merge upstream

This commit is contained in:
Miriam Baglioni 2020-07-16 18:49:38 +02:00
commit 44e1c40c42
44 changed files with 1365 additions and 215 deletions

View File

@ -59,7 +59,6 @@
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dnet-openaire-broker-common</artifactId>
<version>[3.0.0,)</version>
</dependency>
</dependencies>

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@ -11,6 +11,8 @@ import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DateUtils;
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
import eu.dnetlib.dhp.broker.oa.util.BrokerConstants;
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
public class EventFactory {
@ -52,9 +54,11 @@ public class EventFactory {
final OaBrokerMainEntity source = updateInfo.getSource();
final OaBrokerMainEntity target = updateInfo.getTarget();
map.setTargetDatasourceId(target.getCollectedFromId());
map.setTargetDatasourceName(target.getCollectedFromName());
map.setTargetDatasourceType(target.getCollectedFromType());
final OaBrokerRelatedDatasource targetDs = updateInfo.getTargetDs();
map.setTargetDatasourceId(targetDs.getOpenaireId());
map.setTargetDatasourceName(targetDs.getName());
map.setTargetDatasourceType(targetDs.getType());
map.setTargetResultId(target.getOpenaireId());
@ -73,11 +77,19 @@ public class EventFactory {
// PROVENANCE INFO
map.setTrust(updateInfo.getTrust());
map.setProvenanceDatasourceId(source.getCollectedFromId());
map.setProvenanceDatasourceName(source.getCollectedFromName());
map.setProvenanceDatasourceType(source.getCollectedFromType());
map.setProvenanceResultId(source.getOpenaireId());
source
.getDatasources()
.stream()
.filter(ds -> ds.getRelType().equals(BrokerConstants.COLLECTED_FROM_REL))
.findFirst()
.ifPresent(ds -> {
map.setProvenanceDatasourceId(ds.getOpenaireId());
map.setProvenanceDatasourceName(ds.getName());
map.setProvenanceDatasourceType(ds.getType());
});
return map;
}

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@ -17,8 +17,8 @@ import org.slf4j.LoggerFactory;
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.AddDatasourceTypeAggregator;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.SimpleDatasourceInfo;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDatasource;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDatasourceAggregator;
import scala.Tuple2;
public class JoinStep0Job {
@ -45,33 +45,33 @@ public class JoinStep0Job {
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String outputPath = workingPath + "/joinedEntities_step0";
log.info("outputPath: {}", outputPath);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step0";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
ClusterUtils.removeDir(spark, outputPath);
ClusterUtils.removeDir(spark, joinedEntitiesPath);
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/simpleEntities", OaBrokerMainEntity.class);
final Dataset<SimpleDatasourceInfo> datasources = ClusterUtils
.readPath(spark, workingPath + "/datasources", SimpleDatasourceInfo.class);
final Dataset<RelatedDatasource> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedDatasources", RelatedDatasource.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, SimpleDatasourceInfo>, OaBrokerMainEntity> aggr = new AddDatasourceTypeAggregator()
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedDatasource>, OaBrokerMainEntity> aggr = new RelatedDatasourceAggregator()
.toColumn();
final Dataset<OaBrokerMainEntity> dataset = sources
.joinWith(datasources, sources.col("collectedFromId").equalTo(datasources.col("id")), "inner")
.joinWith(typedRels, sources.col("openaireId").equalTo(typedRels.col("source")), "left_outer")
.groupByKey(t -> t._1.getOpenaireId(), Encoders.STRING())
.agg(aggr)
.map(t -> t._2, Encoders.bean(OaBrokerMainEntity.class));
ClusterUtils.save(dataset, outputPath, OaBrokerMainEntity.class, total);
ClusterUtils.save(dataset, joinedEntitiesPath, OaBrokerMainEntity.class, total);
});

