass);
final Dataset<ResultWithRelations> results = expandResultsWithRelations(spark, graphPath, sourceClass);
final Dataset<Relation> mergedRels = readPath(spark, graphPath + "/relation", Relation.class)
.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
final TypedColumn<Tuple2<ResultWithRelations, Relation>, ResultGroup> aggr = new ResultAggregator()
.toColumn();
return results
.joinWith(mergedRels, results.col("result.id").equalTo(mergedRels.col("source")), "inner")
.groupByKey(
(MapFunction<Tuple2<ResultWithRelations, Relation>, String>) t -> t._2.getTarget(), Encoders.STRING())
.agg(aggr)
.map((MapFunction<Tuple2<String, ResultGroup>, ResultGroup>) t -> t._2, Encoders.kryo(ResultGroup.class))
.filter(ResultGroup::isValid)
.map(
(MapFunction<ResultGroup, EventGroup>) g -> EventFinder.generateEvents(g, dedupConfig),
Encoders.kryo(EventGroup.class))
.flatMap(group -> group.getData().iterator(), Encoders.kryo(Event.class));
}
private static <SRC extends Result> Dataset<ResultWithRelations> expandResultsWithRelations(
final SparkSession spark,
final String graphPath,
final Class<SRC> sourceClass) {
final Dataset<Project> projects = readPath(spark, graphPath + "/project", Project.class);
final Dataset<eu.dnetlib.dhp.schema.oaf.Dataset> datasets = readPath(
spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
final Dataset<Software> softwares = readPath(spark, graphPath + "/software", Software.class);
final Dataset<Publication> publications = readPath(spark, graphPath + "/publication", Publication.class);
final Dataset<Relation> rels = readPath(spark, graphPath + "/relation", Relation.class)
.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
if (targetClass == Project.class) {
// TODO join using: generateProjectsEvents
} else if (targetClass == Software.class) {
// TODO join using: generateSoftwareEvents
} else if (targetClass == Publication.class) {
// TODO join using: generatePublicationRelatedEvents
} else if (targetClass == eu.dnetlib.dhp.schema.oaf.Dataset.class) {
// TODO join using: generateDatasetRelatedEvents
final Dataset<ResultWithRelations> r0 = readPath(
spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), Result.class)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.map(r -> new ResultWithRelations(r), Encoders.kryo(ResultWithRelations.class));
final Dataset<ResultWithRelations> r1 = join(r0, rels, relatedEntities(projects, rels, RelatedProject.class));
final Dataset<ResultWithRelations> r2 = join(r1, rels, relatedEntities(softwares, rels, RelatedProject.class));
final Dataset<ResultWithRelations> r3 = join(r2, rels, relatedEntities(datasets, rels, RelatedProject.class));
final Dataset<ResultWithRelations> r4 = join(
r3, rels, relatedEntities(publications, rels, RelatedProject.class));
;
return r4;
}
return null;
private static <T, RT> Dataset<RT> relatedEntities(final Dataset<T> targets,
final Dataset<Relation> rels,
final Class<RT> clazz) {
return rels
.joinWith(targets, targets.col("id").equalTo(rels.col("target")), "inner")
.map(
t -> RelatedEntityFactory.newRelatedEntity(t._1.getSource(), t._1.getRelType(), t._2, clazz),
Encoders.kryo(clazz));
}
private List<Event> generateProjectsEvents(final Collection<Pair<Result, List<Project>>> childrenWithProjects) {
final List<UpdateInfo<?>> list = new ArrayList<>();
private static <T> Dataset<ResultWithRelations> join(final Dataset<ResultWithRelations> sources,
final Dataset<Relation> rels,
final Dataset<T> typedRels) {
for (final Pair<Result, List<Project>> target : childrenWithProjects) {
list.addAll(enrichMissingProject.searchUpdatesForRecord(target, childrenWithProjects));
list.addAll(enrichMoreProject.searchUpdatesForRecord(target, childrenWithProjects));
}
return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
}
private List<Event> generateSoftwareEvents(final Collection<Pair<Result, List<Software>>> childrenWithSoftwares) {
final List<UpdateInfo<?>> list = new ArrayList<>();
for (final Pair<Result, List<Software>> target : childrenWithSoftwares) {
list.addAll(enrichMissingSoftware.searchUpdatesForRecord(target, childrenWithSoftwares));
list.addAll(enrichMoreSoftware.searchUpdatesForRecord(target, childrenWithSoftwares));
}
return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
}
private List<Event> generatePublicationRelatedEvents(final String relType,
final Collection<Pair<Result, Map<String, List<Publication>>>> childrenWithRels) {
final List<UpdateInfo<?>> list = new ArrayList<>();
final List<Pair<Result, List<Publication>>> cleanedChildrens = childrenWithRels
.stream()
.filter(p -> p.getRight().containsKey(relType))
.map(p -> Pair.of(p.getLeft(), p.getRight().get(relType)))
.filter(p -> p.getRight().size() > 0)
.collect(Collectors.toList());
for (final Pair<Result, List<Publication>> target : cleanedChildrens) {
if (relType.equals("isRelatedTo")) {
list.addAll(enrichMisissingPublicationIsRelatedTo.searchUpdatesForRecord(target, cleanedChildrens));
} else if (relType.equals("references")) {
list.addAll(enrichMissingPublicationReferences.searchUpdatesForRecord(target, cleanedChildrens));
} else if (relType.equals("isReferencedBy")) {
list.addAll(enrichMissingPublicationIsReferencedBy.searchUpdatesForRecord(target, cleanedChildrens));
} else if (relType.equals("isSupplementedTo")) {
list.addAll(enrichMissingPublicationIsSupplementedTo.searchUpdatesForRecord(target, cleanedChildrens));
} else if (relType.equals("isSupplementedBy")) {
list.addAll(enrichMissingPublicationIsSupplementedBy.searchUpdatesForRecord(target, cleanedChildrens));
}
}
return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
}
private List<Event> generateDatasetRelatedEvents(final String relType,
final Collection<Pair<Result, Map<String, List<eu.dnetlib.dhp.schema.oaf.Dataset>>>> childrenWithRels) {
final List<UpdateInfo<?>> list = new ArrayList<>();
final List<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>> cleanedChildrens = childrenWithRels
.stream()
.filter(p -> p.getRight().containsKey(relType))
.map(p -> Pair.of(p.getLeft(), p.getRight().get(relType)))
.filter(p -> p.getRight().size() > 0)
.collect(Collectors.toList());
for (final Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>> target : cleanedChildrens) {
if (relType.equals("isRelatedTo")) {
list.addAll(enrichMisissingDatasetIsRelatedTo.searchUpdatesForRecord(target, cleanedChildrens));
} else if (relType.equals("references")) {
list.addAll(enrichMissingDatasetReferences.searchUpdatesForRecord(target, cleanedChildrens));
} else if (relType.equals("isReferencedBy")) {
list.addAll(enrichMissingDatasetIsReferencedBy.searchUpdatesForRecord(target, cleanedChildrens));
} else if (relType.equals("isSupplementedTo")) {
list.addAll(enrichMissingDatasetIsSupplementedTo.searchUpdatesForRecord(target, cleanedChildrens));
} else if (relType.equals("isSupplementedBy")) {
list.addAll(enrichMissingDatasetIsSupplementedBy.searchUpdatesForRecord(target, cleanedChildrens));
}
}
return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
final TypedColumn<Tuple2<ResultWithRelations, T>, ResultWithRelations> aggr = new ResultWithRelationsAggregator<T>()
.toColumn();
;
return sources
.joinWith(typedRels, sources.col("result.id").equalTo(rels.col("source")), "left_outer")
.groupByKey(
(MapFunction<Tuple2<ResultWithRelations, T>, String>) t -> t._1.getResult().getId(), Encoders.STRING())
.agg(aggr)
.map(t -> t._2, Encoders.kryo(ResultWithRelations.class));
}
public static <R> Dataset<R> readPath(
@ -313,4 +184,23 @@ public class GenerateEventsApplication {
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
private static DedupConfig loadDedupConfig(final String isLookupUrl, final String profId) throws Exception {
final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl);
final String conf = isLookUpService
.getResourceProfileByQuery(
String
.format(
"for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()",
profId));
final DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class);
dedupConfig.getPace().initModel();
dedupConfig.getPace().initTranslationMap();
// dedupConfig.getWf().setConfigurationId("???");
return dedupConfig;
}
}

52
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java
View File

@ -6,28 +6,48 @@ import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.function.BiConsumer;
import java.util.function.Function;
import org.apache.commons.codec.digest.DigestUtils;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.broker.objects.Publication;
import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.pace.config.DedupConfig;
public abstract class UpdateMatcher<K, T> {
public abstract class UpdateMatcher<T> {
private final boolean multipleUpdate;
private final Function<T, Topic> topicFunction;
private final BiConsumer<Publication, T> compileHighlightFunction;
private final Function<T, String> highlightToStringFunction;
public UpdateMatcher(final boolean multipleUpdate) {
public UpdateMatcher(final boolean multipleUpdate, final Function<T, Topic> topicFunction,
final BiConsumer<Publication, T> compileHighlightFunction,
final Function<T, String> highlightToStringFunction) {
this.multipleUpdate = multipleUpdate;
this.topicFunction = topicFunction;
this.compileHighlightFunction = compileHighlightFunction;
this.highlightToStringFunction = highlightToStringFunction;
}
public Collection<UpdateInfo<T>> searchUpdatesForRecord(final K res, final Collection<K> others) {
public Collection<UpdateInfo<T>> searchUpdatesForRecord(final ResultWithRelations res,
final Collection<ResultWithRelations> others,
final DedupConfig dedupConfig) {
final Map<String, UpdateInfo<T>> infoMap = new HashMap<>();
for (final K source : others) {
for (final ResultWithRelations source : others) {
if (source != res) {
for (final UpdateInfo<T> info : findUpdates(source, res)) {
for (final T hl : findDifferences(source, res)) {
final Topic topic = getTopicFunction().apply(hl);
final UpdateInfo<T> info = new UpdateInfo<>(topic, hl, source, res, getCompileHighlightFunction(),
getHighlightToStringFunction(),
dedupConfig);
final String s = DigestUtils.md5Hex(info.getHighlightValueAsString());
if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) {
} else {
@ -51,11 +71,7 @@ public abstract class UpdateMatcher<K, T> {
}
}
protected abstract List<UpdateInfo<T>> findUpdates(K source, K target);
protected abstract UpdateInfo<T> generateUpdateInfo(final T highlightValue,
final K source,
final K target);
protected abstract List<T> findDifferences(ResultWithRelations source, ResultWithRelations target);
protected static boolean isMissing(final List<Field<String>> list) {
return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0).getValue());
@ -65,4 +81,20 @@ public abstract class UpdateMatcher<K, T> {
return field == null || StringUtils.isBlank(field.getValue());
}
public boolean isMultipleUpdate() {
return multipleUpdate;
}
public Function<T, Topic> getTopicFunction() {
return topicFunction;
}
public BiConsumer<Publication, T> getCompileHighlightFunction() {
return compileHighlightFunction;
}
public Function<T, String> getHighlightToStringFunction() {
return highlightToStringFunction;
}
}

72
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java
View File

@ -5,59 +5,47 @@ 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.broker.oa.util.aggregators.withRels.RelatedDataset;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Result;
public abstract class AbstractEnrichMissingDataset
extends UpdateMatcher<Pair<Result, List<Dataset>>, eu.dnetlib.broker.objects.Dataset> {
private final Topic topic;
extends UpdateMatcher<eu.dnetlib.broker.objects.Dataset> {
public AbstractEnrichMissingDataset(final Topic topic) {
super(true);
this.topic = topic;
}
@Override
protected final List<UpdateInfo<eu.dnetlib.broker.objects.Dataset>> findUpdates(
final Pair<Result, List<Dataset>> source,
final Pair<Result, List<Dataset>> target) {
final Set<String> 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<eu.dnetlib.broker.objects.Dataset> generateUpdateInfo(
final eu.dnetlib.broker.objects.Dataset highlightValue,
final Pair<Result, List<Dataset>> source,
final Pair<Result, List<Dataset>> target) {
return new UpdateInfo<>(
getTopic(),
highlightValue, source.getLeft(), target.getLeft(),
super(true,
rel -> topic,
(p, rel) -> p.getDatasets().add(rel),
rel -> rel.getInstances().get(0).getUrl());
}
public Topic getTopic() {
return topic;
protected abstract boolean filterByType(String relType);
@Override
protected final List<eu.dnetlib.broker.objects.Dataset> findDifferences(
final ResultWithRelations source,
final ResultWithRelations target) {
final Set<String> existingDatasets = target
.getDatasets()
.stream()
.filter(rel -> filterByType(rel.getRelType()))
.map(RelatedDataset::getRelDataset)
.map(Dataset::getId)
.collect(Collectors.toSet());
return source
.getDatasets()
.stream()
.filter(rel -> filterByType(rel.getRelType()))
.map(RelatedDataset::getRelDataset)
.filter(d -> !existingDatasets.contains(d.getId()))
.map(ConversionUtils::oafDatasetToBrokerDataset)
.collect(Collectors.toList());
}
}

