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dnet-hadoop
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merged with master

This commit is contained in:
Miriam Baglioni 2020-05-11 10:20:00 +02:00
parent 7e66bc2527 622ba87ec2
commit 871e079b45
56 changed files with 1133 additions and 296 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>1.1.7-SNAPSHOT</version>
<version>1.2.0-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>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
</parent>
<artifactId>dhp-build-properties-maven-plugin</artifactId>

6
dhp-build/dhp-code-style/pom.xml
View File

@ -1,13 +1,11 @@
<?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">
<modelVersion>4.0.0</modelVersion>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-code-style</artifactId>
<version>1.1.7-SNAPSHOT</version>
<version>1.2.0-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>1.1.7-SNAPSHOT</version>
<version>1.2.0-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>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>

2
dhp-schemas/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>

3
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
View File

@ -49,6 +49,9 @@ public class ModelConstants {
public static final String HAS_PARTICIPANT = "hasParticipant";
public static final String IS_PARTICIPANT = "isParticipant";
public static final String UNKNOWN = "UNKNOWN";
public static final String NOT_AVAILABLE = "not available";
public static final Qualifier PUBLICATION_DEFAULT_RESULTTYPE = qualifier(
PUBLICATION_RESULTTYPE_CLASSID, PUBLICATION_RESULTTYPE_CLASSID,
DNET_RESULT_TYPOLOGIES, DNET_RESULT_TYPOLOGIES);

14
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java
View File

@ -41,6 +41,12 @@ public class Relation extends Oaf {
*/
private String target;
/**
* List of relation specific properties. Values include 'similarityLevel', indicating the similarity score between a
* pair of publications.
*/
private List<KeyValue> properties = new ArrayList<>();
public String getRelType() {
return relType;
}
@ -81,6 +87,14 @@ public class Relation extends Oaf {
this.target = target;
}
public List<KeyValue> getProperties() {
return properties;
}
public void setProperties(List<KeyValue> properties) {
this.properties = properties;
}
public void mergeFrom(final Relation r) {
checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal");

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

@ -1,11 +1,10 @@
<?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">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-workflows</artifactId>
<version>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
</parent>
<artifactId>dhp-actionmanager</artifactId>

12
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java
View File

@ -84,8 +84,11 @@ public class MigrateActionSet {
final List<Path> sourcePaths = getSourcePaths(sourceNN, isLookUp);
log
.info(
"paths to process:\n{}",
sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n")));
"paths to process:\n{}", sourcePaths
.stream()
.map(p -> p.toString())
.collect(Collectors.joining("\n")));
for (Path source : sourcePaths) {
if (!sourceFS.exists(source)) {
@ -119,9 +122,8 @@ public class MigrateActionSet {
}
}
props
.setProperty(
TARGET_PATHS, targetPaths.stream().map(p -> p.toString()).collect(Collectors.joining(",")));
final String targetPathsCsv = targetPaths.stream().map(p -> p.toString()).collect(Collectors.joining(","));
props.setProperty(TARGET_PATHS, targetPathsCsv);
File file = new File(System.getProperty("oozie.action.output.properties"));
try (OutputStream os = new FileOutputStream(file)) {

44
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java
View File

@ -1,12 +1,10 @@
package eu.dnetlib.dhp.actionmanager.migration;
import static eu.dnetlib.data.proto.KindProtos.Kind.entity;
import static eu.dnetlib.data.proto.KindProtos.Kind.relation;
import static eu.dnetlib.data.proto.TypeProtos.*;
import static eu.dnetlib.data.proto.TypeProtos.Type.*;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
@ -21,10 +19,6 @@ import eu.dnetlib.dhp.schema.oaf.*;
public class ProtoConverter implements Serializable {
public static final String UNKNOWN = "UNKNOWN";
public static final String NOT_AVAILABLE = "not available";
public static final String DNET_ACCESS_MODES = "dnet:access_modes";
public static Oaf convert(OafProtos.Oaf oaf) {
try {
switch (oaf.getKind()) {
@ -64,6 +58,7 @@ public class ProtoConverter implements Serializable {
case result:
final Result r = convertResult(oaf);
r.setInstance(convertInstances(oaf));
r.setExternalReference(convertExternalRefs(oaf));
return r;
case project:
return convertProject(oaf);
@ -94,13 +89,44 @@ public class ProtoConverter implements Serializable {
i.setHostedby(mapKV(ri.getHostedby()));
i.setInstancetype(mapQualifier(ri.getInstancetype()));
i.setLicense(mapStringField(ri.getLicense()));
i.setUrl(ri.getUrlList());
i
.setUrl(
ri.getUrlList() != null ? ri
.getUrlList()
.stream()
.distinct()
.collect(Collectors.toCollection(ArrayList::new)) : null);
i.setRefereed(mapStringField(ri.getRefereed()));
i.setProcessingchargeamount(mapStringField(ri.getProcessingchargeamount()));
i.setProcessingchargecurrency(mapStringField(ri.getProcessingchargecurrency()));
return i;
}
private static List<ExternalReference> convertExternalRefs(OafProtos.Oaf oaf) {
ResultProtos.Result r = oaf.getEntity().getResult();
if (r.getExternalReferenceCount() > 0) {
return r
.getExternalReferenceList()
.stream()
.map(e -> convertExtRef(e))
.collect(Collectors.toList());
}
return Lists.newArrayList();
}
private static ExternalReference convertExtRef(ResultProtos.Result.ExternalReference e) {
ExternalReference ex = new ExternalReference();
ex.setUrl(e.getUrl());
ex.setSitename(e.getSitename());
ex.setRefidentifier(e.getRefidentifier());
ex.setQuery(e.getQuery());
ex.setQualifier(mapQualifier(e.getQualifier()));
ex.setLabel(e.getLabel());
ex.setDescription(e.getDescription());
ex.setDataInfo(ex.getDataInfo());
return ex;
}
private static Organization convertOrganization(OafProtos.Oaf oaf) {
final OrganizationProtos.Organization.Metadata m = oaf.getEntity().getOrganization().getMetadata();
final Organization org = setOaf(new Organization(), oaf);