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@ -9,14 +9,23 @@ import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.util.LongAccumulator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.SimpleDatasourceInfo;
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
import eu.dnetlib.dhp.broker.oa.util.DatasourceRelationsAccumulator;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDatasource;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import scala.Tuple3;
public class PrepareRelatedDatasourcesJob {
@ -42,7 +51,7 @@ public class PrepareRelatedDatasourcesJob {
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String relsPath = workingPath + "/datasources";
final String relsPath = workingPath + "/relatedDatasources";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -53,16 +62,46 @@ public class PrepareRelatedDatasourcesJob {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_datasources");
final Dataset<SimpleDatasourceInfo> dataset = ClusterUtils
.readPath(spark, graphPath + "/datasource", Datasource.class)
.map(
ds -> new SimpleDatasourceInfo(ds.getId(), ds.getDatasourcetype().getClassid()),
Encoders.bean(SimpleDatasourceInfo.class));
final Dataset<Tuple3<String, String, String>> rels = prepareResultTuples(
spark, graphPath, Publication.class)
.union(prepareResultTuples(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class))
.union(prepareResultTuples(spark, graphPath, Software.class))
.union(prepareResultTuples(spark, graphPath, OtherResearchProduct.class));
ClusterUtils.save(dataset, relsPath, SimpleDatasourceInfo.class, total);
final Dataset<OaBrokerRelatedDatasource> datasources = ClusterUtils
.readPath(spark, graphPath + "/datasource", Datasource.class)
.map(ConversionUtils::oafDatasourceToBrokerDatasource, Encoders.bean(OaBrokerRelatedDatasource.class));
final Dataset<RelatedDatasource> dataset = rels
.joinWith(datasources, datasources.col("openaireId").equalTo(rels.col("_2")), "inner")
.map(t -> {
final RelatedDatasource r = new RelatedDatasource();
r.setSource(t._1._1());
r.setRelDatasource(t._2);
r.getRelDatasource().setRelType(t._1._3());
return r;
}, Encoders.bean(RelatedDatasource.class));
ClusterUtils.save(dataset, relsPath, RelatedDatasource.class, total);
});
}
private static final Dataset<Tuple3<String, String, String>> prepareResultTuples(final SparkSession spark,
final String graphPath,
final Class<? extends Result> sourceClass) {
return ClusterUtils
.readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass)
.filter(r -> !ClusterUtils.isDedupRoot(r.getId()))
.filter(r -> r.getDataInfo().getDeletedbyinference())
.map(
r -> DatasourceRelationsAccumulator.calculateTuples(r),
Encoders.bean(DatasourceRelationsAccumulator.class))
.flatMap(
acc -> acc.getRels().iterator(),
Encoders.tuple(Encoders.STRING(), Encoders.STRING(), Encoders.STRING()));
}
}

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@ -15,6 +15,7 @@ import org.apache.commons.lang3.StringUtils;
import org.apache.spark.util.LongAccumulator;
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
@ -34,18 +35,19 @@ public abstract class UpdateMatcher<T> {
this.highlightToStringFunction = highlightToStringFunction;
}
public Collection<UpdateInfo<T>> searchUpdatesForRecord(final OaBrokerMainEntity res,
public Collection<UpdateInfo<T>> searchUpdatesForRecord(final OaBrokerMainEntity target,
final OaBrokerRelatedDatasource targetDs,
final Collection<OaBrokerMainEntity> others,
final Map<String, LongAccumulator> accumulators) {
final Map<String, UpdateInfo<T>> infoMap = new HashMap<>();
for (final OaBrokerMainEntity source : others) {
if (source != res) {
for (final T hl : findDifferences(source, res)) {
if (source != target) {
for (final T hl : findDifferences(source, target)) {
final Topic topic = getTopicFunction().apply(hl);
if (topic != null) {
final UpdateInfo<T> info = new UpdateInfo<>(topic, hl, source, res,
final UpdateInfo<T> info = new UpdateInfo<>(topic, hl, source, target, targetDs,
getCompileHighlightFunction(),
getHighlightToStringFunction());

View File

@ -14,6 +14,10 @@ public class BrokerConstants {
public static final String OPEN_ACCESS = "OPEN";
public static final String IS_MERGED_IN_CLASS = "isMergedIn";
public static final String COLLECTED_FROM_REL = "collectedFrom";
public static final String HOSTED_BY_REL = "hostedBy";
public static final float MIN_TRUST = 0.25f;
public static final float MAX_TRUST = 1.00f;

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@ -22,11 +22,13 @@ import eu.dnetlib.broker.objects.OaBrokerJournal;
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.broker.objects.OaBrokerProject;
import eu.dnetlib.broker.objects.OaBrokerRelatedDataset;
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
import eu.dnetlib.broker.objects.OaBrokerRelatedPublication;
import eu.dnetlib.broker.objects.OaBrokerRelatedSoftware;
import eu.dnetlib.broker.objects.OaBrokerTypedValue;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.ExternalReference;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Instance;
@ -119,8 +121,6 @@ public class ConversionUtils {
res
.setJournal(
result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null);
res.setCollectedFromId(mappedFirst(result.getCollectedfrom(), KeyValue::getKey));
res.setCollectedFromName(mappedFirst(result.getCollectedfrom(), KeyValue::getValue));
res.setPids(mappedList(result.getPid(), ConversionUtils::oafPidToBrokerPid));
res.setInstances(flatMappedList(result.getInstance(), ConversionUtils::oafInstanceToBrokerInstances));
res
@ -223,6 +223,18 @@ public class ConversionUtils {
return res;
}
public static final OaBrokerRelatedDatasource oafDatasourceToBrokerDatasource(final Datasource ds) {
if (ds == null) {
return null;
}
final OaBrokerRelatedDatasource res = new OaBrokerRelatedDatasource();
res.setName(StringUtils.defaultIfBlank(fieldValue(ds.getOfficialname()), fieldValue(ds.getEnglishname())));
res.setOpenaireId(ds.getId());
res.setType(classId(ds.getDatasourcetype()));
return res;
}
private static String first(final List<String> list) {
return list != null && list.size() > 0 ? list.get(0) : null;
}