5
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java
View File

@ -9,4 +9,9 @@ public class EnrichMissingDatasetIsReferencedBy extends AbstractEnrichMissingDat
super(Topic.ENRICH_MISSING_DATASET_IS_REFERENCED_BY);
}
@Override
protected boolean filterByType(final String relType) {
return relType.equals("isReferencedBy");
}
}

5
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java
View File

@ -9,4 +9,9 @@ public class EnrichMissingDatasetIsRelatedTo extends AbstractEnrichMissingDatase
super(Topic.ENRICH_MISSING_DATASET_IS_RELATED_TO);
}
@Override
protected boolean filterByType(final String relType) {
return relType.equals("isRelatedTo");
}
}

5
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java
View File

@ -9,4 +9,9 @@ public class EnrichMissingDatasetIsSupplementedBy extends AbstractEnrichMissingD
super(Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_BY);
}
@Override
protected boolean filterByType(final String relType) {
return relType.equals("isSupplementedBy");
}
}

5
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java
View File

@ -9,4 +9,9 @@ public class EnrichMissingDatasetIsSupplementedTo extends AbstractEnrichMissingD
super(Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_TO);
}
@Override
protected boolean filterByType(final String relType) {
return relType.equals("isSupplementedTo");
}
}

5
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java
View File

@ -9,4 +9,9 @@ public class EnrichMissingDatasetReferences extends AbstractEnrichMissingDataset
super(Topic.ENRICH_MISSING_DATASET_REFERENCES);
}
@Override
protected boolean filterByType(final String relType) {
return relType.equals("references");
}
}

52
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java
View File

@ -5,48 +5,34 @@ import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.lang3.tuple.Pair;
import eu.dnetlib.broker.objects.Project;
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.Project;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
public class EnrichMissingProject
extends UpdateMatcher<Pair<Result, List<Project>>, eu.dnetlib.broker.objects.Project> {
extends UpdateMatcher<eu.dnetlib.broker.objects.Project> {
public EnrichMissingProject() {
super(true);
}
@Override
protected List<UpdateInfo<eu.dnetlib.broker.objects.Project>> findUpdates(final Pair<Result, List<Project>> source,
final Pair<Result, List<Project>> target) {
if (source.getRight().isEmpty()) {
return Arrays.asList();
} else {
return target
.getRight()
.stream()
.map(ConversionUtils::oafProjectToBrokerProject)
.map(p -> generateUpdateInfo(p, source, target))
.collect(Collectors.toList());
}
}
@Override
public UpdateInfo<eu.dnetlib.broker.objects.Project> generateUpdateInfo(
final eu.dnetlib.broker.objects.Project highlightValue,
final Pair<Result, List<Project>> source,
final Pair<Result, List<Project>> target) {
return new UpdateInfo<>(
Topic.ENRICH_MISSING_PROJECT,
highlightValue, source.getLeft(), target.getLeft(),
super(true,
prj -> Topic.ENRICH_MISSING_PROJECT,
(p, prj) -> p.getProjects().add(prj),
prj -> prj.getFunder() + "::" + prj.getFundingProgram() + prj.getCode());
}
@Override
protected List<Project> findDifferences(final ResultWithRelations source, final ResultWithRelations target) {
if (source.getProjects().isEmpty()) {
return Arrays.asList();
} else {
return target
.getProjects()
.stream()
.map(RelatedProject::getRelProject)
.map(ConversionUtils::oafProjectToBrokerProject)
.collect(Collectors.toList());
}
}
}

60
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java
View File

@ -5,50 +5,40 @@ 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.broker.oa.util.aggregators.withRels.RelatedProject;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Result;
public class EnrichMoreProject extends UpdateMatcher<Pair<Result, List<Project>>, eu.dnetlib.broker.objects.Project> {
public class EnrichMoreProject extends UpdateMatcher<eu.dnetlib.broker.objects.Project> {
public EnrichMoreProject() {
super(true);
}
@Override
protected List<UpdateInfo<eu.dnetlib.broker.objects.Project>> findUpdates(final Pair<Result, List<Project>> source,
final Pair<Result, List<Project>> target) {
final Set<String> existingProjects = source
.getRight()
.stream()
.map(Project::getId)
.collect(Collectors.toSet());
return target
.getRight()
.stream()
.filter(p -> !existingProjects.contains(p.getId()))
.map(ConversionUtils::oafProjectToBrokerProject)
.map(p -> generateUpdateInfo(p, source, target))
.collect(Collectors.toList());
}
@Override
public UpdateInfo<eu.dnetlib.broker.objects.Project> generateUpdateInfo(
final eu.dnetlib.broker.objects.Project highlightValue,
final Pair<Result, List<Project>> source,
final Pair<Result, List<Project>> target) {
return new UpdateInfo<>(
Topic.ENRICH_MORE_PROJECT,
highlightValue, source.getLeft(), target.getLeft(),
super(true,
prj -> Topic.ENRICH_MORE_PROJECT,
(p, prj) -> p.getProjects().add(prj),
prj -> prj.getFunder() + "::" + prj.getFundingProgram() + prj.getCode());
}
@Override
protected List<eu.dnetlib.broker.objects.Project> findDifferences(final ResultWithRelations source,
final ResultWithRelations target) {
final Set<String> existingProjects = source
.getProjects()
.stream()
.map(RelatedProject::getRelProject)
.map(Project::getId)
.collect(Collectors.toSet());
return target
.getProjects()
.stream()
.map(RelatedProject::getRelProject)
.filter(p -> !existingProjects.contains(p.getId()))
.map(ConversionUtils::oafProjectToBrokerProject)
.collect(Collectors.toList());
}
}

50
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java
View File

@ -5,59 +5,47 @@ 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.broker.oa.util.aggregators.withRels.RelatedPublication;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Result;
public abstract class AbstractEnrichMissingPublication
extends UpdateMatcher<Pair<Result, List<Publication>>, eu.dnetlib.broker.objects.Publication> {
private final Topic topic;
extends UpdateMatcher<eu.dnetlib.broker.objects.Publication> {
public AbstractEnrichMissingPublication(final Topic topic) {
super(true);
this.topic = topic;
super(true,
rel -> topic,
(p, rel) -> p.getPublications().add(rel),
rel -> rel.getInstances().get(0).getUrl());
}
protected abstract boolean filterByType(String relType);
@Override
protected final List<UpdateInfo<eu.dnetlib.broker.objects.Publication>> findUpdates(
final Pair<Result, List<Publication>> source,
final Pair<Result, List<Publication>> target) {
protected final List<eu.dnetlib.broker.objects.Publication> findDifferences(
final ResultWithRelations source,
final ResultWithRelations target) {
final Set<String> existingPublications = target
.getRight()
.getPublications()
.stream()
.filter(rel -> filterByType(rel.getRelType()))
.map(RelatedPublication::getRelPublication)
.map(Publication::getId)
.collect(Collectors.toSet());
return source
.getRight()
.getPublications()
.stream()
.filter(rel -> filterByType(rel.getRelType()))
.map(RelatedPublication::getRelPublication)
.filter(d -> !existingPublications.contains(d.getId()))
.map(ConversionUtils::oafResultToBrokerPublication)
.map(i -> generateUpdateInfo(i, source, target))
.collect(Collectors.toList());
}
@Override
protected final UpdateInfo<eu.dnetlib.broker.objects.Publication> generateUpdateInfo(
final eu.dnetlib.broker.objects.Publication highlightValue,
final Pair<Result, List<Publication>> source,
final Pair<Result, List<Publication>> 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;
}
}

4
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java
View File

@ -9,4 +9,8 @@ public class EnrichMissingPublicationIsReferencedBy extends AbstractEnrichMissin
super(Topic.ENRICH_MISSING_PUBLICATION_IS_REFERENCED_BY);
}
@Override
protected boolean filterByType(final String relType) {
return relType.equals("isReferencedBy");
}
}

5
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java
View File

@ -9,4 +9,9 @@ public class EnrichMissingPublicationIsRelatedTo extends AbstractEnrichMissingPu
super(Topic.ENRICH_MISSING_PUBLICATION_IS_RELATED_TO);
}
@Override
protected boolean filterByType(final String relType) {
return relType.equals("isRelatedTo");
}
}

4
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java
View File

@ -9,4 +9,8 @@ public class EnrichMissingPublicationIsSupplementedBy extends AbstractEnrichMiss
super(Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_BY);
}
@Override
protected boolean filterByType(final String relType) {
return relType.equals("isSupplementedBy");
}
}

5
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java
View File

@ -9,4 +9,9 @@ public class EnrichMissingPublicationIsSupplementedTo extends AbstractEnrichMiss
super(Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_TO);
}
@Override
protected boolean filterByType(final String relType) {
return relType.equals("isSupplementedTo");
}
}

5
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java
View File

@ -9,4 +9,9 @@ public class EnrichMissingPublicationReferences extends AbstractEnrichMissingPub
super(Topic.ENRICH_MISSING_PUBLICATION_REFERENCES);
}
@Override
protected boolean filterByType(final String relType) {
return relType.equals("references");
}
}

56
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java
View File

@ -5,49 +5,37 @@ import java.util.Arrays;
import java.util.List;
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;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
public class EnrichMissingSoftware
extends UpdateMatcher<Pair<Result, List<Software>>, eu.dnetlib.broker.objects.Software> {
extends UpdateMatcher<eu.dnetlib.broker.objects.Software> {
public EnrichMissingSoftware() {
super(true);
}
@Override
protected List<UpdateInfo<eu.dnetlib.broker.objects.Software>> findUpdates(
final Pair<Result, List<Software>> source,
final Pair<Result, List<Software>> target) {
if (source.getRight().isEmpty()) {
return Arrays.asList();
} else {
return target
.getRight()
.stream()
.map(ConversionUtils::oafSoftwareToBrokerSoftware)
.map(p -> generateUpdateInfo(p, source, target))
.collect(Collectors.toList());
}
}
@Override
public UpdateInfo<eu.dnetlib.broker.objects.Software> generateUpdateInfo(
final eu.dnetlib.broker.objects.Software highlightValue,
final Pair<Result, List<Software>> source,
final Pair<Result, List<Software>> target) {
return new UpdateInfo<>(
Topic.ENRICH_MISSING_SOFTWARE,
highlightValue, source.getLeft(), target.getLeft(),
super(true,
s -> Topic.ENRICH_MISSING_SOFTWARE,
(p, s) -> p.getSoftwares().add(s),
s -> s.getName());
}
@Override
protected List<eu.dnetlib.broker.objects.Software> findDifferences(
final ResultWithRelations source,
final ResultWithRelations target) {
if (source.getSoftwares().isEmpty()) {
return Arrays.asList();
} else {
return target
.getSoftwares()
.stream()
.map(RelatedSoftware::getRelSoftware)
.map(ConversionUtils::oafSoftwareToBrokerSoftware)
.collect(Collectors.toList());
}
}
}