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

@ -4,7 +4,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-workflows</artifactId>
<version>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
</parent>
<artifactId>dhp-aggregation</artifactId>

2
dhp-workflows/dhp-broker-events/pom.xml
View File

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

104
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Event.java Normal file
View File

@ -0,0 +1,104 @@
package eu.dnetlib.dhp.broker.model;
import java.util.Map;
public class Event {
private String eventId;
private String producerId;
private String topic;
private String payload;
private Long creationDate;
private Long expiryDate;
private boolean instantMessage;
private Map<String, Object> map;
public Event() {
}
public Event(final String producerId, final String eventId, final String topic, final String payload,
final Long creationDate, final Long expiryDate,
final boolean instantMessage,
final Map<String, Object> map) {
this.producerId = producerId;
this.eventId = eventId;
this.topic = topic;
this.payload = payload;
this.creationDate = creationDate;
this.expiryDate = expiryDate;
this.instantMessage = instantMessage;
this.map = map;
}
public String getProducerId() {
return this.producerId;
}
public void setProducerId(final String producerId) {
this.producerId = producerId;
}
public String getEventId() {
return this.eventId;
}
public void setEventId(final String eventId) {
this.eventId = eventId;
}
public String getTopic() {
return this.topic;
}
public void setTopic(final String topic) {
this.topic = topic;
}
public String getPayload() {
return this.payload;
}
public void setPayload(final String payload) {
this.payload = payload;
}
public Long getCreationDate() {
return this.creationDate;
}
public void setCreationDate(final Long creationDate) {
this.creationDate = creationDate;
}
public Long getExpiryDate() {
return this.expiryDate;
}
public void setExpiryDate(final Long expiryDate) {
this.expiryDate = expiryDate;
}
public boolean isInstantMessage() {
return this.instantMessage;
}
public void setInstantMessage(final boolean instantMessage) {
this.instantMessage = instantMessage;
}
public Map<String, Object> getMap() {
return this.map;
}
public void setMap(final Map<String, Object> map) {
this.map = map;
}
}

140
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java Normal file
View File

@ -0,0 +1,140 @@
package eu.dnetlib.dhp.broker.model;
import java.text.ParseException;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import org.apache.commons.codec.digest.DigestUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DateUtils;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class EventFactory {
private final static String PRODUCER_ID = "OpenAIRE";
private static final int TTH_DAYS = 365;
private final static String[] DATE_PATTERNS = {
"yyyy-MM-dd"
};
public static Event newBrokerEvent(final Result source, final Result target, final UpdateInfo<?> updateInfo) {
final long now = new Date().getTime();
final Event res = new Event();
final Map<String, Object> map = createMapFromResult(target, source, updateInfo);
final String payload = createPayload(target, updateInfo);
final String eventId = calculateEventId(
updateInfo.getTopic(), target.getOriginalId().get(0), updateInfo.getHighlightValueAsString());
res.setEventId(eventId);
res.setProducerId(PRODUCER_ID);
res.setPayload(payload);
res.setMap(map);
res.setTopic(updateInfo.getTopic());
res.setCreationDate(now);
res.setExpiryDate(calculateExpiryDate(now));
res.setInstantMessage(false);
return res;
}
private static String createPayload(final Result result, final UpdateInfo<?> updateInfo) {
final OpenAireEventPayload payload = new OpenAireEventPayload();
// TODO
updateInfo.compileHighlight(payload);
return payload.toJSON();
}
private static Map<String, Object> createMapFromResult(final Result oaf, final Result source,
final UpdateInfo<?> updateInfo) {
final Map<String, Object> map = new HashMap<>();
final List<KeyValue> collectedFrom = oaf.getCollectedfrom();
if (collectedFrom.size() == 1) {
map.put("target_datasource_id", collectedFrom.get(0).getKey());
map.put("target_datasource_name", collectedFrom.get(0).getValue());
}
final List<String> ids = oaf.getOriginalId();
if (ids.size() > 0) {
map.put("target_publication_id", ids.get(0));
}
final List<StructuredProperty> titles = oaf.getTitle();
if (titles.size() > 0) {
map.put("target_publication_title", titles.get(0));
}
final long date = parseDateTolong(oaf.getDateofacceptance().getValue());
if (date > 0) {
map.put("target_dateofacceptance", date);
}
final List<StructuredProperty> subjects = oaf.getSubject();
if (subjects.size() > 0) {
map
.put(
"target_publication_subject_list",
subjects.stream().map(StructuredProperty::getValue).collect(Collectors.toList()));
}
final List<Author> authors = oaf.getAuthor();
if (authors.size() > 0) {
map
.put(
"target_publication_author_list",
authors.stream().map(Author::getFullname).collect(Collectors.toList()));
}
// PROVENANCE INFO
map.put("trust", updateInfo.getTrust());
final List<KeyValue> sourceCollectedFrom = source.getCollectedfrom();
if (sourceCollectedFrom.size() == 1) {
map.put("provenance_datasource_id", sourceCollectedFrom.get(0).getKey());
map.put("provenance_datasource_name", sourceCollectedFrom.get(0).getValue());
}
map.put("provenance_publication_id_list", source.getOriginalId());
return map;
}
private static String calculateEventId(final String topic, final String publicationId, final String value) {
return "event-"
+ DigestUtils.md5Hex(topic).substring(0, 6) + "-"
+ DigestUtils.md5Hex(publicationId).substring(0, 8) + "-"
+ DigestUtils.md5Hex(value).substring(0, 8);
}
private static long calculateExpiryDate(final long now) {
return now + TTH_DAYS * 24 * 60 * 60 * 1000;
}
private static long parseDateTolong(final String date) {
if (StringUtils.isBlank(date)) {
return -1;
}
try {
return DateUtils.parseDate(date, DATE_PATTERNS).getTime();
} catch (final ParseException e) {
return -1;
}
}
}

112
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java Normal file
View File