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@ -0,0 +1,68 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.Result;
import scala.Tuple3;
public class DatasourceRelationsAccumulator implements Serializable {
/**
*
*/
private static final long serialVersionUID = 3256220670651218957L;
private List<Tuple3<String, String, String>> rels = new ArrayList<>();
public List<Tuple3<String, String, String>> getRels() {
return rels;
}
public void setRels(final List<Tuple3<String, String, String>> rels) {
this.rels = rels;
}
protected void addTuple(final Tuple3<String, String, String> t) {
rels.add(t);
}
public static final DatasourceRelationsAccumulator calculateTuples(final Result r) {
final Set<String> collectedFromSet = r
.getCollectedfrom()
.stream()
.map(kv -> kv.getKey())
.filter(StringUtils::isNotBlank)
.distinct()
.collect(Collectors.toSet());
final Set<String> hostedBySet = r
.getInstance()
.stream()
.map(i -> i.getHostedby())
.filter(Objects::nonNull)
.filter(kv -> !StringUtils.equalsIgnoreCase(kv.getValue(), "Unknown Repository"))
.map(kv -> kv.getKey())
.filter(StringUtils::isNotBlank)
.distinct()
.filter(id -> !collectedFromSet.contains(id))
.collect(Collectors.toSet());
final DatasourceRelationsAccumulator res = new DatasourceRelationsAccumulator();
collectedFromSet
.stream()
.map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.COLLECTED_FROM_REL))
.forEach(res::addTuple);
hostedBySet.stream().map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.HOSTED_BY_REL)).forEach(res::addTuple);
return res;
}
}

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@ -11,6 +11,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
import eu.dnetlib.dhp.broker.model.EventFactory;
import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher;
import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsReferencedBy;
@ -80,9 +81,11 @@ public class EventFinder {
final List<UpdateInfo<?>> list = new ArrayList<>();
for (final OaBrokerMainEntity target : results.getData()) {
if (verifyTarget(target, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) {
for (final UpdateMatcher<?> matcher : matchers) {
list.addAll(matcher.searchUpdatesForRecord(target, results.getData(), accumulators));
for (final OaBrokerRelatedDatasource targetDs : target.getDatasources()) {
if (verifyTarget(targetDs, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) {
for (final UpdateMatcher<?> matcher : matchers) {
list.addAll(matcher.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators));
}
}
}
}
@ -90,17 +93,17 @@ public class EventFinder {
return asEventGroup(list);
}
private static boolean verifyTarget(final OaBrokerMainEntity target,
private static boolean verifyTarget(final OaBrokerRelatedDatasource target,
final Set<String> dsIdWhitelist,
final Set<String> dsIdBlacklist,
final Set<String> dsTypeWhitelist) {
if (dsIdWhitelist.contains(target.getCollectedFromId())) {
if (dsIdWhitelist.contains(target.getOpenaireId())) {
return true;
} else if (dsIdBlacklist.contains(target.getCollectedFromId())) {
} else if (dsIdBlacklist.contains(target.getOpenaireId())) {
return false;
} else {
return dsTypeWhitelist.contains(target.getCollectedFromType());
return dsTypeWhitelist.contains(target.getType());
}
}