62
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java
View File

@ -5,52 +5,42 @@ 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.Result;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
import eu.dnetlib.dhp.schema.oaf.Software;
public class EnrichMoreSoftware
extends UpdateMatcher<Pair<Result, List<Software>>, eu.dnetlib.broker.objects.Software> {
extends UpdateMatcher<eu.dnetlib.broker.objects.Software> {
public EnrichMoreSoftware() {
super(true);
}
@Override
protected List<UpdateInfo<eu.dnetlib.broker.objects.Software>> findUpdates(
final Pair<Result, List<Software>> source,
final Pair<Result, List<Software>> target) {
final Set<String> existingSoftwares = source
.getRight()
.stream()
.map(Software::getId)
.collect(Collectors.toSet());
return target
.getRight()
.stream()
.filter(p -> !existingSoftwares.contains(p.getId()))
.map(ConversionUtils::oafSoftwareToBrokerSoftware)
.map(p -> generateUpdateInfo(p, source, target))
.collect(Collectors.toList());
}
@Override
public UpdateInfo<eu.dnetlib.broker.objects.Software> generateUpdateInfo(
final eu.dnetlib.broker.objects.Software highlightValue,
final Pair<Result, List<Software>> source,
final Pair<Result, List<Software>> target) {
return new UpdateInfo<>(
Topic.ENRICH_MORE_SOFTWARE,
highlightValue, source.getLeft(), target.getLeft(),
super(true,
s -> Topic.ENRICH_MORE_SOFTWARE,
(p, s) -> p.getSoftwares().add(s),
s -> s.getName());
}
@Override
protected List<eu.dnetlib.broker.objects.Software> findDifferences(
final ResultWithRelations source,
final ResultWithRelations target) {
final Set<String> existingSoftwares = source
.getSoftwares()
.stream()
.map(RelatedSoftware::getRelSoftware)
.map(Software::getId)
.collect(Collectors.toSet());
return target
.getSoftwares()
.stream()
.map(RelatedSoftware::getRelSoftware)
.filter(p -> !existingSoftwares.contains(p.getId()))
.map(ConversionUtils::oafSoftwareToBrokerSoftware)
.collect(Collectors.toList());
}
}

35
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java
View File

@ -7,32 +7,25 @@ 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;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
public class EnrichMissingAbstract extends UpdateMatcher<Result, String> {
public class EnrichMissingAbstract extends UpdateMatcher<String> {
public EnrichMissingAbstract() {
super(false);
}
@Override
protected List<UpdateInfo<String>> findUpdates(final Result source, final Result target) {
if (isMissing(target.getDescription()) && !isMissing(source.getDescription())) {
return Arrays.asList(generateUpdateInfo(source.getDescription().get(0).getValue(), source, target));
}
return new ArrayList<>();
}
@Override
public UpdateInfo<String> generateUpdateInfo(final String highlightValue,
final Result source,
final Result target) {
return new UpdateInfo<>(
Topic.ENRICH_MISSING_ABSTRACT,
highlightValue, source, target,
super(false,
s -> Topic.ENRICH_MISSING_ABSTRACT,
(p, s) -> p.getAbstracts().add(s),
s -> s);
}
@Override
protected List<String> findDifferences(final ResultWithRelations source,
final ResultWithRelations target) {
if (isMissing(target.getResult().getDescription()) && !isMissing(source.getResult().getDescription())) {
return Arrays
.asList(source.getResult().getDescription().get(0).getValue());
}
return new ArrayList<>();
}
}

55
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java
View File

@ -1,36 +1,53 @@
package eu.dnetlib.dhp.broker.oa.matchers.simple;
import java.util.Arrays;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang3.tuple.Pair;
import java.util.Set;
import java.util.stream.Collectors;
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.broker.oa.util.aggregators.withRels.ResultWithRelations;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class EnrichMissingAuthorOrcid extends UpdateMatcher<Result, Pair<String, String>> {
public class EnrichMissingAuthorOrcid extends UpdateMatcher<String> {
public EnrichMissingAuthorOrcid() {
super(true);
super(true,
aut -> Topic.ENRICH_MISSING_AUTHOR_ORCID,
(p, aut) -> p.getCreators().add(aut),
aut -> aut);
}
@Override
protected List<UpdateInfo<Pair<String, String>>> findUpdates(final Result source, final Result target) {
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
return Arrays.asList();
protected List<String> findDifferences(final ResultWithRelations source,
final ResultWithRelations target) {
final Set<String> existingOrcids = target
.getResult()
.getAuthor()
.stream()
.map(Author::getPid)
.flatMap(List::stream)
.filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid"))
.map(pid -> pid.getValue())
.collect(Collectors.toSet());
final List<String> list = new ArrayList<>();
for (final Author author : source.getResult().getAuthor()) {
final String name = author.getFullname();
for (final StructuredProperty pid : author.getPid()) {
if (pid.getQualifier().getClassid().equalsIgnoreCase("orcid")
&& !existingOrcids.contains(pid.getValue())) {
list.add(name + " [ORCID: " + pid.getValue() + "]");
}
}
}
@Override
public UpdateInfo<Pair<String, String>> generateUpdateInfo(final Pair<String, String> highlightValue,
final Result source,
final Result target) {
return new UpdateInfo<>(
Topic.ENRICH_MISSING_AUTHOR_ORCID,
highlightValue, source, target,
(p, pair) -> p.getCreators().add(pair.getLeft() + " - ORCID: " + pair.getRight()),
pair -> pair.getLeft() + "::" + pair.getRight());
return list;
}
}

27
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java
View File

@ -10,18 +10,22 @@ 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;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
public class EnrichMissingOpenAccess extends UpdateMatcher<Result, Instance> {
public class EnrichMissingOpenAccess extends UpdateMatcher<Instance> {
public EnrichMissingOpenAccess() {
super(true);
super(true,
i -> Topic.ENRICH_MISSING_OA_VERSION,
(p, i) -> p.getInstances().add(i),
Instance::getUrl);
}
@Override
protected List<UpdateInfo<Instance>> findUpdates(final Result source, final Result target) {
protected List<Instance> findDifferences(final ResultWithRelations source,
final ResultWithRelations target) {
final long count = target
.getResult()
.getInstance()
.stream()
.map(i -> i.getAccessright().getClassid())
@ -33,24 +37,13 @@ public class EnrichMissingOpenAccess extends UpdateMatcher<Result, Instance> {
}
return source
.getResult()
.getInstance()
.stream()
.filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS))
.map(ConversionUtils::oafInstanceToBrokerInstances)
.flatMap(List::stream)
.map(i -> generateUpdateInfo(i, source, target))
.collect(Collectors.toList());
}
@Override
public UpdateInfo<Instance> generateUpdateInfo(final Instance highlightValue,
final Result source,
final Result target) {
return new UpdateInfo<>(
Topic.ENRICH_MISSING_OA_VERSION,
highlightValue, source, target,
(p, i) -> p.getInstances().add(i),
Instance::getUrl);
}
}

26
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java
View File

@ -9,38 +9,32 @@ 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;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
public class EnrichMissingPid extends UpdateMatcher<Result, Pid> {
public class EnrichMissingPid extends UpdateMatcher<Pid> {
public EnrichMissingPid() {
super(true);
super(true,
pid -> Topic.ENRICH_MISSING_PID,
(p, pid) -> p.getPids().add(pid),
pid -> pid.getType() + "::" + pid.getValue());
}
@Override
protected List<UpdateInfo<Pid>> findUpdates(final Result source, final Result target) {
final long count = target.getPid().size();
protected List<Pid> findDifferences(final ResultWithRelations source,
final ResultWithRelations target) {
final long count = target.getResult().getPid().size();
if (count > 0) {
return Arrays.asList();
}
return source
.getResult()
.getPid()
.stream()
.map(ConversionUtils::oafPidToBrokerPid)
.map(i -> generateUpdateInfo(i, source, target))
.collect(Collectors.toList());
}
@Override
public UpdateInfo<Pid> generateUpdateInfo(final Pid highlightValue, final Result source, final Result target) {
return new UpdateInfo<>(
Topic.ENRICH_MISSING_PID,
highlightValue, source, target,
(p, pid) -> p.getPids().add(pid),
pid -> pid.getType() + "::" + pid.getValue());
}
}

35
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java
View File

@ -7,32 +7,25 @@ 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;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
public class EnrichMissingPublicationDate extends UpdateMatcher<Result, String> {
public class EnrichMissingPublicationDate extends UpdateMatcher<String> {
public EnrichMissingPublicationDate() {
super(false);
}
@Override
protected List<UpdateInfo<String>> findUpdates(final Result source, final Result target) {
if (isMissing(target.getDateofacceptance()) && !isMissing(source.getDateofacceptance())) {
return Arrays.asList(generateUpdateInfo(source.getDateofacceptance().getValue(), source, target));
}
return new ArrayList<>();
}
@Override
public UpdateInfo<String> generateUpdateInfo(final String highlightValue,
final Result source,
final Result target) {
return new UpdateInfo<>(
Topic.ENRICH_MISSING_PUBLICATION_DATE,
highlightValue, source, target,
super(false,
date -> Topic.ENRICH_MISSING_PUBLICATION_DATE,
(p, date) -> p.setPublicationdate(date),
s -> s);
}
@Override
protected List<String> findDifferences(final ResultWithRelations source,
final ResultWithRelations target) {
if (isMissing(target.getResult().getDateofacceptance())
&& !isMissing(source.getResult().getDateofacceptance())) {
return Arrays.asList(source.getResult().getDateofacceptance().getValue());
}
return new ArrayList<>();
}
}

28
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java
View File

@ -10,20 +10,24 @@ 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.broker.oa.util.aggregators.withRels.ResultWithRelations;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class EnrichMissingSubject extends UpdateMatcher<Result, Pair<String, String>> {
public class EnrichMissingSubject extends UpdateMatcher<Pair<String, String>> {
public EnrichMissingSubject() {
super(true);
super(true,
pair -> Topic.fromPath("ENRICH/MISSING/SUBJECT/" + pair.getLeft()),
(p, pair) -> p.getSubjects().add(pair.getRight()),
pair -> pair.getLeft() + "::" + pair.getRight());
}
@Override
protected List<UpdateInfo<Pair<String, String>>> findUpdates(final Result source, final Result target) {
protected List<Pair<String, String>> findDifferences(final ResultWithRelations source,
final ResultWithRelations target) {
final Set<String> existingTypes = target
.getResult()
.getSubject()
.stream()
.map(StructuredProperty::getQualifier)
@ -31,24 +35,12 @@ public class EnrichMissingSubject extends UpdateMatcher<Result, Pair<String, Str
.collect(Collectors.toSet());
return source
.getResult()
.getPid()
.stream()
.filter(pid -> !existingTypes.contains(pid.getQualifier().getClassid()))
.map(ConversionUtils::oafSubjectToPair)
.map(i -> generateUpdateInfo(i, source, target))
.collect(Collectors.toList());
}
@Override
public UpdateInfo<Pair<String, String>> generateUpdateInfo(final Pair<String, String> highlightValue,
final Result source,
final Result target) {
return new UpdateInfo<>(
Topic.fromPath("ENRICH/MISSING/SUBJECT/" + highlightValue.getLeft()),
highlightValue, source, target,
(p, pair) -> p.getSubjects().add(pair.getRight()),
pair -> pair.getLeft() + "::" + pair.getRight());
}
}

27
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java
View File

@ -10,18 +10,22 @@ 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;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
public class EnrichMoreOpenAccess extends UpdateMatcher<Result, Instance> {
public class EnrichMoreOpenAccess extends UpdateMatcher<Instance> {
public EnrichMoreOpenAccess() {
super(true);
super(true,
i -> Topic.ENRICH_MORE_OA_VERSION,
(p, i) -> p.getInstances().add(i),
Instance::getUrl);
}
@Override
protected List<UpdateInfo<Instance>> findUpdates(final Result source, final Result target) {
protected List<Instance> findDifferences(final ResultWithRelations source,
final ResultWithRelations target) {
final Set<String> urls = target
.getResult()
.getInstance()
.stream()
.filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS))
@ -30,25 +34,14 @@ public class EnrichMoreOpenAccess extends UpdateMatcher<Result, Instance> {
.collect(Collectors.toSet());
return source
.getResult()
.getInstance()
.stream()
.filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS))
.map(ConversionUtils::oafInstanceToBrokerInstances)
.flatMap(List::stream)
.filter(i -> !urls.contains(i.getUrl()))
.map(i -> generateUpdateInfo(i, source, target))
.collect(Collectors.toList());
}
@Override
public UpdateInfo<Instance> generateUpdateInfo(final Instance highlightValue,
final Result source,
final Result target) {
return new UpdateInfo<>(
Topic.ENRICH_MORE_OA_VERSION,
highlightValue, source, target,
(p, i) -> p.getInstances().add(i),
Instance::getUrl);
}
}