@ -0,0 +1,112 @@
package eu.dnetlib.dhp.broker.oa;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
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.broker.model.Event;
import eu.dnetlib.dhp.broker.model.EventFactory;
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingAbstract;
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingAuthorOrcid;
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingOpenAccess;
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingPid;
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingProject;
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingPublicationDate;
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingSubject;
import eu.dnetlib.dhp.broker.oa.util.EnrichMoreOpenAccess;
import eu.dnetlib.dhp.broker.oa.util.EnrichMorePid;
import eu.dnetlib.dhp.broker.oa.util.EnrichMoreSubject;
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.Result;
public class GenerateEventsApplication {
private static final Logger log = LoggerFactory.getLogger(GenerateEventsApplication.class);
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")));
parser.parseArgument(args);
final Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String eventsPath = parser.get("eventsPath");
log.info("eventsPath: {}", eventsPath);
final SparkConf conf = new SparkConf();
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
removeOutputDir(spark, eventsPath);
generateEvents(spark, graphPath, eventsPath);
});
}
private static void removeOutputDir(final SparkSession spark, final String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
private static void generateEvents(final SparkSession spark, final String graphPath, final String eventsPath) {
// TODO
}
private List<Event> generateEvents(final Result... children) {
final List<Event> list = new ArrayList<>();
for (final Result source : children) {
for (final Result target : children) {
if (source != target) {
list
.addAll(
findUpdates(source, target)
.stream()
.map(info -> EventFactory.newBrokerEvent(source, target, info))
.collect(Collectors.toList()));
}
}
}
return list;
}
private List<UpdateInfo<?>> findUpdates(final Result source, final Result target) {
final List<UpdateInfo<?>> list = new ArrayList<>();
list.addAll(EnrichMissingAbstract.findUpdates(source, target));
list.addAll(EnrichMissingAuthorOrcid.findUpdates(source, target));
list.addAll(EnrichMissingOpenAccess.findUpdates(source, target));
list.addAll(EnrichMissingPid.findUpdates(source, target));
list.addAll(EnrichMissingProject.findUpdates(source, target));
list.addAll(EnrichMissingPublicationDate.findUpdates(source, target));
list.addAll(EnrichMissingSubject.findUpdates(source, target));
list.addAll(EnrichMoreOpenAccess.findUpdates(source, target));
list.addAll(EnrichMorePid.findUpdates(source, target));
list.addAll(EnrichMoreSubject.findUpdates(source, target));
return list;
}
}

31
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAbstract.java Normal file
View File

@ -0,0 +1,31 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.dhp.schema.oaf.Result;
public class EnrichMissingAbstract extends UpdateInfo<String> {
public static List<EnrichMissingAbstract> findUpdates(final Result source, final Result target) {
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
return Arrays.asList();
}
private EnrichMissingAbstract(final String highlightValue, final float trust) {
super("ENRICH/MISSING/ABSTRACT", highlightValue, trust);
}
@Override
public void compileHighlight(final OpenAireEventPayload payload) {
payload.getHighlight().getAbstracts().add(getHighlightValue());
}
@Override
public String getHighlightValueAsString() {
return getHighlightValue();
}
}

31
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAuthorOrcid.java Normal file
View File

@ -0,0 +1,31 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.dhp.schema.oaf.Result;
public class EnrichMissingAuthorOrcid extends UpdateInfo<String> {
public static List<EnrichMissingAuthorOrcid> findUpdates(final Result source, final Result target) {
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
return Arrays.asList();
}
private EnrichMissingAuthorOrcid(final String highlightValue, final float trust) {
super("ENRICH/MISSING/AUTHOR/ORCID", highlightValue, trust);
}
@Override
public void compileHighlight(final OpenAireEventPayload payload) {
// TODO
}
@Override
public String getHighlightValueAsString() {
return getHighlightValue();
}
}

32
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java Normal file
View File

@ -0,0 +1,32 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.broker.objects.Instance;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.dhp.schema.oaf.Result;
public class EnrichMissingOpenAccess extends UpdateInfo<Instance> {
public static List<EnrichMissingOpenAccess> findUpdates(final Result source, final Result target) {
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
return Arrays.asList();
}
private EnrichMissingOpenAccess(final Instance highlightValue, final float trust) {
super("ENRICH/MISSING/OPENACCESS_VERSION", highlightValue, trust);
}
@Override
public void compileHighlight(final OpenAireEventPayload payload) {
payload.getHighlight().getInstances().add(getHighlightValue());
}
@Override
public String getHighlightValueAsString() {
return getHighlightValue().getUrl();
}
}

32
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPid.java Normal file
View File

@ -0,0 +1,32 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.broker.objects.Pid;
import eu.dnetlib.dhp.schema.oaf.Result;
public class EnrichMissingPid extends UpdateInfo<Pid> {
public static List<EnrichMissingPid> findUpdates(final Result source, final Result target) {
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
return Arrays.asList();
}
private EnrichMissingPid(final Pid highlightValue, final float trust) {
super("ENRICH/MISSING/PID", highlightValue, trust);
}
@Override
public void compileHighlight(final OpenAireEventPayload payload) {
payload.getHighlight().getPids().add(getHighlightValue());
}
@Override
public String getHighlightValueAsString() {
return getHighlightValue().getType() + "::" + getHighlightValue().getValue();
}
}

33
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingProject.java Normal file
View File

@ -0,0 +1,33 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.broker.objects.Project;
import eu.dnetlib.dhp.schema.oaf.Result;
public class EnrichMissingProject extends UpdateInfo<Project> {
public static List<EnrichMissingProject> findUpdates(final Result source, final Result target) {
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
return Arrays.asList();
}
private EnrichMissingProject(final Project highlightValue, final float trust) {
super("ENRICH/MISSING/PROJECT", highlightValue, trust);
}
@Override
public void compileHighlight(final OpenAireEventPayload payload) {
payload.getHighlight().getProjects().add(getHighlightValue());
}
@Override
public String getHighlightValueAsString() {
return getHighlightValue().getFunder() + "::" + getHighlightValue().getFundingProgram()
+ getHighlightValue().getCode();
}
}

31
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPublicationDate.java Normal file
View File