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@ -8,6 +8,7 @@ import eu.dnetlib.broker.objects.OaBrokerEventPayload;
import eu.dnetlib.broker.objects.OaBrokerInstance;
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.broker.objects.OaBrokerProvenance;
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
import eu.dnetlib.dhp.broker.model.Topic;
public final class UpdateInfo<T> {
@ -20,6 +21,8 @@ public final class UpdateInfo<T> {
private final OaBrokerMainEntity target;
private final OaBrokerRelatedDatasource targetDs;
private final BiConsumer<OaBrokerMainEntity, T> compileHighlight;
private final Function<T, String> highlightToString;
@ -28,12 +31,14 @@ public final class UpdateInfo<T> {
public UpdateInfo(final Topic topic, final T highlightValue, final OaBrokerMainEntity source,
final OaBrokerMainEntity target,
final OaBrokerRelatedDatasource targetDs,
final BiConsumer<OaBrokerMainEntity, T> compileHighlight,
final Function<T, String> highlightToString) {
this.topic = topic;
this.highlightValue = highlightValue;
this.source = source;
this.target = target;
this.targetDs = targetDs;
this.compileHighlight = compileHighlight;
this.highlightToString = highlightToString;
this.trust = TrustUtils.calculateTrust(source, target);
@ -51,6 +56,10 @@ public final class UpdateInfo<T> {
return target;
}
public OaBrokerRelatedDatasource getTargetDs() {
return targetDs;
}
protected Topic getTopic() {
return topic;
}
@ -75,8 +84,20 @@ public final class UpdateInfo<T> {
compileHighlight.accept(hl, getHighlightValue());
final String provId = getSource().getOpenaireId();
final String provRepo = getSource().getCollectedFromName();
final String provType = getSource().getCollectedFromType();
final String provRepo = getSource()
.getDatasources()
.stream()
.filter(ds -> ds.getRelType().equals(BrokerConstants.COLLECTED_FROM_REL))
.map(ds -> ds.getName())
.findFirst()
.orElse("");
final String provType = getSource()
.getDatasources()
.stream()
.filter(ds -> ds.getRelType().equals(BrokerConstants.COLLECTED_FROM_REL))
.map(ds -> ds.getType())
.findFirst()
.orElse("");
final String provUrl = getSource()
.getInstances()

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@ -0,0 +1,42 @@
package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels;
import java.io.Serializable;
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
public class RelatedDatasource implements Serializable {
/**
*
*/
private static final long serialVersionUID = 3015550240920424010L;
private String source;
private OaBrokerRelatedDatasource relDatasource;
public RelatedDatasource() {
}
public RelatedDatasource(final String source, final OaBrokerRelatedDatasource relDatasource) {
this.source = source;
this.relDatasource = relDatasource;
}
public String getSource() {
return source;
}
public void setSource(final String source) {
this.source = source;
}
public OaBrokerRelatedDatasource getRelDatasource() {
return relDatasource;
}
public void setRelDatasource(final OaBrokerRelatedDatasource relDatasource) {
this.relDatasource = relDatasource;
}
}

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@ -7,15 +7,16 @@ import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.expressions.Aggregator;
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.dhp.broker.oa.util.BrokerConstants;
import scala.Tuple2;
public class AddDatasourceTypeAggregator
extends Aggregator<Tuple2<OaBrokerMainEntity, SimpleDatasourceInfo>, OaBrokerMainEntity, OaBrokerMainEntity> {
public class RelatedDatasourceAggregator
extends Aggregator<Tuple2<OaBrokerMainEntity, RelatedDatasource>, OaBrokerMainEntity, OaBrokerMainEntity> {
/**
*
*/
private static final long serialVersionUID = 8788588975496014728L;
private static final long serialVersionUID = -7212121913834713672L;
@Override
public OaBrokerMainEntity zero() {
@ -29,10 +30,10 @@ public class AddDatasourceTypeAggregator
@Override
public OaBrokerMainEntity reduce(final OaBrokerMainEntity g,
final Tuple2<OaBrokerMainEntity, SimpleDatasourceInfo> t) {
final Tuple2<OaBrokerMainEntity, RelatedDatasource> t) {
final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOpenaireId()) ? g : t._1;
if (t._2 != null && StringUtils.isNotBlank(t._2.getType())) {
res.setCollectedFromType(t._2.getType());
if (t._2 != null && res.getDatasources().size() < BrokerConstants.MAX_NUMBER_OF_RELS) {
res.getDatasources().add(t._2.getRelDatasource());
}
return res;
@ -40,7 +41,15 @@ public class AddDatasourceTypeAggregator
@Override
public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) {
if (StringUtils.isNotBlank(g1.getOpenaireId()) && StringUtils.isNotBlank(g1.getCollectedFromType())) {
if (StringUtils.isNotBlank(g1.getOpenaireId())) {
final int availables = BrokerConstants.MAX_NUMBER_OF_RELS - g1.getDatasources().size();
if (availables > 0) {
if (g2.getDatasources().size() <= availables) {
g1.getDatasources().addAll(g2.getDatasources());
} else {
g1.getDatasources().addAll(g2.getDatasources().subList(0, availables));
}
}
return g1;
} else {
return g2;
@ -56,4 +65,5 @@ public class AddDatasourceTypeAggregator
public Encoder<OaBrokerMainEntity> outputEncoder() {
return Encoders.bean(OaBrokerMainEntity.class);
}
}