25
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java
View File

@ -9,39 +9,34 @@ 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;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
public class EnrichMorePid extends UpdateMatcher<Result, Pid> {
public class EnrichMorePid extends UpdateMatcher<Pid> {
public EnrichMorePid() {
super(true);
super(true,
pid -> Topic.ENRICH_MORE_PID,
(p, pid) -> p.getPids().add(pid),
pid -> pid.getType() + "::" + pid.getValue());
}
@Override
protected List<UpdateInfo<Pid>> findUpdates(final Result source, final Result target) {
protected List<Pid> findDifferences(final ResultWithRelations source,
final ResultWithRelations target) {
final Set<String> existingPids = target
.getResult()
.getPid()
.stream()
.map(pid -> pid.getQualifier().getClassid() + "::" + pid.getValue())
.collect(Collectors.toSet());
return source
.getResult()
.getPid()
.stream()
.filter(pid -> !existingPids.contains(pid.getQualifier().getClassid() + "::" + pid.getValue()))
.map(ConversionUtils::oafPidToBrokerPid)
.map(i -> generateUpdateInfo(i, source, target))
.collect(Collectors.toList());
}
@Override
public UpdateInfo<Pid> generateUpdateInfo(final Pid highlightValue, final Result source, final Result target) {
return new UpdateInfo<>(
Topic.ENRICH_MORE_PID,
highlightValue, source, target,
(p, pid) -> p.getPids().add(pid),
pid -> pid.getType() + "::" + pid.getValue());
}
}

28
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java
View File

@ -10,42 +10,34 @@ 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;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
public class EnrichMoreSubject extends UpdateMatcher<Result, Pair<String, String>> {
public class EnrichMoreSubject extends UpdateMatcher<Pair<String, String>> {
public EnrichMoreSubject() {
super(true);
super(true,
pair -> Topic.fromPath("ENRICH/MORE/SUBJECT/" + pair.getLeft()),
(p, pair) -> p.getSubjects().add(pair.getRight()),
pair -> pair.getLeft() + "::" + pair.getRight());
}
@Override
protected List<UpdateInfo<Pair<String, String>>> findUpdates(final Result source, final Result target) {
protected List<Pair<String, String>> findDifferences(final ResultWithRelations source,
final ResultWithRelations target) {
final Set<String> existingSubjects = target
.getResult()
.getSubject()
.stream()
.map(pid -> pid.getQualifier().getClassid() + "::" + pid.getValue())
.collect(Collectors.toSet());
return source
.getResult()
.getPid()
.stream()
.filter(pid -> !existingSubjects.contains(pid.getQualifier().getClassid() + "::" + pid.getValue()))
.map(ConversionUtils::oafSubjectToPair)
.map(i -> generateUpdateInfo(i, source, target))
.collect(Collectors.toList());
}
@Override
public UpdateInfo<Pair<String, String>> generateUpdateInfo(final Pair<String, String> highlightValue,
final Result source,
final Result target) {
return new UpdateInfo<>(
Topic.fromPath("ENRICH/MORE/SUBJECT/" + highlightValue.getLeft()),
highlightValue, source, target,
(p, pair) -> p.getSubjects().add(pair.getRight()),
pair -> pair.getLeft() + "::" + pair.getRight());
}
}

3
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java
View File

@ -15,6 +15,9 @@ public class BrokerConstants {
public static final String OPEN_ACCESS = "OPEN";
public static final String IS_MERGED_IN_CLASS = "isMergedIn";
public static final float MIN_TRUST = 0.25f;
public static final float MAX_TRUST = 1.00f;
public static final List<Class<? extends Result>> RESULT_CLASSES = Arrays
.asList(Publication.class, Dataset.class, Software.class, OtherResearchProduct.class);

86
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java Normal file
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@ -0,0 +1,86 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.ArrayList;
import java.util.List;
import eu.dnetlib.dhp.broker.model.EventFactory;
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.relatedSoftware.EnrichMissingSoftware;
import eu.dnetlib.dhp.broker.oa.matchers.relatedSoftware.EnrichMoreSoftware;
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.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.EnrichMoreSubject;
import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
import eu.dnetlib.pace.config.DedupConfig;
public class EventFinder {
private static List<UpdateMatcher<?>> matchers = new ArrayList<>();
static {
matchers.add(new EnrichMissingAbstract());
matchers.add(new EnrichMissingAuthorOrcid());
matchers.add(new EnrichMissingOpenAccess());
matchers.add(new EnrichMissingPid());
matchers.add(new EnrichMissingPublicationDate());
matchers.add(new EnrichMissingSubject());
matchers.add(new EnrichMoreOpenAccess());
matchers.add(new EnrichMorePid());
matchers.add(new EnrichMoreSubject());
// Advanced matchers
matchers.add(new EnrichMissingProject());
matchers.add(new EnrichMoreProject());
matchers.add(new EnrichMissingSoftware());
matchers.add(new EnrichMoreSoftware());
matchers.add(new EnrichMissingPublicationIsRelatedTo());
matchers.add(new EnrichMissingPublicationIsReferencedBy());
matchers.add(new EnrichMissingPublicationReferences());
matchers.add(new EnrichMissingPublicationIsSupplementedTo());
matchers.add(new EnrichMissingPublicationIsSupplementedBy());
matchers.add(new EnrichMissingDatasetIsRelatedTo());
matchers.add(new EnrichMissingDatasetIsReferencedBy());
matchers.add(new EnrichMissingDatasetReferences());
matchers.add(new EnrichMissingDatasetIsSupplementedTo());
matchers.add(new EnrichMissingDatasetIsSupplementedBy());
matchers.add(new EnrichMissingAbstract());
}
public static EventGroup generateEvents(final ResultGroup results, final DedupConfig dedupConfig) {
final List<UpdateInfo<?>> list = new ArrayList<>();
for (final ResultWithRelations target : results.getData()) {
for (final UpdateMatcher<?> matcher : matchers) {
list.addAll(matcher.searchUpdatesForRecord(target, results.getData(), dedupConfig));
}
}
return asEventGroup(list);
}
private static EventGroup asEventGroup(final List<UpdateInfo<?>> list) {
final EventGroup events = new EventGroup();
list.stream().map(EventFactory::newBrokerEvent).forEach(events::addElement);
return events;
}
}

1
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventGroup.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.io.Serializable;

23
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/TrustUtils.java Normal file
View File

@ -0,0 +1,23 @@
package eu.dnetlib.dhp.broker.oa.util;
public class TrustUtils {
public static float rescale(final double score, final double threshold) {
if (score >= BrokerConstants.MAX_TRUST) {
return BrokerConstants.MAX_TRUST;
}
final double val = (score - threshold) * (BrokerConstants.MAX_TRUST - BrokerConstants.MIN_TRUST)
/ (BrokerConstants.MAX_TRUST - threshold);
if (val < BrokerConstants.MIN_TRUST) {
return BrokerConstants.MIN_TRUST;
}
if (val > BrokerConstants.MAX_TRUST) {
return BrokerConstants.MAX_TRUST;
}
return (float) val;
}
}

53
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java
View File

@ -5,13 +5,23 @@ import java.util.List;
import java.util.function.BiConsumer;
import java.util.function.Function;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.broker.objects.Provenance;
import eu.dnetlib.broker.objects.Publication;
import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.tree.support.TreeProcessor;
import eu.dnetlib.pace.util.MapDocumentUtil;
public final class UpdateInfo<T> {
@ -19,9 +29,9 @@ public final class UpdateInfo<T> {
private final T highlightValue;
private final Result source;
private final ResultWithRelations source;
private final Result target;
private final ResultWithRelations target;
private final BiConsumer<Publication, T> compileHighlight;
@ -29,33 +39,50 @@ public final class UpdateInfo<T> {
private final float trust;
public UpdateInfo(final Topic topic, final T highlightValue, final Result source, final Result target,
private static final Logger log = LoggerFactory.getLogger(UpdateInfo.class);
public UpdateInfo(final Topic topic, final T highlightValue, final ResultWithRelations source,
final ResultWithRelations target,
final BiConsumer<Publication, T> compileHighlight,
final Function<T, String> highlightToString) {
final Function<T, String> highlightToString,
final DedupConfig dedupConfig) {
this.topic = topic;
this.highlightValue = highlightValue;
this.source = source;
this.target = target;
this.compileHighlight = compileHighlight;
this.highlightToString = highlightToString;
this.trust = calculateTrust(source, target);
this.trust = calculateTrust(dedupConfig, source.getResult(), target.getResult());
}
public T getHighlightValue() {
return highlightValue;
}
public Result getSource() {
public ResultWithRelations getSource() {
return source;
}
public Result getTarget() {
public ResultWithRelations getTarget() {
return target;
}
private float calculateTrust(final Result source, final Result target) {
// TODO
return 0.9f;
private float calculateTrust(final DedupConfig dedupConfig, final Result r1, final Result r2) {
try {
final ObjectMapper objectMapper = new ObjectMapper();
final MapDocument doc1 = MapDocumentUtil
.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r1));
final MapDocument doc2 = MapDocumentUtil
.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r2));
final double score = new TreeProcessor(dedupConfig).computeScore(doc1, doc2);
final double threshold = dedupConfig.getWf().getThreshold();
return TrustUtils.rescale(score, threshold);
} catch (final Exception e) {
log.error("Error computing score between results", e);
return BrokerConstants.MIN_TRUST;
}
}
protected Topic getTopic() {
@ -76,20 +103,22 @@ public final class UpdateInfo<T> {
public OpenAireEventPayload asBrokerPayload() {
final Publication p = ConversionUtils.oafResultToBrokerPublication(getSource());
final Publication p = ConversionUtils.oafResultToBrokerPublication(getSource().getResult());
compileHighlight.accept(p, getHighlightValue());
final Publication hl = new Publication();
compileHighlight.accept(hl, getHighlightValue());
final String provId = getSource().getOriginalId().stream().findFirst().orElse(null);
final String provId = getSource().getResult().getOriginalId().stream().findFirst().orElse(null);
final String provRepo = getSource()
.getResult()
.getCollectedfrom()
.stream()
.map(KeyValue::getValue)
.findFirst()
.orElse(null);
final String provUrl = getSource()
.getResult()
.getInstance()
.stream()
.map(Instance::getUrl)

9
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ResultAggregator.java → dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultAggregator.java
View File

@ -1,14 +1,15 @@
package eu.dnetlib.dhp.broker.oa.util;
package eu.dnetlib.dhp.broker.oa.util.aggregators.simple;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.expressions.Aggregator;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import scala.Tuple2;
public class ResultAggregator extends Aggregator<Tuple2<Result, Relation>, ResultGroup, ResultGroup> {
public class ResultAggregator extends Aggregator<Tuple2<ResultWithRelations, Relation>, ResultGroup, ResultGroup> {
/**
*
@ -21,7 +22,7 @@ public class ResultAggregator extends Aggregator<Tuple2<Result, Relation>, Resul
}
@Override
public ResultGroup reduce(final ResultGroup group, final Tuple2<Result, Relation> t) {
public ResultGroup reduce(final ResultGroup group, final Tuple2<ResultWithRelations, Relation> t) {
return group.addElement(t._1);
}

11
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ResultGroup.java → dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultGroup.java
View File

@ -1,10 +1,11 @@
package eu.dnetlib.dhp.broker.oa.util;
package eu.dnetlib.dhp.broker.oa.util.aggregators.simple;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations;
public class ResultGroup implements Serializable {
@ -13,13 +14,13 @@ public class ResultGroup implements Serializable {
*/
private static final long serialVersionUID = -3360828477088669296L;
private final List<Result> data = new ArrayList<>();
private final List<ResultWithRelations> data = new ArrayList<>();
public List<Result> getData() {
public List<ResultWithRelations> getData() {
return data;
}
public ResultGroup addElement(final Result elem) {
public ResultGroup addElement(final ResultWithRelations elem) {
data.add(elem);
return this;
}

30
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java Normal file
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@ -0,0 +1,30 @@
package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels;
import eu.dnetlib.dhp.schema.oaf.Dataset;
public class RelatedDataset {
private final String source;
private final String relType;
private final Dataset relDataset;
public RelatedDataset(final String source, final String relType, final Dataset relDataset) {
this.source = source;
this.relType = relType;
this.relDataset = relDataset;
}
public String getSource() {
return source;
}
public String getRelType() {
return relType;
}
public Dataset getRelDataset() {
return relDataset;
}
}