@ -0,0 +1,31 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.dhp.schema.oaf.Result;
public class EnrichMissingPublicationDate extends UpdateInfo<String> {
public static List<EnrichMissingPublicationDate> findUpdates(final Result source, final Result target) {
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
return Arrays.asList();
}
private EnrichMissingPublicationDate(final String highlightValue, final float trust) {
super("ENRICH/MISSING/PUBLICATION_DATE", highlightValue, trust);
}
@Override
public void compileHighlight(final OpenAireEventPayload payload) {
payload.getHighlight().setPublicationdate(getHighlightValue());
}
@Override
public String getHighlightValueAsString() {
return getHighlightValue();
}
}

36
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java Normal file
View File

@ -0,0 +1,36 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.dhp.schema.oaf.Result;
public class EnrichMissingSubject extends UpdateInfo<String> {
public static List<EnrichMissingSubject> findUpdates(final Result source, final Result target) {
// MESHEUROPMC
// ARXIV
// JEL
// DDC
// ACM
return Arrays.asList();
}
private EnrichMissingSubject(final String subjectClassification, final String highlightValue, final float trust) {
super("ENRICH/MISSING/SUBJECT/" + subjectClassification, highlightValue, trust);
}
@Override
public void compileHighlight(final OpenAireEventPayload payload) {
payload.getHighlight().getSubjects().add(getHighlightValue());
}
@Override
public String getHighlightValueAsString() {
return getHighlightValue();
}
}

32
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java Normal file
View File

@ -0,0 +1,32 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.broker.objects.Instance;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.dhp.schema.oaf.Result;
public class EnrichMoreOpenAccess extends UpdateInfo<Instance> {
public static List<EnrichMoreOpenAccess> findUpdates(final Result source, final Result target) {
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
return Arrays.asList();
}
private EnrichMoreOpenAccess(final Instance highlightValue, final float trust) {
super("ENRICH/MORE/OPENACCESS_VERSION", highlightValue, trust);
}
@Override
public void compileHighlight(final OpenAireEventPayload payload) {
payload.getHighlight().getInstances().add(getHighlightValue());
}
@Override
public String getHighlightValueAsString() {
return getHighlightValue().getUrl();
}
}

32
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMorePid.java Normal file
View File

@ -0,0 +1,32 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.broker.objects.Pid;
import eu.dnetlib.dhp.schema.oaf.Result;
public class EnrichMorePid extends UpdateInfo<Pid> {
public static List<EnrichMorePid> findUpdates(final Result source, final Result target) {
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
return Arrays.asList();
}
private EnrichMorePid(final Pid highlightValue, final float trust) {
super("ENRICH/MORE/PID", highlightValue, trust);
}
@Override
public void compileHighlight(final OpenAireEventPayload payload) {
payload.getHighlight().getPids().add(getHighlightValue());
}
@Override
public String getHighlightValueAsString() {
return getHighlightValue().getType() + "::" + getHighlightValue().getValue();
}
}

36
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreSubject.java Normal file
View File

@ -0,0 +1,36 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.dhp.schema.oaf.Result;
public class EnrichMoreSubject extends UpdateInfo<String> {
public static List<EnrichMoreSubject> findUpdates(final Result source, final Result target) {
// MESHEUROPMC
// ARXIV
// JEL
// DDC
// ACM
return Arrays.asList();
}
private EnrichMoreSubject(final String subjectClassification, final String highlightValue, final float trust) {
super("ENRICH/MORE/SUBJECT/" + subjectClassification, highlightValue, trust);
}
@Override
public void compileHighlight(final OpenAireEventPayload payload) {
payload.getHighlight().getSubjects().add(getHighlightValue());
}
@Override
public String getHighlightValueAsString() {
return getHighlightValue();
}
}

36
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java Normal file
View File

@ -0,0 +1,36 @@
package eu.dnetlib.dhp.broker.oa.util;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
public abstract class UpdateInfo<T> {
private final String topic;
private final T highlightValue;
private final float trust;
protected UpdateInfo(final String topic, final T highlightValue, final float trust) {
this.topic = topic;
this.highlightValue = highlightValue;
this.trust = trust;
}
public T getHighlightValue() {
return highlightValue;
}
public float getTrust() {
return trust;
}
public String getTopic() {
return topic;
}
abstract public void compileHighlight(OpenAireEventPayload payload);
abstract public String getHighlightValueAsString();
}

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

@ -5,7 +5,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.7-SNAPSHOT</version>
<version>1.1.8-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

9
dhp-workflows/dhp-bulktag/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
View File

@ -25,6 +25,7 @@ import eu.dnetlib.dhp.schema.oaf.*;
public class SparkBulkTagJob {
private static final Logger log = LoggerFactory.getLogger(SparkBulkTagJob.class);
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
@ -108,12 +109,12 @@ public class SparkBulkTagJob {
.json(outputPath);
}
private static <R> Dataset<R> readPath(
SparkSession spark, String inputEntityPath, Class<R> clazz) {
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark
.read()
.json(inputEntityPath)
.as(Encoders.bean(clazz));
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
}

80
dhp-workflows/dhp-bulktag/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml
View File

@ -1,39 +1,33 @@
<workflow-app name="bulk_tagging" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>isLookUpUrl</name>
<description>the isLookup service endpoint</description>
</property>
<property>
<name>pathMap</name>
<description>the json path associated to each selection field</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
</parameters>
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>isLookUpUrl</name>
<description>the isLookup service endpoint</description>
</property>
<property>
<name>pathMap</name>
<description>the json path associated to each selection field</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
</parameters>
<start to="reset-outputpath"/>
<start to="reset_outputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset-outputpath">
<action name="reset_outputpath">
<fs>
<delete path='${outputPath}/relation'/>
<delete path='${outputPath}/dataset'/>
<delete path='${outputPath}/software'/>
<delete path='${outputPath}/publication'/>
<delete path='${outputPath}/otherresearchproduct'/>
<delete path='${outputPath}/project'/>
<delete path='${outputPath}/organization'/>
<delete path='${outputPath}/datasource'/>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<error to="Kill"/>
@ -67,6 +61,7 @@
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<action name="copy_projects">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
@ -91,14 +86,13 @@
<join name="copy_wait" to="fork_exec_bulktag"/>
<fork name="fork_exec_bulktag">
<path start="join_bulktag_publication"/>
<path start="join_bulktag_dataset"/>
<path start="join_bulktag_otherresearchproduct"/>
<path start="join_bulktag_software"/>
</fork>
<fork name="fork_exec_bulktag">
<path start="join_bulktag_publication"/>
<path start="join_bulktag_dataset"/>
<path start="join_bulktag_otherresearchproduct"/>
<path start="join_bulktag_software"/>
</fork>
<action name="join_bulktag_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
@ -127,6 +121,7 @@
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_bulktag_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
@ -155,6 +150,7 @@
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_bulktag_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
@ -183,6 +179,7 @@
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_bulktag_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
@ -211,6 +208,9 @@
<ok to="wait"/>
<error to="Kill"/>
</action>
<join name="wait" to="End"/>
<end name="End"/>
<join name="wait" to="End"/>
<end name="End"/>
</workflow-app>