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@ -1,40 +0,0 @@
package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels;
import java.io.Serializable;
public class SimpleDatasourceInfo implements Serializable {
/**
*
*/
private static final long serialVersionUID = 2996609859416024734L;
private String id;
private String type;
public SimpleDatasourceInfo() {
}
public SimpleDatasourceInfo(final String id, final String type) {
this.id = id;
this.type = type;
}
public String getId() {
return id;
}
public void setId(final String id) {
this.id = id;
}
public String getType() {
return type;
}
public void setType(final String type) {
this.type = type;
}
}

View File

@ -448,6 +448,30 @@
<arg>--index</arg><arg>${esIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
</spark>
<ok to="stats"/>
<error to="Kill"/>
</action>
<action name="stats">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>GenerateStatsJob</name>
<class>eu.dnetlib.dhp.broker.oa.GenerateStatsJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${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}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>

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@ -64,14 +64,209 @@
</configuration>
</global>
<start to="stats"/>
<start to="join_entities_step0"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="join_entities_step0">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>JoinStep0</name>
<class>eu.dnetlib.dhp.broker.oa.JoinStep0Job</class>
<jar>dhp-broker-events-${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=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="join_entities_step1"/>
<error to="Kill"/>
</action>
<action name="join_entities_step1">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>JoinStep1</name>
<class>eu.dnetlib.dhp.broker.oa.JoinStep1Job</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${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}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="join_entities_step2"/>
<error to="Kill"/>
</action>
<action name="join_entities_step2">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>JoinStep2</name>
<class>eu.dnetlib.dhp.broker.oa.JoinStep2Job</class>
<jar>dhp-broker-events-${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=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="join_entities_step3"/>
<error to="Kill"/>
</action>
<action name="join_entities_step3">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>JoinStep3</name>
<class>eu.dnetlib.dhp.broker.oa.JoinStep3Job</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${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}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="join_entities_step4"/>
<error to="Kill"/>
</action>
<action name="join_entities_step4">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>JoinStep4</name>
<class>eu.dnetlib.dhp.broker.oa.JoinStep4Job</class>
<jar>dhp-broker-events-${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=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="prepare_groups"/>
<error to="Kill"/>
</action>
<action name="stats">
<action name="prepare_groups">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>PrepareGroupsJob</name>
<class>eu.dnetlib.dhp.broker.oa.PrepareGroupsJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${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}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="generate_events"/>
<error to="Kill"/>
</action>
<action name="generate_events">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>GenerateEventsJob</name>
<class>eu.dnetlib.dhp.broker.oa.GenerateEventsJob</class>
<jar>dhp-broker-events-${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=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--datasourceIdWhitelist</arg><arg>${datasourceIdWhitelist}</arg>
<arg>--datasourceTypeWhitelist</arg><arg>${datasourceTypeWhitelist}</arg>
<arg>--datasourceIdBlacklist</arg><arg>${datasourceIdBlacklist}</arg>
</spark>
<ok to="index_es"/>
<error to="Kill"/>
</action>
<action name="index_es">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>IndexOnESJob</name>
<class>eu.dnetlib.dhp.broker.oa.IndexOnESJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.dynamicAllocation.maxExecutors="8"
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--index</arg><arg>${esIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
</spark>
<ok to="stats"/>
<error to="Kill"/>
</action>
<action name="stats">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>

View File

@ -8,15 +8,23 @@ import java.util.Collection;
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 eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPublicationDate;
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
@ExtendWith(MockitoExtension.class)
class UpdateMatcherTest {
UpdateMatcher<String> matcher = new EnrichMissingPublicationDate();
@Mock
private OaBrokerRelatedDatasource targetDs;
@BeforeEach
void setUp() throws Exception {
}
@ -30,7 +38,7 @@ class UpdateMatcherTest {
final OaBrokerMainEntity p4 = new OaBrokerMainEntity();
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.isEmpty());
}
@ -46,7 +54,7 @@ class UpdateMatcherTest {
res.setPublicationdate("2018");
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.isEmpty());
}
@ -62,7 +70,7 @@ class UpdateMatcherTest {
p2.setPublicationdate("2018");
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.size() == 1);
}
@ -79,7 +87,7 @@ class UpdateMatcherTest {
p2.setPublicationdate("2018");
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.isEmpty());
}
@ -98,7 +106,7 @@ class UpdateMatcherTest {
p4.setPublicationdate("2018");
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.isEmpty());
}
@ -117,7 +125,7 @@ class UpdateMatcherTest {
p4.setPublicationdate("2018");
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.size() == 1);
}

View File

@ -28,6 +28,8 @@ import eu.dnetlib.pace.config.DedupConfig;
abstract class AbstractSparkAction implements Serializable {
protected static final int NUM_PARTITIONS = 1000;
protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);