28
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java Normal file
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@ -0,0 +1,28 @@
package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Software;
public class RelatedEntityFactory {
@SuppressWarnings("unchecked")
public static <RT, T> RT newRelatedEntity(final String sourceId, final String relType, final T target,
final Class<RT> clazz) {
if (clazz == RelatedProject.class) {
return (RT) new RelatedProject(sourceId, relType, (Project) target);
}
if (clazz == RelatedSoftware.class) {
return (RT) new RelatedSoftware(sourceId, relType, (Software) target);
}
if (clazz == RelatedDataset.class) {
return (RT) new RelatedDataset(sourceId, relType, (Dataset) target);
}
if (clazz == RelatedPublication.class) {
return (RT) new RelatedPublication(sourceId, relType, (Publication) target);
}
return null;
}
}

30
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java Normal file
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@ -0,0 +1,30 @@
package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels;
import eu.dnetlib.dhp.schema.oaf.Project;
public class RelatedProject {
private final String source;
private final String relType;
private final Project relProject;
public RelatedProject(final String source, final String relType, final Project relProject) {
this.source = source;
this.relType = relType;
this.relProject = relProject;
}
public String getSource() {
return source;
}
public String getRelType() {
return relType;
}
public Project getRelProject() {
return relProject;
}
}

30
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java Normal file
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@ -0,0 +1,30 @@
package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class RelatedPublication {
private final String source;
private final String relType;
private final Publication relPublication;
public RelatedPublication(final String source, final String relType, final Publication relPublication) {
this.source = source;
this.relType = relType;
this.relPublication = relPublication;
}
public String getSource() {
return source;
}
public String getRelType() {
return relType;
}
public Publication getRelPublication() {
return relPublication;
}
}

30
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java Normal file
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@ -0,0 +1,30 @@
package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels;
import eu.dnetlib.dhp.schema.oaf.Software;
public class RelatedSoftware {
private final String source;
private final String relType;
private final Software relSoftware;
public RelatedSoftware(final String source, final String relType, final Software relSoftware) {
this.source = source;
this.relType = relType;
this.relSoftware = relSoftware;
}
public String getSource() {
return source;
}
public String getRelType() {
return relType;
}
public Software getRelSoftware() {
return relSoftware;
}
}

55
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/ResultWithRelations.java Normal file
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@ -0,0 +1,55 @@
package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import eu.dnetlib.dhp.schema.oaf.Result;
public class ResultWithRelations implements Serializable {
/**
*
*/
private static final long serialVersionUID = -1368401915974311571L;
private Result result;
private final List<RelatedDataset> datasets = new ArrayList<>();
private final List<RelatedPublication> publications = new ArrayList<>();
private final List<RelatedSoftware> softwares = new ArrayList<>();
private final List<RelatedProject> projects = new ArrayList<>();
public ResultWithRelations() {
}
public ResultWithRelations(final Result result) {
this.result = result;
}
public Result getResult() {
return result;
}
public List<RelatedDataset> getDatasets() {
return datasets;
}
public List<RelatedPublication> getPublications() {
return publications;
}
public List<RelatedSoftware> getSoftwares() {
return softwares;
}
public List<RelatedProject> getProjects() {
return projects;
}
public void setResult(final Result result) {
this.result = result;
}
}

68
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/ResultWithRelationsAggregator.java Normal file
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@ -0,0 +1,68 @@
package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.expressions.Aggregator;
import scala.Tuple2;
public class ResultWithRelationsAggregator<T>
extends Aggregator<Tuple2<ResultWithRelations, T>, ResultWithRelations, ResultWithRelations> {
/**
*
*/
private static final long serialVersionUID = -3687878788861013488L;
@Override
public ResultWithRelations zero() {
return new ResultWithRelations();
}
@Override
public ResultWithRelations finish(final ResultWithRelations g) {
return g;
}
@Override
public ResultWithRelations reduce(final ResultWithRelations g, final Tuple2<ResultWithRelations, T> t) {
if (g.getResult() == null) {
return t._1;
} else if (t._2 instanceof RelatedSoftware) {
g.getSoftwares().add((RelatedSoftware) t._2);
} else if (t._2 instanceof RelatedDataset) {
g.getDatasets().add((RelatedDataset) t._2);
} else if (t._2 instanceof RelatedPublication) {
g.getPublications().add((RelatedPublication) t._2);
} else if (t._2 instanceof RelatedProject) {
g.getProjects().add((RelatedProject) t._2);
}
return g;
}
@Override
public ResultWithRelations merge(final ResultWithRelations g1, final ResultWithRelations g2) {
if (g1.getResult() != null) {
g1.getSoftwares().addAll(g2.getSoftwares());
g1.getDatasets().addAll(g2.getDatasets());
g1.getPublications().addAll(g2.getPublications());
g1.getProjects().addAll(g2.getProjects());
return g1;
} else {
return g2;
}
}
@Override
public Encoder<ResultWithRelations> bufferEncoder() {
return Encoders.kryo(ResultWithRelations.class);
}
@Override
public Encoder<ResultWithRelations> outputEncoder() {
return Encoders.kryo(ResultWithRelations.class);
}
}

18
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/config-default.xml Normal file
View File

@ -0,0 +1,18 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

99
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml Normal file
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@ -0,0 +1,99 @@
<workflow-app name="create broker events" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>graphInputPath</name>
<description>the path where the graph is stored</description>
</property>
<property>
<name>eventsOutputPath</name>
<description>the path where the the events will be stored</description>
</property>
<property>
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>dedupConfProfId</name>
<description>the id of a valid Dedup Configuration Profile</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="generate_events"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="generate_events">
<java>
<prepare>
<delete path="${eventsOutputPath}"/>
</prepare>
<main-class>eu.dnetlib.dhp.broker.oa.GenerateEventsApplication</main-class>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--eventsPath</arg><arg>${eventsOutputPath}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--dedupConfProfile</arg><arg>${dedupConfProfId}</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

26
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_broker_events.json Normal file
View File

@ -0,0 +1,26 @@
[
{
"paramName": "g",
"paramLongName": "graphPath",
"paramDescription": "the path where there the graph is stored",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "eventsPath",
"paramDescription": "the path where the generated events will be stored",
"paramRequired": true
},
{
"paramName": "lu",
"paramLongName": "isLookupUrl",
"paramDescription": "the address of the ISLookUpService",
"paramRequired": true
},
{
"paramName": "d",
"paramLongName": "dedupConfProfile",
"paramDescription": "the id of a valid Dedup Configuration Profile",
"paramRequired": true
}
]

73
dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java Normal file
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@ -0,0 +1,73 @@
package eu.dnetlib.dhp.broker.oa.util;
import static org.junit.jupiter.api.Assertions.assertTrue;
import org.junit.jupiter.api.Test;
public class TrustUtilsTest {
private static final double THRESHOLD = 0.95;
@Test
public void rescaleTest_1() {
verifyValue(-0.3, BrokerConstants.MIN_TRUST);
}
@Test
public void rescaleTest_2() {
verifyValue(0.0, BrokerConstants.MIN_TRUST);
}
@Test
public void rescaleTest_3() {
verifyValue(0.5, BrokerConstants.MIN_TRUST);
}
@Test
public void rescaleTest_4() {
verifyValue(0.95, BrokerConstants.MIN_TRUST);
}
@Test
public void rescaleTest_5() {
verifyValue(0.96, BrokerConstants.MIN_TRUST);
}
@Test
public void rescaleTest_6() {
verifyValue(0.97, 0.3f);
}
@Test
public void rescaleTest_7() {
verifyValue(0.98, 0.45f);
}
@Test
public void rescaleTest_8() {
verifyValue(0.99, 0.6f);
}
@Test
public void rescaleTest_9() {
verifyValue(1.00, BrokerConstants.MAX_TRUST);
}
@Test
public void rescaleTest_10() {
verifyValue(1.01, BrokerConstants.MAX_TRUST);
}
@Test
public void rescaleTest_11() {
verifyValue(2.00, BrokerConstants.MAX_TRUST);
}
private void verifyValue(final double originalScore, final float expectedTrust) {
final float trust = TrustUtils.rescale(originalScore, THRESHOLD);
System.out.println(trust);
assertTrue(Math.abs(trust - expectedTrust) < 0.01);
}
}

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>1.2.2-SNAPSHOT</version>
<version>1.2.3-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-dedup-openaire</artifactId>

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>1.2.2-SNAPSHOT</version>
<version>1.2.3-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>1.2.2-SNAPSHOT</version>
<version>1.2.3-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

5
dhp-workflows/dhp-doiboost/pom.xml
View File

@ -1,10 +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>1.2.2-SNAPSHOT</version>
<version>1.2.3-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

10
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
View File

@ -166,8 +166,10 @@ case object Crossref2Oaf {
val has_review = (json \ "relation" \"has-review" \ "id")
if(has_review != JNothing)
instance.setRefereed(asField("peerReviewed"))
if(has_review != JNothing) {
instance.setRefereed(
createQualifier("0001", "peerReviewed", "dnet:review_levels", "dnet:review_levels"))
}
instance.setAccessright(getRestrictedQualifier())
@ -243,7 +245,7 @@ case object Crossref2Oaf {
val queue = new mutable.Queue[Relation]
def snfRule(award:String): String = {
def snsfRule(award:String): String = {
var tmp1 = StringUtils.substringAfter(award,"_")
val tmp2 = StringUtils.substringBefore(tmp1,"/")
logger.debug(s"From $award to $tmp2")
@ -318,7 +320,7 @@ case object Crossref2Oaf {
case "10.13039/501100006588" |
"10.13039/501100004488" => generateSimpleRelationFromAward(funder, "irb_hr______", a=>a.replaceAll("Project No.", "").replaceAll("HRZZ-","") )
case "10.13039/501100006769"=> generateSimpleRelationFromAward(funder, "rsf_________", a=>a)
case "10.13039/501100001711"=> generateSimpleRelationFromAward(funder, "snsf________", snfRule)
case "10.13039/501100001711"=> generateSimpleRelationFromAward(funder, "snsf________", snsfRule)
case "10.13039/501100004410"=> generateSimpleRelationFromAward(funder, "tubitakf____", a =>a)
case "10.10.13039/100004440"=> generateSimpleRelationFromAward(funder, "wt__________", a =>a)
case "10.13039/100004440"=> queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "wt__________" )

12
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala
View File

@ -1,16 +1,10 @@
package eu.dnetlib.doiboost.orcid
import java.io.IOException
import eu.dnetlib.dhp.schema.oaf.{Author, Publication}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier}
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
import org.apache.commons.lang.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
@ -22,7 +16,7 @@ case class ORCIDItem(oid:String,name:String,surname:String,creditName:String,err
case class ORCIDElement(doi:String, authors:List[ORCIDItem]) {}
object ORCIDToOAF {
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass)
val mapper = new ObjectMapper
def isJsonValid(inputStr: String): Boolean = {
@ -57,7 +51,7 @@ object ORCIDToOAF {
pub.setId(generateIdentifier(pub, doi.toLowerCase))
try{
pub.setAuthor(input.authors.map(a=> {
generateAuhtor(a.name, a.surname, a.creditName, a.oid)
generateAuthor(a.name, a.surname, a.creditName, a.oid)
}).asJava)
pub.setCollectedfrom(List(DoiBoostMappingUtil.createORIDCollectedFrom()).asJava)
pub.setDataInfo(DoiBoostMappingUtil.generateDataInfo())
@ -69,7 +63,7 @@ object ORCIDToOAF {
}
}
def generateAuhtor(given: String, family: String, fullName:String, orcid: String): Author = {
def generateAuthor(given: String, family: String, fullName:String, orcid: String): Author = {
val a = new Author
a.setName(given)
a.setSurname(family)

2
dhp-workflows/dhp-doiboost/src/main/resources/eu.dnetlib.dhp.doiboost.mappings/crossref_mapping.csv
View File

@ -58,3 +58,5 @@ reference,Array of Reference,No,List of references made by the work,,Future impr
content-domain,Content Domain,No,Information on domains that support Crossmark for this work,N/A,
relation,Relations,No,Relations to other works,Result/Instance/refereed,"if(relation.has-review) instance.refereed = ""peerReviewed"". "
review,Review,No,Peer review metadata,N/A,
funder,Array of Funder,No,,Relation between Result and Project,"The mapping between Crossref funder elements and OpenAIRE projects is implemented in eu.dnetlib.doiboost.crossref.Crossref2Oaf.mappingFunderToRelations.
The matching is based on Funder DOIs, Funder names, and grant codes. Different mapping approaches are applied to cover the different cases in Crossref records."