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>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-dedup-openaire</artifactId>

4
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java
View File

@ -137,10 +137,14 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
}
private Relation rel(String source, String target, String relClass, DedupConfig dedupConf) {
String entityType = dedupConf.getWf().getEntityType();
Relation r = new Relation();
r.setSource(source);
r.setTarget(target);
r.setRelClass(relClass);
r.setRelType(entityType + entityType.substring(0, 1).toUpperCase() + entityType.substring(1));
r.setSubRelType("dedup");
DataInfo info = new DataInfo();

3
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
View File

@ -86,7 +86,8 @@ public class SparkPropagateRelation extends AbstractSparkAction {
mergedIds,
FieldType.TARGET,
getFixRelFn(FieldType.TARGET))
.filter(SparkPropagateRelation::containsDedup);
.filter(SparkPropagateRelation::containsDedup)
.distinct();
Dataset<Relation> updated = processDataset(
processDataset(rels, mergedIds, FieldType.SOURCE, getDeletedFn()),

24
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
View File

@ -18,6 +18,7 @@ import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
@ -29,6 +30,8 @@ import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -420,7 +423,7 @@ public class SparkDedupTest implements Serializable {
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
assertEquals(5022, relations);
assertEquals(4975, relations);
// check deletedbyinference
final Dataset<Relation> mergeRels = spark
@ -450,6 +453,25 @@ public class SparkDedupTest implements Serializable {
assertEquals(updated, deletedbyinference);
}
@Test
@Order(6)
public void testRelations() throws Exception {
testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_1.json", 12, 10);
testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2);
}
private void testUniqueness(String path, int expected_total, int expected_unique) {
Dataset<Relation> rel = spark
.read()
.textFile(getClass().getResource(path).getPath())
.map(
(MapFunction<String, Relation>) s -> new ObjectMapper().readValue(s, Relation.class),
Encoders.bean(Relation.class));
assertEquals(expected_total, rel.count());
assertEquals(expected_unique, rel.distinct().count());
}
@AfterAll
public static void finalCleanUp() throws IOException {
FileUtils.deleteDirectory(new File(testOutputBasePath));

12
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/test/relation_1.json Normal file
View File

@ -0,0 +1,12 @@
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|doajarticles::40c7b1dfa18c3693d374dafd21ef852f","subRelType":"provision","target":"10|doajarticles::618df40624078491acfd93ca3ff6921c"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|doajarticles::0b4e756a73338f60b84de98d080f6422","subRelType":"provision","target":"10|doajarticles::6d01e689db13b6977b411f4170b6143b"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|doajarticles::fe2f7c9d350b9c5aa658ec384d761e33","subRelType":"provision","target":"10|doajarticles::9b8a956b0703854ba79e52ddf7dc552e"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|doajarticles::a116734108ba011ef715b012f095e3f5","subRelType":"provision","target":"10|doajarticles::c5de04b1a35da2cc4468e299bc9ffa16"}
{"collectedfrom":[{"key":"10|openaire____::47ce9e9f4fad46e732cff06419ecaabb","value":"OpenDOAR"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|opendoar____::8b83abbbcad5496fe43cda88d0045aa4","subRelType":"provision","target":"10|opendoar____::6855456e2fe46a9d49d3d3af4f57443d"}
{"collectedfrom":[{"key":"10|openaire____::47ce9e9f4fad46e732cff06419ecaabb","value":"OpenDOAR"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|opendoar____::88034de0247d9d36e22783e9319c5ba3","subRelType":"provision","target":"10|opendoar____::c17028c9b6e0c5deaad29665d582284a"}
{"collectedfrom":[{"key":"10|openaire____::47ce9e9f4fad46e732cff06419ecaabb","value":"OpenDOAR"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|opendoar____::dfb21c796f33e9acf505cc960a3d8d2c","subRelType":"provision","target":"10|opendoar____::dfa037a53e121ecc9e0926800c3e814e"}
{"collectedfrom":[{"key":"10|openaire____::21f8a223b9925c2f87c404096080b046","value":"Registry of Research Data Repository"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|re3data_____::b526b1aa1562038881a31be59896985f","subRelType":"provision","target":"10|re3data_____::2e457773b62df3534cc04441bf406a70"}
{"collectedfrom":[{"key":"10|openaire____::21f8a223b9925c2f87c404096080b046","value":"Registry of Research Data Repository"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|re3data_____::6b306183bc051b5aaa5376f2fab6e6e5","subRelType":"provision","target":"10|re3data_____::6371ff9ee1ec7073416cb83c868b10a3"}
{"collectedfrom":[{"key":"10|openaire____::21f8a223b9925c2f87c404096080b046","value":"Registry of Research Data Repository"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|re3data_____::0f697c2543a43bc0da793bf78ecd4996","subRelType":"provision","target":"10|re3data_____::770ef1f8eb03f174c0add746523c6f28"}
{"collectedfrom":[{"key":"10|openaire____::21f8a223b9925c2f87c404096080b046","value":"Registry of Research Data Repository"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|re3data_____::0f697c2543a43bc0da793bf78ecd4996","subRelType":"provision","target":"10|re3data_____::770ef1f8eb03f174c0add746523c6f28"}
{"collectedfrom":[{"key":"10|openaire____::21f8a223b9925c2f87c404096080b046","value":"Registry of Research Data Repository"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"provides","relType":"datasourceOrganization","source":"20|re3data_____::0f697c2543a43bc0da793bf78ecd4996","subRelType":"provision","target":"10|re3data_____::770ef1f8eb03f174c0add746523c6f28"}