View File

@ -100,6 +100,11 @@ public class DedupUtility {
return String.format("%s/%s/%s_mergerel", basePath, actionSetId, entityType);
}
public static String createBlockStatsPath(
final String basePath, final String actionSetId, final String entityType) {
return String.format("%s/%s/%s_blockstats", basePath, actionSetId, entityType);
}
public static List<DedupConfig> getConfigurations(String isLookUpUrl, String orchestrator)
throws ISLookUpException, DocumentException {
final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookUpUrl);

View File

@ -52,6 +52,7 @@ public class Deduper implements Serializable {
.collect(Collectors.toList())
.iterator())
.mapToPair(block -> new Tuple2<>(block.getKey(), block))
.reduceByKey((b1, b2) -> Block.from(b1, b2, of, maxQueueSize));
.reduceByKey((b1, b2) -> Block.from(b1, b2, of, maxQueueSize))
.filter(b -> b._2().getDocuments().size() > 1);
}
}

View File

@ -0,0 +1,57 @@
package eu.dnetlib.dhp.oa.dedup;
import java.util.Objects;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.expressions.Aggregator;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class RelationAggregator extends Aggregator<Relation, Relation, Relation> {
private static Relation ZERO = new Relation();
@Override
public Relation zero() {
return ZERO;
}
@Override
public Relation reduce(Relation b, Relation a) {
return mergeRel(b, a);
}
@Override
public Relation merge(Relation b, Relation a) {
return mergeRel(b, a);
}
@Override
public Relation finish(Relation r) {
return r;
}
private Relation mergeRel(Relation b, Relation a) {
if (Objects.equals(b, ZERO)) {
return a;
}
if (Objects.equals(a, ZERO)) {
return b;
}
b.mergeFrom(a);
return b;
}
@Override
public Encoder<Relation> bufferEncoder() {
return Encoders.kryo(Relation.class);
}
@Override
public Encoder<Relation> outputEncoder() {
return Encoders.kryo(Relation.class);
}
}

View File

@ -0,0 +1,126 @@
package eu.dnetlib.dhp.oa.dedup;
import java.io.IOException;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
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.FilterFunction;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.dedup.model.Block;
import eu.dnetlib.dhp.oa.dedup.model.BlockStats;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
public class SparkBlockStats extends AbstractSparkAction {
private static final Logger log = LoggerFactory.getLogger(SparkBlockStats.class);
public SparkBlockStats(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
}
public static void main(String[] args) throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkBlockStats.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/createBlockStats_parameters.json")));
parser.parseArgument(args);
SparkConf conf = new SparkConf();
new SparkBlockStats(parser, getSparkSession(conf))
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
}
public Long computeComparisons(Long blockSize, Long slidingWindowSize) {
if (slidingWindowSize >= blockSize)
return (slidingWindowSize * (slidingWindowSize - 1)) / 2;
else {
return (blockSize - slidingWindowSize + 1) * (slidingWindowSize * (slidingWindowSize - 1)) / 2;
}
}
@Override
public void run(ISLookUpService isLookUpService)
throws DocumentException, IOException, ISLookUpException {
// read oozie parameters
final String graphBasePath = parser.get("graphBasePath");
final String isLookUpUrl = parser.get("isLookUpUrl");
final String actionSetId = parser.get("actionSetId");
final String workingPath = parser.get("workingPath");
final int numPartitions = Optional
.ofNullable(parser.get("numPartitions"))
.map(Integer::valueOf)
.orElse(NUM_PARTITIONS);
log.info("graphBasePath: '{}'", graphBasePath);
log.info("isLookUpUrl: '{}'", isLookUpUrl);
log.info("actionSetId: '{}'", actionSetId);
log.info("workingPath: '{}'", workingPath);
// for each dedup configuration
for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
final String subEntity = dedupConf.getWf().getSubEntityValue();
log.info("Creating blockstats for: '{}'", subEntity);
final String outputPath = DedupUtility.createBlockStatsPath(workingPath, actionSetId, subEntity);
removeOutputDir(spark, outputPath);
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaPairRDD<String, MapDocument> mapDocuments = sc
.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
.repartition(numPartitions)
.mapToPair(
(PairFunction<String, String, MapDocument>) s -> {
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
return new Tuple2<>(d.getIdentifier(), d);
});
// create blocks for deduplication
JavaRDD<BlockStats> blockStats = Deduper
.createSortedBlocks(mapDocuments, dedupConf)
.repartition(numPartitions)
.map(b -> asBlockStats(dedupConf, b));
// save the blockstats in the workingdir
spark
.createDataset(blockStats.rdd(), Encoders.bean(BlockStats.class))
.write()
.mode(SaveMode.Overwrite)
.save(outputPath);
}
}
private BlockStats asBlockStats(DedupConfig dedupConf, Tuple2<String, Block> b) {
return new BlockStats(
b._1(),
(long) b._2().getDocuments().size(),
computeComparisons(
(long) b._2().getDocuments().size(), (long) dedupConf.getWf().getSlidingWindowSize()));
}
}