1 Crossref Field Type Required Description (from Crossref) OAF field Comments
58
59
60
61
62

37
dhp-workflows/dhp-doiboost/src/main/resources/eu.dnetlib.dhp.doiboost.mappings/mag_mapping.csv Normal file
View File

@ -0,0 +1,37 @@
Micorsoft Academic Graph Field,OAF field,Comments
Papers/DOI,OafEntity/originalId,
,OafEntity/PID,
,Oaf/id in the form 50|doiboost____::md5(DOI),
Papers/PaperId,OafEntity/originalId,
Papers/PaperTitle,"Result/Title with Qualifier(""main title"", ""dnet:dataCite_title"")",
Papers/OriginalTitle,"Result/Title with Qualifier(""alternative title"", ""dnet:dataCite_title"")",
Papers/BookTitle,Publication/Source,
Papers/Year,N/A,
Papers/Date,Result/dateofacceptance,
Papers/Publisher,Result/Publisher,Possibly overridden by Journal/Publisher
Papers/JournalId,N/A,
Journal/Rank,N/A,
Journal/NormalizedName,N/A,
Journal/DisplayName,Publication/Journal/Name,
Journal/Issn,Publication/Journal/issnPrinted,
Journal/Publisher,Result/publisher,"If avalable, it overrides value in Papers/Publisher"
Journal/Webpage,N/A,
Journal/PaperCount,N/A,
Journal/CitationCount,N/A,
Journal/CreatedDate,N/A,
ConferenceInstances/DisplayName,Publication/Journal/Name,
ConferenceInstances/Location,Publication/Journal/Conferenceplace,
ConferenceInstances/StartDate,Publication/Journal/Conferencedate,subjectTo be constructed as StartDate - EndDate (only the first 10 chars ofthe dates are kept)
ConferenceInstances/EndDate,Publication/Journal/Conferencedate,To be constructed as StartDate - EndDate (only the first 10 chars ofthe dates are kept)
Papers/Volume,Publication/Journal/vol,
Papers/Issue,Publication/Journal/iss,
Papers/FirstPage,Publication/Journal/sp,
Papers/LastPage,Publication/Journal/ep,
Papers/ReferenceCount,N/A,
Papers/CitationCount,N/A,
Papers/EstimatedCitation,N/A,
Papers/OriginalVenue,N/A,
Papers/FamilyId,N/A,
Papers/CreatedDate,Result/LastUpdateTimeStamp,
Papers/FieldOfStudy/DisplayName,"Result/subject with Qualifier(""keyword"", ""dnet:subject_classification_typologies"")",Some FieldOfStudy come from the UMLS controlled vocabulary. Future releases of DOIBoost will include such terms with a specific Qualifier (i.e. not as generic keywords)
Papers/FieldOfStudy/MainType,"Result/subject with Qualifier(""keyword"", ""dnet:subject_classification_typologies"")","If MainType is splittable on . (like 'food.type_of_dish', 'aviation.airport', 'soccer.team'), then the first token (i.e. food, aviation, soccer) is also added as additional subject."
1 Micorsoft Academic Graph Field OAF field Comments
2 Papers/DOI OafEntity/originalId
3 OafEntity/PID
4 Oaf/id in the form 50|doiboost____::md5(DOI)
5 Papers/PaperId OafEntity/originalId
6 Papers/PaperTitle Result/Title with Qualifier("main title", "dnet:dataCite_title")
7 Papers/OriginalTitle Result/Title with Qualifier("alternative title", "dnet:dataCite_title")
8 Papers/BookTitle Publication/Source
9 Papers/Year N/A
10 Papers/Date Result/dateofacceptance
11 Papers/Publisher Result/Publisher Possibly overridden by Journal/Publisher
12 Papers/JournalId N/A
13 Journal/Rank N/A
14 Journal/NormalizedName N/A
15 Journal/DisplayName Publication/Journal/Name
16 Journal/Issn Publication/Journal/issnPrinted
17 Journal/Publisher Result/publisher If avalable, it overrides value in Papers/Publisher
18 Journal/Webpage N/A
19 Journal/PaperCount N/A
20 Journal/CitationCount N/A
21 Journal/CreatedDate N/A
22 ConferenceInstances/DisplayName Publication/Journal/Name
23 ConferenceInstances/Location Publication/Journal/Conferenceplace
24 ConferenceInstances/StartDate Publication/Journal/Conferencedate subjectTo be constructed as StartDate - EndDate (only the first 10 chars ofthe dates are kept)
25 ConferenceInstances/EndDate Publication/Journal/Conferencedate To be constructed as StartDate - EndDate (only the first 10 chars ofthe dates are kept)
26 Papers/Volume Publication/Journal/vol
27 Papers/Issue Publication/Journal/iss
28 Papers/FirstPage Publication/Journal/sp
29 Papers/LastPage Publication/Journal/ep
30 Papers/ReferenceCount N/A
31 Papers/CitationCount N/A
32 Papers/EstimatedCitation N/A
33 Papers/OriginalVenue N/A
34 Papers/FamilyId N/A
35 Papers/CreatedDate Result/LastUpdateTimeStamp
36 Papers/FieldOfStudy/DisplayName Result/subject with Qualifier("keyword", "dnet:subject_classification_typologies") Some FieldOfStudy come from the UMLS controlled vocabulary. Future releases of DOIBoost will include such terms with a specific Qualifier (i.e. not as generic keywords)
37 Papers/FieldOfStudy/MainType Result/subject with Qualifier("keyword", "dnet:subject_classification_typologies") If MainType is splittable on . (like 'food.type_of_dish', 'aviation.airport', 'soccer.team'), then the first token (i.e. food, aviation, soccer) is also added as additional subject.

6
dhp-workflows/dhp-doiboost/src/main/resources/eu.dnetlib.dhp.doiboost.mappings/orcid_mapping.csv Normal file
View File

@ -0,0 +1,6 @@
ORCID field,OAF mapping,Comment
doi,Result/pid,
oid,Result/Author/pid,
name,Result/Author/name,
surname,Result/Author/surname,
creditName,N/A,Result/Author/fullname is generated by concatenating name and surname
1 ORCID field OAF mapping Comment
2 doi Result/pid
3 oid Result/Author/pid
4 name Result/Author/name
5 surname Result/Author/surname
6 creditName N/A Result/Author/fullname is generated by concatenating name and surname

11
dhp-workflows/dhp-doiboost/src/main/resources/eu.dnetlib.dhp.doiboost.mappings/unpaywall_mapping.csv Normal file
View File

@ -0,0 +1,11 @@
Unpaywall field,Description,OAF Mapping,Comment
doi,The DOI of this resource.,Result/pid,
is_oa,Is there an OA copy of this resource.,N/A,Add a Result/Instance only if is_oa is true
best_oa_location,The best OA Location Object we could find for this DOI.,,Create one Result/Instance with Open Access right
best_oa_location.url,The url_for_pdf if there is one; otherwise landing page URL.,Result/instance/url,
best_oa_location.license,The license under which this copy is published.,Result/instance/license,
oa_status,"The OA status, or color, of this resource. Classifies OA resources by location and license terms as one of: gold, hybrid, bronze, green or closed.",N/A,New field to be introduced in the OpenAIRE data model
published_date,"The date this resource was published. As reported by the publishers, who unfortunately have inconsistent definitions of what counts as officially ""published.""",N/A,"Not used in the mapping. Could be used to improve the coverage of dates, if needed."
title,The title of this resource.,N/A,
oa_locations,List of all the OA Location objects associated with this resource.,N/A,"Coud be useful if we plan to ""patch"" existing instances. If the instance URL is a URL of a oa_location, then it's Open.
"
1 Unpaywall field Description OAF Mapping Comment
2 doi The DOI of this resource. Result/pid
3 is_oa Is there an OA copy of this resource. N/A Add a Result/Instance only if is_oa is true
4 best_oa_location The best OA Location Object we could find for this DOI. Create one Result/Instance with Open Access right
5 best_oa_location.url The url_for_pdf if there is one; otherwise landing page URL. Result/instance/url
6 best_oa_location.license The license under which this copy is published. Result/instance/license
7 oa_status The OA status, or color, of this resource. Classifies OA resources by location and license terms as one of: gold, hybrid, bronze, green or closed. N/A New field to be introduced in the OpenAIRE data model
8 published_date The date this resource was published. As reported by the publishers, who unfortunately have inconsistent definitions of what counts as officially "published." N/A Not used in the mapping. Could be used to improve the coverage of dates, if needed.
9 title The title of this resource. N/A
10 oa_locations List of all the OA Location objects associated with this resource. N/A Coud be useful if we plan to "patch" existing instances. If the instance URL is a URL of a oa_location, then it's Open.

8
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala
View File

@ -1,16 +1,14 @@
package eu.dnetlib.doiboost.orcid
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.codehaus.jackson.map.ObjectMapper
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory}
import org.junit.jupiter.api.Assertions._
import scala.io.Source
class MappingORCIDToOAFTest {
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass)
val mapper = new ObjectMapper()
@Test

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

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.2-SNAPSHOT</version>
<version>1.2.3-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>1.2.2-SNAPSHOT</version>
<version>1.2.3-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

109
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java Normal file
View File

@ -0,0 +1,109 @@
package eu.dnetlib.dhp.oa.graph.clean;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class CleanGraphSparkJob {
private static final Logger log = LoggerFactory.getLogger(CleanGraphSparkJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
CleanGraphSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath);
String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
String graphTableClassName = parser.get("graphTableClassName");
log.info("graphTableClassName: {}", graphTableClassName);
Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
fixGraphTable(spark, vocs, inputPath, entityClazz, outputPath);
});
}
private static <T extends Oaf> void fixGraphTable(
SparkSession spark,
VocabularyGroup vocs,
String inputPath,
Class<T> clazz,
String outputPath) {
final CleaningRuleMap mapping = CleaningRuleMap.create(vocs);
readTableFromPath(spark, inputPath, clazz)
.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static <T extends Oaf> Dataset<T> readTableFromPath(
SparkSession spark, String inputEntityPath, Class<T> clazz) {
log.info("Reading Graph table from: {}", inputEntityPath);
return spark
.read()
.textFile(inputEntityPath)
.map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz),
Encoders.bean(clazz));
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
}

40
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java Normal file
View File

@ -0,0 +1,40 @@
package eu.dnetlib.dhp.oa.graph.clean;
import java.io.Serializable;
import java.util.HashMap;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableConsumer;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class CleaningRuleMap extends HashMap<Class, SerializableConsumer<Object>> implements Serializable {
/**
* Creates the mapping for the Oaf types subject to cleaning
*
* @param vocabularies
*/
public static CleaningRuleMap create(VocabularyGroup vocabularies) {
CleaningRuleMap mapping = new CleaningRuleMap();
mapping.put(Qualifier.class, o -> {
Qualifier q = (Qualifier) o;
if (vocabularies.vocabularyExists(q.getSchemeid())) {
Qualifier newValue = vocabularies.lookup(q.getSchemeid(), q.getClassid());
q.setClassid(newValue.getClassid());
q.setClassname(newValue.getClassname());
}
});
mapping.put(StructuredProperty.class, o -> {
StructuredProperty sp = (StructuredProperty) o;
// TODO implement a policy
/*
* if (StringUtils.isBlank(sp.getValue())) { sp.setValue(null); sp.setQualifier(null); sp.setDataInfo(null);
* }
*/
});
return mapping;
}
}

82
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafCleaner.java Normal file
View File