10
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/test/relation_2.json Normal file
View File

@ -0,0 +1,10 @@
{"collectedfrom":null,"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null},"lastupdatetimestamp":null,"relClass":"isMergedIn","relType":"resultResult","source":"50|dedup_wf_001::498c4e6cfff198831b488a6c62221241","subRelType":"dedup","target":"50|doiboost____::8e5e14d80d0f2ebe6a6a55d972681628"}
{"collectedfrom":null,"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null},"lastupdatetimestamp":null,"relClass":"isMergedIn","relType":"resultResult","source":"50|dedup_wf_001::498c4e6cfff198831b488a6c62221241","subRelType":"dedup","target":"50|doiboost____::8e5e14d80d0f2ebe6a6a55d972681628"}
{"collectedfrom":null,"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null},"lastupdatetimestamp":null,"relClass":"isMergedIn","relType":"resultResult","source":"50|dedup_wf_001::498c4e6cfff198831b488a6c62221241","subRelType":"dedup","target":"50|doiboost____::8e5e14d80d0f2ebe6a6a55d972681628"}
{"collectedfrom":null,"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null},"lastupdatetimestamp":null,"relClass":"isMergedIn","relType":"resultResult","source":"50|dedup_wf_001::498c4e6cfff198831b488a6c62221241","subRelType":"dedup","target":"50|doiboost____::8e5e14d80d0f2ebe6a6a55d972681628"}
{"collectedfrom":null,"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null},"lastupdatetimestamp":null,"relClass":"isMergedIn","relType":"resultResult","source":"50|dedup_wf_001::498c4e6cfff198831b488a6c62221241","subRelType":"dedup","target":"50|doiboost____::8e5e14d80d0f2ebe6a6a55d972681628"}
{"collectedfrom":null,"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null},"lastupdatetimestamp":null,"relClass":"isMergedIn","relType":"resultResult","source":"50|dedup_wf_001::498c4e6cfff198831b488a6c62221241","subRelType":"dedup","target":"50|doiboost____::8e5e14d80d0f2ebe6a6a55d972681628"}
{"collectedfrom":null,"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null},"lastupdatetimestamp":null,"relClass":"isMergedIn","relType":"resultResult","source":"50|dedup_wf_001::498c4e6cfff198831b488a6c62221241","subRelType":"dedup","target":"50|doiboost____::8e5e14d80d0f2ebe6a6a55d972681628"}
{"collectedfrom":null,"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null},"lastupdatetimestamp":null,"relClass":"isMergedIn","relType":"resultResult","source":"50|dedup_wf_001::498c4e6cfff198831b488a6c62221241","subRelType":"dedup","target":"50|doiboost____::8e5e14d80d0f2ebe6a6a55d972681628"}
{"collectedfrom":null,"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null},"lastupdatetimestamp":null,"relClass":"isMergedIn","relType":"resultResult","source":"50|dedup_wf_001::498c4e6cfff198831b488a6c62221241","subRelType":"dedup","target":"50|doiboost____::8e5e14d80d0f2ebe6a6a55d972681628"}
{"collectedfrom":null,"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null},"lastupdatetimestamp":null,"relClass":"isMergedIn","relType":"resultResult","source":"50|dedup_wf_001::498c4e6cfff198831b488a6c62221241","subRelType":"dedup","target":"50|doiboost____::8e5e14d80d0f2ebe6a6a55d972681629"}

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>1.1.7-SNAPSHOT</version>
<version>1.2.0-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>1.1.7-SNAPSHOT</version>
<version>1.2.0-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>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

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

@ -5,10 +5,8 @@ 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.schema.common.ModelConstants.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
@ -115,12 +113,17 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
.setProcessingchargecurrency(
field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
for (final Object o : doc.selectNodes("//dc:identifier")) {
final String url = ((Node) o).getText().trim();
if (url.startsWith("http")) {
instance.setUrl(Arrays.asList(url));
}
}
List<Node> nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier"));
instance
.setUrl(
nodes
.stream()
.filter(n -> StringUtils.isNotBlank(n.getText()))
.map(n -> n.getText().trim())
.filter(u -> u.startsWith("http"))
.distinct()
.collect(Collectors.toCollection(ArrayList::new)));
return Lists.newArrayList(instance);
}

15
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
View File

@ -6,10 +6,7 @@ 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.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.*;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
@ -80,6 +77,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
final KeyValue hostedby) {
final Instance instance = new Instance();
final Set<String> url = new HashSet<>();
instance.setUrl(new ArrayList<>());
instance
.setInstancetype(
@ -100,17 +98,18 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
instance.getUrl().add(((Node) o).getText().trim());
url.add(((Node) o).getText().trim());
}
for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='URL']")) {
instance.getUrl().add(((Node) o).getText().trim());
url.add(((Node) o).getText().trim());
}
for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='DOI']")) {
instance.getUrl().add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim());
url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim());
}
for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='DOI']")) {
instance.getUrl().add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim());
url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim());
}
instance.getUrl().addAll(url);
return Arrays.asList(instance);
}

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

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

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

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

3
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
View File

@ -405,6 +405,9 @@
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.speculation=false
--conf spark.hadoop.mapreduce.map.speculative=false
--conf spark.hadoop.mapreduce.reduce.speculative=false
</spark-opts>
<arg>--inputPath</arg><arg>${workingDir}/xml</arg>
<arg>--isLookupUrl</arg> <arg>${isLookupUrl}</arg>

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

@ -5,7 +5,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.7-SNAPSHOT</version>
<version>1.1.8-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

10
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml
View File

@ -27,14 +27,8 @@
<action name="reset_outputpath">
<fs>
<delete path="${outputPath}/relation"/>
<delete path="${outputPath}/dataset"/>
<delete path="${outputPath}/software"/>
<delete path="${outputPath}/publication"/>
<delete path="${outputPath}/otherresearchproduct"/>
<delete path="${outputPath}/project"/>
<delete path="${outputPath}/organization"/>
<delete path="${outputPath}/datasource"/>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<error to="Kill"/>