View File

@ -5,11 +5,13 @@ import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
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.graphx.Edge;
import org.apache.spark.rdd.RDD;
@ -75,7 +77,11 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
final String workingPath = parser.get("workingPath");
final String isLookUpUrl = parser.get("isLookUpUrl");
final String actionSetId = parser.get("actionSetId");
int cut = Optional
.ofNullable(parser.get("cutConnectedComponent"))
.map(Integer::valueOf)
.orElse(0);
log.info("connected component cut: '{}'", cut);
log.info("graphBasePath: '{}'", graphBasePath);
log.info("isLookUpUrl: '{}'", isLookUpUrl);
log.info("actionSetId: '{}'", actionSetId);
@ -100,8 +106,10 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
final RDD<Edge<String>> edgeRdd = spark
.read()
.load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity))
.as(Encoders.bean(Relation.class))
.textFile(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity))
.map(
(MapFunction<String, Relation>) r -> OBJECT_MAPPER.readValue(r, Relation.class),
Encoders.bean(Relation.class))
.javaRDD()
.map(it -> new Edge<>(hash(it.getSource()), hash(it.getTarget()), it.getRelClass()))
.rdd();
@ -109,7 +117,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
final Dataset<Relation> mergeRels = spark
.createDataset(
GraphProcessor
.findCCs(vertexes.rdd(), edgeRdd, maxIterations)
.findCCs(vertexes.rdd(), edgeRdd, maxIterations, cut)
.toJavaRDD()
.filter(k -> k.getDocIds().size() > 1)
.flatMap(cc -> ccToMergeRel(cc, dedupConf))
@ -117,6 +125,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
Encoders.bean(Relation.class));
mergeRels.write().mode(SaveMode.Append).parquet(mergeRelPath);
}
}

View File

@ -2,6 +2,7 @@
package eu.dnetlib.dhp.oa.dedup;
import java.io.IOException;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
@ -48,13 +49,6 @@ public class SparkCreateSimRels extends AbstractSparkAction {
parser.parseArgument(args);
SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf
.registerKryoClasses(
new Class[] {
MapDocument.class, FieldListImpl.class, FieldValueImpl.class, Block.class
});
new SparkCreateSimRels(parser, getSparkSession(conf))
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
}
@ -68,7 +62,12 @@ public class SparkCreateSimRels extends AbstractSparkAction {
final String isLookUpUrl = parser.get("isLookUpUrl");
final String actionSetId = parser.get("actionSetId");
final String workingPath = parser.get("workingPath");
final int numPartitions = Optional
.ofNullable(parser.get("numPartitions"))
.map(Integer::valueOf)
.orElse(NUM_PARTITIONS);
log.info("numPartitions: '{}'", numPartitions);
log.info("graphBasePath: '{}'", graphBasePath);
log.info("isLookUpUrl: '{}'", isLookUpUrl);
log.info("actionSetId: '{}'", actionSetId);
@ -88,6 +87,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
JavaPairRDD<String, MapDocument> mapDocuments = sc
.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
.repartition(numPartitions)
.mapToPair(
(PairFunction<String, String, MapDocument>) s -> {
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
@ -95,19 +95,17 @@ public class SparkCreateSimRels extends AbstractSparkAction {
});
// create blocks for deduplication
JavaPairRDD<String, Block> blocks = Deduper.createSortedBlocks(mapDocuments, dedupConf);
JavaPairRDD<String, Block> blocks = Deduper
.createSortedBlocks(mapDocuments, dedupConf)
.repartition(numPartitions);
// create relations by comparing only elements in the same group
JavaRDD<Relation> relations = Deduper
Deduper
.computeRelations(sc, blocks, dedupConf)
.map(t -> createSimRel(t._1(), t._2(), entity));
// save the simrel in the workingdir
spark
.createDataset(relations.rdd(), Encoders.bean(Relation.class))
.write()
.mode(SaveMode.Append)
.save(outputPath);
.map(t -> createSimRel(t._1(), t._2(), entity))
.repartition(numPartitions)
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
.saveAsTextFile(outputPath);
}
}