@ -0,0 +1,82 @@
package eu.dnetlib.dhp.oa.graph.clean;
import java.io.Serializable;
import java.lang.reflect.Field;
import java.util.Arrays;
import java.util.LinkedList;
import java.util.List;
import java.util.Objects;
import eu.dnetlib.dhp.schema.oaf.Oaf;
public class OafCleaner implements Serializable {
public static <E extends Oaf> E apply(E oaf, CleaningRuleMap mapping) {
try {
navigate(oaf, mapping);
} catch (IllegalAccessException e) {
throw new RuntimeException(e);
}
return oaf;
}
private static void navigate(Object o, CleaningRuleMap mapping) throws IllegalAccessException {
if (isPrimitive(o)) {
return;
} else if (isIterable(o.getClass())) {
for (final Object elem : (Iterable<?>) o) {
navigate(elem, mapping);
}
} else if (hasMapping(o, mapping)) {
mapping.get(o.getClass()).accept(o);
} else {
for (final Field f : getAllFields(o.getClass())) {
f.setAccessible(true);
final Object val = f.get(o);
if (!isPrimitive(val) && hasMapping(val, mapping)) {
mapping.get(val.getClass()).accept(val);
} else {
navigate(f.get(o), mapping);
}
}
}
}
private static boolean hasMapping(Object o, CleaningRuleMap mapping) {
return mapping.containsKey(o.getClass());
}
private static boolean isIterable(final Class<?> cl) {
return Iterable.class.isAssignableFrom(cl);
}
private static boolean isPrimitive(Object o) {
return Objects.isNull(o)
|| o.getClass().isPrimitive()
|| o instanceof Class
|| o instanceof Integer
|| o instanceof Double
|| o instanceof Float
|| o instanceof Long
|| o instanceof Boolean
|| o instanceof String
|| o instanceof Byte;
}
private static List<Field> getAllFields(Class<?> clazz) {
return getAllFields(new LinkedList<>(), clazz);
}
private static List<Field> getAllFields(List<Field> fields, Class<?> clazz) {
fields.addAll(Arrays.asList(clazz.getDeclaredFields()));
final Class<?> superclass = clazz.getSuperclass();
if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) {
getAllFields(fields, superclass);
}
return fields;
}
}

13
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -63,6 +63,8 @@ public abstract class AbstractMdRecordToOafMapper {
protected final VocabularyGroup vocs;
private final boolean invisible;
protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4";
protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3";
protected static final Qualifier ORCID_PID_TYPE = qualifier(
@ -85,8 +87,9 @@ public abstract class AbstractMdRecordToOafMapper {
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
"main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs) {
protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible) {
this.vocs = vocs;
this.invisible = invisible;
}
public List<Oaf> processMdRecord(final String xml) {
@ -112,7 +115,7 @@ public abstract class AbstractMdRecordToOafMapper {
return null;
}
final DataInfo info = prepareDataInfo(doc);
final DataInfo info = prepareDataInfo(doc, invisible);
final long lastUpdateTimestamp = new Date().getTime();
return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp);
@ -510,11 +513,11 @@ public abstract class AbstractMdRecordToOafMapper {
return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
}
protected DataInfo prepareDataInfo(final Document doc) {
protected DataInfo prepareDataInfo(final Document doc, final boolean invisible) {
final Node n = doc.selectSingleNode("//oaf:datainfo");
if (n == null) {
return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9");
return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9");
}
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
@ -528,7 +531,7 @@ public abstract class AbstractMdRecordToOafMapper {
final String trust = n.valueOf("./oaf:trust");
return dataInfo(
deletedbyinference, inferenceprovenance, inferred, false,
deletedbyinference, inferenceprovenance, inferred, invisible,
qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
}

19
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
View File

@ -39,6 +39,8 @@ import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import scala.Tuple2;
public class GenerateEntitiesApplication {
@ -71,7 +73,8 @@ public class GenerateEntitiesApplication {
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupUrl);
final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
final SparkConf conf = new SparkConf();
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
@ -137,10 +140,16 @@ public class GenerateEntitiesApplication {
final String type = StringUtils.substringAfter(id, ":");
switch (type.toLowerCase()) {
case "native_oaf":
return new OafToOafMapper(vocs).processMdRecord(s);
case "native_odf":
return new OdfToOafMapper(vocs).processMdRecord(s);
case "oaf-store-cleaned":
case "oaf-store-claim":
return new OafToOafMapper(vocs, false).processMdRecord(s);
case "odf-store-cleaned":
case "odf-store-claim":
return new OdfToOafMapper(vocs, false).processMdRecord(s);
case "oaf-store-intersection":
return new OafToOafMapper(vocs, true).processMdRecord(s);
case "odf-store-intersection":
return new OdfToOafMapper(vocs, true).processMdRecord(s);
case "datasource":
return Arrays.asList(convertFromJson(s, Datasource.class));
case "organization":

3
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -71,6 +71,7 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable {
@ -151,7 +152,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
super(hdfsPath);
this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
this.lastUpdateTimestamp = new Date().getTime();
this.vocs = VocabularyGroup.loadVocsFromIS(isLookupUrl);
this.vocs = VocabularyGroup.loadVocsFromIS(ISLookupClientFactory.getLookUpService(isLookupUrl));
}
public void execute(final String sqlFile, final Function<ResultSet, List<Oaf>> producer)

5
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateMongoMdstoresApplication.java
View File

@ -26,8 +26,7 @@ public class MigrateMongoMdstoresApplication extends AbstractMigrationApplicatio
IOUtils
.toString(
MigrateMongoMdstoresApplication.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/migrate_mongo_mstores_parameters.json")));
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_mongo_mstores_parameters.json")));
parser.parseArgument(args);
final String mongoBaseUrl = parser.get("mongoBaseUrl");
@ -60,7 +59,7 @@ public class MigrateMongoMdstoresApplication extends AbstractMigrationApplicatio
final String currentColl = entry.getValue();
for (final String xml : mdstoreClient.listRecords(currentColl)) {
emit(xml, "native_" + format);
emit(xml, String.format("%s-%s-%s", format, layout, interpretation));
}
}
}

18
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
View File

@ -4,13 +4,7 @@ package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DATASET;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.util.ArrayList;
import java.util.List;
@ -37,8 +31,8 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class OafToOafMapper extends AbstractMdRecordToOafMapper {
public OafToOafMapper(final VocabularyGroup vocs) {
super(vocs);
public OafToOafMapper(final VocabularyGroup vocs, final boolean invisible) {
super(vocs, invisible);
}
@Override
@ -139,7 +133,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
instance
.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
instance.setRefereed(prepareQualifier(doc, "//oaf:refereed", DNET_REVIEW_LEVELS));
instance
.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
instance
@ -281,12 +275,12 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
res
.add(
getRelation(
docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
docId, otherId, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, collectedFrom, info,
lastUpdateTimestamp));
res
.add(
getRelation(
otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
otherId, docId, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, collectedFrom, info,
lastUpdateTimestamp));
}
}

20
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
View File

@ -4,19 +4,7 @@ package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_DATE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_RESOURCE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTS;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PART_OF;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_SUPPLEMENTED_BY;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_SUPPLEMENT_TO;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PART;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.SUPPLEMENT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.util.ArrayList;
import java.util.Arrays;
@ -44,8 +32,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
public static final String HTTP_DX_DOI_PREIFX = "http://dx.doi.org/";
public OdfToOafMapper(final VocabularyGroup vocs) {
super(vocs);
public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible) {
super(vocs, invisible);
}
@Override
@ -129,7 +117,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
instance
.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
instance.setRefereed(prepareQualifier(doc, "//oaf:refereed", DNET_REVIEW_LEVELS));
instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
instance
.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java
View File

@ -60,6 +60,10 @@ public class OafMapperUtils {
.collect(Collectors.toList());
}
public static Qualifier unknown(final String schemeid, final String schemename) {
return qualifier("UNKNOWN", "Unknown", schemeid, schemename);
}
public static Qualifier qualifier(
final String classid,
final String classname,

45
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java
View File

@ -4,14 +4,29 @@ package eu.dnetlib.dhp.oa.graph.raw.common;
import java.io.Serializable;
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class Vocabulary implements Serializable {
private final String id;
private final String name;
/**
* Code to Term mappings for this Vocabulary.
*/
private final Map<String, VocabularyTerm> terms = new HashMap<>();
/**
* Synonym to Code mappings for this Vocabulary.
*/
private final Map<String, String> synonyms = Maps.newHashMap();
public Vocabulary(final String id, final String name) {
this.id = id;
this.name = name;
@ -30,7 +45,7 @@ public class Vocabulary implements Serializable {
}
public VocabularyTerm getTerm(final String id) {
return terms.get(id.toLowerCase());
return Optional.ofNullable(id).map(s -> s.toLowerCase()).map(s -> terms.get(s)).orElse(null);
}
protected void addTerm(final String id, final String name) {
@ -40,4 +55,32 @@ public class Vocabulary implements Serializable {
protected boolean termExists(final String id) {
return terms.containsKey(id.toLowerCase());
}
protected void addSynonym(final String syn, final String termCode) {
synonyms.put(syn, termCode.toLowerCase());
}
public VocabularyTerm getTermBySynonym(final String syn) {
return getTerm(synonyms.get(syn));
}
public Qualifier getTermAsQualifier(final String termId) {
if (StringUtils.isBlank(termId)) {
return OafMapperUtils.unknown(getId(), getName());
} else if (termExists(termId)) {
final VocabularyTerm t = getTerm(termId);
return OafMapperUtils.qualifier(t.getId(), t.getName(), getId(), getName());
} else {
return OafMapperUtils.qualifier(termId, termId, getId(), getName());
}
}
public Qualifier getSynonymAsQualifier(final String syn) {
return Optional
.ofNullable(getTermBySynonym(syn))
.map(term -> getTermAsQualifier(term.getId()))
.orElse(null);
// .orElse(OafMapperUtils.unknown(getId(), getName()));
}
}

96
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java
View File

@ -1,33 +1,39 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
import java.io.IOException;
import java.io.Serializable;
import java.util.HashMap;
import java.util.Map;
import java.util.*;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class VocabularyGroup implements Serializable {
public static VocabularyGroup loadVocsFromIS(final String isLookupUrl) throws IOException, ISLookUpException {
final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl);
public static final String VOCABULARIES_XQUERY = "for $x in collection(' /db/DRIVER/VocabularyDSResources/VocabularyDSResourceType') \n"
+
"let $vocid := $x//VOCABULARY_NAME/@code\n" +
"let $vocname := $x//VOCABULARY_NAME/text()\n" +
"for $term in ($x//TERM)\n" +
"return concat($vocid,' @=@ ',$vocname,' @=@ ',$term/@code,' @=@ ',$term/@english_name)";
final String xquery = IOUtils
.toString(
GenerateEntitiesApplication.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery"));
public static final String VOCABULARY_SYNONYMS_XQUERY = "for $x in collection('/db/DRIVER/VocabularyDSResources/VocabularyDSResourceType')\n"
+
"let $vocid := $x//VOCABULARY_NAME/@code\n" +
"let $vocname := $x//VOCABULARY_NAME/text()\n" +
"for $term in ($x//TERM)\n" +
"for $syn in ($term//SYNONYM/@term)\n" +
"return concat($vocid,' @=@ ',$term/@code,' @=@ ', $syn)\n";
public static VocabularyGroup loadVocsFromIS(ISLookUpService isLookUpService) throws ISLookUpException {
final VocabularyGroup vocs = new VocabularyGroup();
for (final String s : isLookUpService.quickSearchProfile(xquery)) {
for (final String s : isLookUpService.quickSearchProfile(VOCABULARIES_XQUERY)) {
final String[] arr = s.split("@=@");
if (arr.length == 4) {
final String vocId = arr[0].trim();
@ -40,6 +46,19 @@ public class VocabularyGroup implements Serializable {
}
vocs.addTerm(vocId, termId, termName);
vocs.addSynonyms(vocId, termId, termId);
}
}
for (final String s : isLookUpService.quickSearchProfile(VOCABULARY_SYNONYMS_XQUERY)) {
final String[] arr = s.split("@=@");
if (arr.length == 3) {
final String vocId = arr[0].trim();
final String termId = arr[1].trim();
final String syn = arr[2].trim();
vocs.addSynonyms(vocId, termId, syn);
vocs.addSynonyms(vocId, termId, termId);
}
}
@ -66,16 +85,37 @@ public class VocabularyGroup implements Serializable {
}
}
public Qualifier getTermAsQualifier(final String vocId, final String id) {
if (StringUtils.isBlank(id)) {
return OafMapperUtils.qualifier("UNKNOWN", "UNKNOWN", vocId, vocId);
} else if (termExists(vocId, id)) {
final Vocabulary v = vocs.get(vocId.toLowerCase());
final VocabularyTerm t = v.getTerm(id);
return OafMapperUtils.qualifier(t.getId(), t.getName(), v.getId(), v.getName());
} else {
return OafMapperUtils.qualifier(id, id, vocId, vocId);
public Set<String> getTerms(String vocId) {
if (!vocabularyExists(vocId)) {
return new HashSet<>();
}
return vocs
.get(vocId.toLowerCase())
.getTerms()
.values()
.stream()
.map(t -> t.getId())
.collect(Collectors.toCollection(HashSet::new));
}
public Qualifier lookup(String vocId, String id) {
return Optional
.ofNullable(getSynonymAsQualifier(vocId, id))
.orElse(getTermAsQualifier(vocId, id));
}
public Qualifier getTermAsQualifier(final String vocId, final String id) {
if (vocabularyExists(vocId)) {
return vocs.get(vocId.toLowerCase()).getTermAsQualifier(id);
}
return OafMapperUtils.qualifier(id, id, "", "");
}
public Qualifier getSynonymAsQualifier(final String vocId, final String syn) {
if (StringUtils.isBlank(vocId)) {
return OafMapperUtils.unknown("", "");
}
return vocs.get(vocId.toLowerCase()).getSynonymAsQualifier(syn);
}
public boolean termExists(final String vocId, final String id) {
@ -86,4 +126,16 @@ public class VocabularyGroup implements Serializable {
return vocs.containsKey(vocId.toLowerCase());
}
private void addSynonyms(final String vocId, final String termId, final String syn) {
String id = Optional
.ofNullable(vocId)
.map(s -> s.toLowerCase())
.orElseThrow(
() -> new IllegalArgumentException(String.format("empty vocabulary id for [term:%s, synonym:%s]")));
Optional
.ofNullable(vocs.get(id))
.orElseThrow(() -> new IllegalArgumentException("missing vocabulary id: " + vocId))
.addSynonym(syn, termId);
}
}