192
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml
View File

@ -1,37 +1,29 @@
<workflow-app name="orcid_to_result_from_semrel_propagation" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>allowedsemrels</name>
<description>the semantic relationships allowed for propagation</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
</parameters>
<start to="reset-outputpath"/>
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>allowedsemrels</name>
<description>the semantic relationships allowed for propagation</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
</parameters>
<start to="reset_outputpath"/>
<!-- <start to="fork_prepare_assoc_step1"/>-->
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset-outputpath">
<action name="reset_outputpath">
<fs>
<delete path='${workingDir}/preparedInfo'/>
<delete path='${outputPath}/relation'/>
<delete path='${outputPath}/dataset'/>
<delete path='${outputPath}/software'/>
<delete path='${outputPath}/publication'/>
<delete path='${outputPath}/otherresearchproduct'/>
<delete path='${outputPath}/project'/>
<delete path='${outputPath}/organization'/>
<delete path='${outputPath}/datasource'/>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<error to="Kill"/>
@ -119,11 +111,16 @@
--conf spark.hadoop.mapreduce.map.speculative=false
--conf spark.hadoop.mapreduce.reduce.speculative=false
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
<arg>--sourcePath</arg>
<arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg>
<arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg>
<arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg>
<arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg>
<arg>${allowedsemrels}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
@ -147,11 +144,16 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
<arg>--sourcePath</arg>
<arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg>
<arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg>
<arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg>
<arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg>
<arg>${allowedsemrels}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
@ -175,11 +177,16 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
<arg>--sourcePath</arg>
<arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg>
<arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg>
<arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg>
<arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg>
<arg>${allowedsemrels}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
@ -203,11 +210,16 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
<arg>--sourcePath</arg>
<arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg>
<arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg>
<arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg>
<arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg>
<arg>${allowedsemrels}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
@ -233,11 +245,13 @@
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg>
<arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
<arg>--outputPath</arg>
<arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
</spark>
<ok to="fork-join-exec-propagation"/>
<!-- <ok to="End"/>-->
<!-- <ok to="End"/>-->
<error to="Kill"/>
</action>
@ -270,12 +284,18 @@
--conf spark.hadoop.mapreduce.reduce.speculative=false
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--possibleUpdatesPath</arg>
<arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg>
<arg>${sourcePath}/publication</arg>
<arg>--hive_metastore_uris</arg>
<arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg>
<arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg>
<arg>${outputPath}/publication</arg>
<arg>--saveGraph</arg>
<arg>${saveGraph}</arg>
</spark>
<ok to="wait2"/>
<error to="Kill"/>
@ -301,12 +321,18 @@
--conf spark.hadoop.mapreduce.map.speculative=false
--conf spark.hadoop.mapreduce.reduce.speculative=false
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--possibleUpdatesPath</arg>
<arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg>
<arg>${sourcePath}/dataset</arg>
<arg>--hive_metastore_uris</arg>
<arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg>
<arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg>
<arg>${outputPath}/dataset</arg>
<arg>--saveGraph</arg>
<arg>${saveGraph}</arg>
</spark>
<ok to="wait2"/>
<error to="Kill"/>
@ -332,12 +358,18 @@
--conf spark.hadoop.mapreduce.map.speculative=false
--conf spark.hadoop.mapreduce.reduce.speculative=false
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--possibleUpdatesPath</arg>
<arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg>
<arg>${sourcePath}/otherresearchproduct</arg>
<arg>--hive_metastore_uris</arg>
<arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg>
<arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg>
<arg>${outputPath}/otherresearchproduct</arg>
<arg>--saveGraph</arg>
<arg>${saveGraph}</arg>
</spark>
<ok to="wait2"/>
<error to="Kill"/>
@ -363,16 +395,22 @@
--conf spark.hadoop.mapreduce.map.speculative=false
--conf spark.hadoop.mapreduce.reduce.speculative=false
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--possibleUpdatesPath</arg>
<arg>${workingDir}/preparedInfo/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg>
<arg>${sourcePath}/software</arg>
<arg>--hive_metastore_uris</arg>
<arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg>
<arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg>
<arg>${outputPath}/software</arg>
<arg>--saveGraph</arg>
<arg>${saveGraph}</arg>
</spark>
<ok to="wait2"/>
<error to="Kill"/>
</action>
<join name="wait2" to="End"/>
<end name="End"/>
<end name="End"/>
</workflow-app>

19
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml
View File

@ -14,27 +14,21 @@
</property>
</parameters>
<start to="reset-outputpath"/>
<!-- <start to="apply_propagation"/>-->
<start to="reset_outputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset-outputpath">
<action name="reset_outputpath">
<fs>
<delete path='${workingDir}/preparedInfo'/>
<delete path='${outputPath}/relation'/>
<delete path='${outputPath}/dataset'/>
<delete path='${outputPath}/software'/>
<delete path='${outputPath}/publication'/>
<delete path='${outputPath}/otherresearchproduct'/>
<delete path='${outputPath}/project'/>
<delete path='${outputPath}/organization'/>
<delete path='${outputPath}/datasource'/>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<error to="Kill"/>
</action>
<fork name="copy_entities">
<path start="copy_relation"/>
<path start="copy_publication"/>
@ -190,4 +184,5 @@
</action>
<end name="End"/>
</workflow-app>

22
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml
View File

@ -14,23 +14,16 @@
</property>
</parameters>
<start to="reset-outputpath"/>
<start to="reset_outputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset-outputpath">
<action name="reset_outputpath">
<fs>
<delete path='${outputPath}/relation'/>
<delete path='${outputPath}/datasource'/>
<delete path='${outputPath}/organization'/>
<delete path='${outputPath}/project'/>
<delete path='${outputPath}/publication'/>
<delete path='${outputPath}/dataset'/>
<delete path='${outputPath}/software'/>
<delete path='${outputPath}/otherresearchproduct'/>
<delete path='${workingDir}/preparedInfo'/>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<error to="Kill"/>
@ -64,6 +57,7 @@
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<action name="copy_projects">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
@ -85,6 +79,7 @@
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<join name="copy_wait" to="prepare_result_communitylist"/>
<action name="prepare_result_communitylist">
@ -111,7 +106,6 @@
<arg>--organizationtoresultcommunitymap</arg><arg>${organizationtoresultcommunitymap}</arg>
</spark>
<ok to="fork-join-exec-propagation"/>
<!-- <ok to="End"/>-->
<error to="Kill"/>
</action>
@ -150,6 +144,7 @@
<ok to="wait2"/>
<error to="Kill"/>
</action>
<action name="join_propagate_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -178,6 +173,7 @@
<ok to="wait2"/>
<error to="Kill"/>
</action>
<action name="join_propagate_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -206,6 +202,7 @@
<ok to="wait2"/>
<error to="Kill"/>
</action>
<action name="join_propagate_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -238,4 +235,5 @@
<join name="wait2" to="End"/>
<end name="End"/>
</workflow-app>

107
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/oozie_app/workflow.xml
View File

@ -1,43 +1,38 @@
<workflow-app name="result_to_community_from_semrel_propagation" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>allowedsemrels</name>
<description>the semantic relationships allowed for propagation</description>
</property>
<property>
<name>isLookUpUrl</name>
<description>the isLookup service endpoint</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
</parameters>
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>allowedsemrels</name>
<description>the semantic relationships allowed for propagation</description>
</property>
<property>
<name>isLookUpUrl</name>
<description>the isLookup service endpoint</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
</parameters>
<start to="reset-outputpath"/>
<start to="reset_outputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset-outputpath">
<action name="reset_outputpath">
<fs>
<delete path='${outputPath}/relation'/>
<delete path='${outputPath}/datasource'/>
<delete path='${outputPath}/organization'/>
<delete path='${outputPath}/project'/>
<delete path='${outputPath}/publication'/>
<delete path='${outputPath}/dataset'/>
<delete path='${outputPath}/software'/>
<delete path='${outputPath}/otherresearchproduct'/>
<delete path='${workingDir}/preparedInfo'/>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<error to="Kill"/>
</action>
<fork name="copy_entities">
<path start="copy_relation"/>
<path start="copy_organization"/>
@ -126,6 +121,7 @@
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_prepare_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -182,6 +178,7 @@
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_prepare_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -214,29 +211,29 @@
<join name="wait" to="prepare_assoc_step2"/>
<action name="prepare_assoc_step2">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ResultToCommunityEmRelPropagation-PreparePhase2</name>
<class>eu.dnetlib.dhp.resulttocommunityfromsemrel.PrepareResultCommunitySetStep2</class>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${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}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/preparedInfo/targetCommunityAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/mergedCommunityAssoc</arg>
</spark>
<ok to="fork-join-exec-propagation"/>
<!-- <ok to="End"/>-->
<error to="Kill"/>
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ResultToCommunityEmRelPropagation-PreparePhase2</name>
<class>eu.dnetlib.dhp.resulttocommunityfromsemrel.PrepareResultCommunitySetStep2</class>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${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}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/preparedInfo/targetCommunityAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/mergedCommunityAssoc</arg>
</spark>
<ok to="fork-join-exec-propagation"/>
<!-- <ok to="End"/>-->
<error to="Kill"/>
</action>
@ -275,6 +272,7 @@
<ok to="wait2"/>
<error to="Kill"/>
</action>
<action name="join_propagate_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -303,6 +301,7 @@
<ok to="wait2"/>
<error to="Kill"/>
</action>
<action name="join_propagate_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -331,6 +330,7 @@
<ok to="wait2"/>
<error to="Kill"/>
</action>
<action name="join_propagate_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -362,5 +362,6 @@
<join name="wait2" to="End"/>
<end name="End"/>
<end name="End"/>
</workflow-app>

50
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml
View File

@ -1,32 +1,25 @@
<workflow-app name="affiliation_from_instrepo_propagation" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>outputPath</name>
<description>sets the outputPath</description>
</property>
</parameters>
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>outputPath</name>
<description>sets the outputPath</description>
</property>
</parameters>
<start to="reset-outputpath"/>
<!--<start to="prepare_result_organization_association"/>-->
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<start to="reset_outputpath"/>
<action name="reset-outputpath">
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset_outputpath">
<fs>
<delete path='${outputPath}/relation'/>
<delete path='${outputPath}/datasource'/>
<delete path='${outputPath}/organization'/>
<delete path='${outputPath}/project'/>
<delete path='${outputPath}/publication'/>
<delete path='${outputPath}/dataset'/>
<delete path='${outputPath}/software'/>
<delete path='${outputPath}/otherresearchproduct'/>
<delete path='${workingDir}/preparedInfo'/>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<error to="Kill"/>
@ -53,6 +46,7 @@
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_publication">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
@ -85,6 +79,7 @@
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_software">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
@ -95,6 +90,7 @@
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="copy_organization">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
@ -151,9 +147,9 @@
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
</spark>
<ok to="fork_join_apply_resulttoorganization_propagation"/>
<!-- <ok to="End"/>-->
<error to="Kill"/>
</action>
<fork name="fork_join_apply_resulttoorganization_propagation">
<path start="join_propagation_publication"/>
<path start="join_propagation_dataset"/>
@ -220,6 +216,7 @@
<ok to="wait2"/>
<error to="Kill"/>
</action>
<action name="join_propagation_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -281,6 +278,7 @@
</action>
<join name="wait2" to="End"/>
<end name="End"/>
</workflow-app>

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

@ -3,7 +3,7 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-stats-update</artifactId>

2
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9_6.sql
View File

@ -1,2 +1,2 @@
DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages;
CREATE TABLE ${stats_db_name}.datasource_languages AS SELECT substr(d.id, 4) as id, langs.languages as language from openaire.datasource d LATERAL VIEW explode(d.odlanguages.value) langs as languages;
CREATE TABLE ${stats_db_name}.datasource_languages AS SELECT substr(d.id, 4) as id, langs.languages as language from ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs as languages;

6
dhp-workflows/dhp-worfklow-profiles/pom.xml
View File

@ -1,11 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

2
dhp-workflows/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>

2
pom.xml
View File

@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.1.7-SNAPSHOT</version>
<version>1.2.0-SNAPSHOT</version>
<packaging>pom</packaging>
<licenses>