18
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/config-default.xml Normal file
View File

@ -0,0 +1,18 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

281
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml Normal file
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@ -0,0 +1,281 @@
<workflow-app name="clean graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>graphInputPath</name>
<description>the input path to read graph content</description>
</property>
<property>
<name>graphOutputPath</name>
<description>the target path to store cleaned graph</description>
</property>
<property>
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<start to="fork_clean_graph"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<fork name="fork_clean_graph">
<path start="clean_publication"/>
<path start="clean_dataset"/>
<path start="clean_otherresearchproduct"/>
<path start="clean_software"/>
<path start="clean_datasource"/>
<path start="clean_organization"/>
<path start="clean_project"/>
<path start="clean_relation"/>
</fork>
<action name="clean_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean publications</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphInputPath}/publication</arg>
<arg>--outputPath</arg><arg>${graphOutputPath}/publication</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="wait_clean"/>
<error to="Kill"/>
</action>
<action name="clean_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean datasets</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphInputPath}/dataset</arg>
<arg>--outputPath</arg><arg>${graphOutputPath}/dataset</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="wait_clean"/>
<error to="Kill"/>
</action>
<action name="clean_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean otherresearchproducts</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphInputPath}/otherresearchproduct</arg>
<arg>--outputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="wait_clean"/>
<error to="Kill"/>
</action>
<action name="clean_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean softwares</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphInputPath}/software</arg>
<arg>--outputPath</arg><arg>${graphOutputPath}/software</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="wait_clean"/>
<error to="Kill"/>
</action>
<action name="clean_datasource">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean datasources</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphInputPath}/datasource</arg>
<arg>--outputPath</arg><arg>${graphOutputPath}/datasource</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="wait_clean"/>
<error to="Kill"/>
</action>
<action name="clean_organization">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean organizations</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphInputPath}/organization</arg>
<arg>--outputPath</arg><arg>${graphOutputPath}/organization</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="wait_clean"/>
<error to="Kill"/>
</action>
<action name="clean_project">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean projects</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphInputPath}/project</arg>
<arg>--outputPath</arg><arg>${graphOutputPath}/project</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="wait_clean"/>
<error to="Kill"/>
</action>
<action name="clean_relation">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean relations</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphInputPath}/relation</arg>
<arg>--outputPath</arg><arg>${graphOutputPath}/relation</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="wait_clean"/>
<error to="Kill"/>
</action>
<join name="wait_clean" to="End"/>
<end name="End"/>
</workflow-app>

32
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json Normal file
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@ -0,0 +1,32 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "in",
"paramLongName": "inputPath",
"paramDescription": "the path to the graph data dump to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path to store the output graph",
"paramRequired": true
},
{
"paramName": "isu",
"paramLongName": "isLookupUrl",
"paramDescription": "url to the ISLookup Service",
"paramRequired": true
},
{
"paramName": "class",
"paramLongName": "graphTableClassName",
"paramDescription": "class name moelling the graph table",
"paramRequired": true
}
]

19
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
View File

@ -210,6 +210,23 @@
<arg>--mdLayout</arg><arg>store</arg>
<arg>--mdInterpretation</arg><arg>cleaned</arg>
</java>
<ok to="ImportOAF_invisible"/>
<error to="Kill"/>
</action>
<action name="ImportOAF_invisible">
<java>
<prepare>
<delete path="${contentPath}/oaf_records_invisible"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
<arg>--hdfsPath</arg><arg>${contentPath}/oaf_records_invisible</arg>
<arg>--mongoBaseUrl</arg><arg>${mongoURL}</arg>
<arg>--mongoDb</arg><arg>${mongoDb}</arg>
<arg>--mdFormat</arg><arg>OAF</arg>
<arg>--mdLayout</arg><arg>store</arg>
<arg>--mdInterpretation</arg><arg>intersection</arg>
</java>
<ok to="wait_import"/>
<error to="Kill"/>
</action>
@ -237,7 +254,7 @@
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims</arg>
<arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims,${contentPath}/oaf_records_invisible</arg>
<arg>--targetPath</arg><arg>${workingDir}/entities_claim</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
</spark>

6
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies_synonyms.xquery Normal file
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@ -0,0 +1,6 @@
for $x in collection('/db/DRIVER/VocabularyDSResources/VocabularyDSResourceType')
let $vocid := $x//VOCABULARY_NAME/@code
let $vocname := $x//VOCABULARY_NAME/text()
for $term in ($x//TERM)
for $syn in ($term//SYNONYM/@term)
return concat($vocid,' @=@ ',$term/@code,' @=@ ', $syn)

106
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java Normal file
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@ -0,0 +1,106 @@
package eu.dnetlib.dhp.oa.graph.clean;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.lenient;
import java.io.IOException;
import java.util.List;
import java.util.Set;
import java.util.stream.Stream;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class)
public class CleaningFunctionTest {
public static final ObjectMapper MAPPER = new ObjectMapper();
@Mock
private ISLookUpService isLookUpService;
private VocabularyGroup vocabularies;
private CleaningRuleMap mapping;
@BeforeEach
public void setUp() throws ISLookUpException, IOException {
lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs());
lenient()
.when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY))
.thenReturn(synonyms());
vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService);
mapping = CleaningRuleMap.create(vocabularies);
}
@Test
public void testCleaning() throws Exception {
assertNotNull(vocabularies);
assertNotNull(mapping);
String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"));
Publication p_in = MAPPER.readValue(json, Publication.class);
Publication p_out = OafCleaner.apply(p_in, mapping);
assertNotNull(p_out);
assertEquals("eng", p_out.getLanguage().getClassid());
assertEquals("English", p_out.getLanguage().getClassname());
assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid());
assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname());
assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid());
assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname());
Set<String> pidTerms = vocabularies.getTerms("dnet:pid_types");
assertTrue(
p_out
.getPid()
.stream()
.map(p -> p.getQualifier())
.allMatch(q -> pidTerms.contains(q.getClassid())));
// TODO add more assertions to verity the cleaned values
System.out.println(MAPPER.writeValueAsString(p_out));
/*
* assertTrue( p_out .getPid() .stream() .allMatch(sp -> StringUtils.isNotBlank(sp.getValue())));
*/
}
private Stream<Qualifier> getAuthorPidTypes(Publication pub) {
return pub
.getAuthor()
.stream()
.map(a -> a.getPid())
.flatMap(p -> p.stream())
.map(s -> s.getQualifier());
}
private List<String> vocs() throws IOException {
return IOUtils
.readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"));
}
private List<String> synonyms() throws IOException {
return IOUtils
.readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"));
}
}

24
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -2,6 +2,7 @@
package eu.dnetlib.dhp.oa.graph.raw;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.ArgumentMatchers.anyString;
@ -55,7 +56,7 @@ public class MappersTest {
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml"));
final List<Oaf> list = new OafToOafMapper(vocs).processMdRecord(xml);
final List<Oaf> list = new OafToOafMapper(vocs, false).processMdRecord(xml);
assertEquals(3, list.size());
assertTrue(list.get(0) instanceof Publication);
@ -69,6 +70,7 @@ public class MappersTest {
assertValidId(p.getId());
assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
assertFalse(p.getDataInfo().getInvisible());
assertTrue(p.getAuthor().size() > 0);
final Optional<Author> author = p
@ -134,11 +136,27 @@ public class MappersTest {
// System.out.println(new ObjectMapper().writeValueAsString(r2));
}
@Test
void testPublicationInvisible() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_record.xml"));
final List<Oaf> list = new OafToOafMapper(vocs, true).processMdRecord(xml);
assertTrue(list.size() > 0);
assertTrue(list.get(0) instanceof Publication);
final Publication p = (Publication) list.get(0);
assertTrue(p.getDataInfo().getInvisible());
}
@Test
void testDataset() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset.xml"));
final List<Oaf> list = new OdfToOafMapper(vocs).processMdRecord(xml);
final List<Oaf> list = new OdfToOafMapper(vocs, false).processMdRecord(xml);
assertEquals(3, list.size());
assertTrue(list.get(0) instanceof Dataset);
@ -220,7 +238,7 @@ public class MappersTest {
void testSoftware() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_software.xml"));
final List<Oaf> list = new OdfToOafMapper(vocs).processMdRecord(xml);
final List<Oaf> list = new OdfToOafMapper(vocs, false).processMdRecord(xml);
assertEquals(1, list.size());
assertTrue(list.get(0) instanceof Software);

757
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json Normal file
View File

@ -0,0 +1,757 @@
{
"author": [
{
"affiliation": [
],
"fullname": "Brien, Tom",
"name": "Tom",
"pid": [
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "ORCID12",
"classname": "ORCID12",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "0000-0001-9613-6639"
}
],
"rank": 1,
"surname": "Brien"
},
{
"affiliation": [
],
"fullname": "Ade, Peter",
"name": "Peter",
"pid": [
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "xyz",
"classname": "XYZ",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "qwerty"
}
],
"rank": 2,
"surname": "Ade"
},
{
"affiliation": [
],
"fullname": "Barry, Peter S.",
"name": "Peter S.",
"pid": [
],
"rank": 3,
"surname": "Barry"
},
{
"affiliation": [
],
"fullname": "Dunscombe, Chris J.",
"name": "Chris J.",
"pid": [
],
"rank": 4,
"surname": "Dunscombe"
},
{
"affiliation": [
],
"fullname": "Leadley, David R.",
"name": "David R.",
"pid": [
],
"rank": 5,
"surname": "Leadley"
},
{
"affiliation": [
],
"fullname": "Morozov, Dmitry V.",
"name": "Dmitry V.",
"pid": [
],
"rank": 6,
"surname": "Morozov"
},
{
"affiliation": [
],
"fullname": "Myronov, Maksym",
"name": "Maksym",
"pid": [
],
"rank": 7,
"surname": "Myronov"
},
{
"affiliation": [
],
"fullname": "Parker, Evan",
"name": "Evan",
"pid": [
],
"rank": 8,
"surname": "Parker"
},
{
"affiliation": [
],
"fullname": "Prest, Martin J.",
"name": "Martin J.",
"pid": [
],
"rank": 9,
"surname": "Prest"
},
{
"affiliation": [
],
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dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt Normal file
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dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt Normal file
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dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml
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@ -3,7 +3,7 @@
<parent>
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<modelVersion>4.0.0</modelVersion>

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