View File

@ -4,12 +4,16 @@ package eu.dnetlib.dhp.oa.dedup;
import static org.apache.spark.sql.functions.col;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.base.Joiner;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
@ -95,7 +99,24 @@ public class SparkPropagateRelation extends AbstractSparkAction {
FieldType.TARGET,
getDeletedFn());
save(newRels.union(updated).union(mergeRels), outputRelationPath, SaveMode.Overwrite);
save(
distinctRelations(
newRels
.union(updated)
.union(mergeRels)
.map((MapFunction<Relation, Relation>) r -> r, Encoders.kryo(Relation.class))),
outputRelationPath, SaveMode.Overwrite);
}
private Dataset<Relation> distinctRelations(Dataset<Relation> rels) {
return rels
.filter(getRelationFilterFunction())
.groupByKey(
(MapFunction<Relation, String>) r -> String
.join(r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()),
Encoders.STRING())
.agg(new RelationAggregator().toColumn())
.map((MapFunction<Tuple2<String, Relation>, Relation>) t -> t._2(), Encoders.bean(Relation.class));
}
private static Dataset<Relation> processDataset(
@ -112,6 +133,14 @@ public class SparkPropagateRelation extends AbstractSparkAction {
.map(mapFn, Encoders.bean(Relation.class));
}
private FilterFunction<Relation> getRelationFilterFunction() {
return (FilterFunction<Relation>) r -> StringUtils.isNotBlank(r.getSource()) ||
StringUtils.isNotBlank(r.getTarget()) ||
StringUtils.isNotBlank(r.getRelClass()) ||
StringUtils.isNotBlank(r.getSubRelType()) ||
StringUtils.isNotBlank(r.getRelClass());
}
private static MapFunction<String, Relation> patchRelFn() {
return value -> {
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);

View File

@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.dedup.graph;
import java.io.IOException;
import java.io.Serializable;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.lang.StringUtils;
import org.codehaus.jackson.annotate.JsonIgnore;
@ -18,12 +19,17 @@ public class ConnectedComponent implements Serializable {
private Set<String> docIds;
private String ccId;
public ConnectedComponent() {
}
public ConnectedComponent(Set<String> docIds) {
public ConnectedComponent(Set<String> docIds, final int cut) {
this.docIds = docIds;
createID();
if (cut > 0 && docIds.size() > cut) {
this.docIds = docIds
.stream()
.filter(s -> !ccId.equalsIgnoreCase(s))
.limit(cut - 1)
.collect(Collectors.toSet());
this.docIds.add(ccId);
}
}
public String createID() {
@ -41,6 +47,7 @@ public class ConnectedComponent implements Serializable {
public String getMin() {
final StringBuilder min = new StringBuilder();
docIds
.forEach(
i -> {

View File

@ -7,7 +7,7 @@ import scala.collection.JavaConversions;
object GraphProcessor {
def findCCs(vertexes: RDD[(VertexId, String)], edges: RDD[Edge[String]], maxIterations: Int): RDD[ConnectedComponent] = {
def findCCs(vertexes: RDD[(VertexId, String)], edges: RDD[Edge[String]], maxIterations: Int, cut:Int): RDD[ConnectedComponent] = {
val graph: Graph[String, String] = Graph(vertexes, edges).partitionBy(PartitionStrategy.RandomVertexCut) //TODO remember to remove partitionby
val cc = graph.connectedComponents(maxIterations).vertices
@ -22,15 +22,15 @@ object GraphProcessor {
}
}
val connectedComponents = joinResult.groupByKey()
.map[ConnectedComponent](cc => asConnectedComponent(cc))
.map[ConnectedComponent](cc => asConnectedComponent(cc, cut))
connectedComponents
}
def asConnectedComponent(group: (VertexId, Iterable[String])): ConnectedComponent = {
def asConnectedComponent(group: (VertexId, Iterable[String]), cut:Int): ConnectedComponent = {
val docs = group._2.toSet[String]
val connectedComponent = new ConnectedComponent(JavaConversions.setAsJavaSet[String](docs));
val connectedComponent = new ConnectedComponent(JavaConversions.setAsJavaSet[String](docs), cut);
connectedComponent
}

View File

@ -0,0 +1,45 @@
package eu.dnetlib.dhp.oa.dedup.model;
import java.io.Serializable;
public class BlockStats implements Serializable {
private String key; // key of the block
private Long size; // number of elements in the block
private Long comparisons; // number of comparisons in the block
public BlockStats() {
}
public BlockStats(String key, Long size, Long comparisons) {
this.key = key;
this.size = size;
this.comparisons = comparisons;
}
public String getKey() {
return key;
}
public void setKey(String key) {
this.key = key;
}
public Long getSize() {
return size;
}
public void setSize(Long size) {
this.size = size;
}
public Long getComparisons() {
return comparisons;
}
public void setComparisons(Long comparisons) {
this.comparisons = comparisons;
}
}

View File

@ -0,0 +1,32 @@
[
{
"paramName": "la",
"paramLongName": "isLookUpUrl",
"paramDescription": "address for the LookUp",
"paramRequired": true
},
{
"paramName": "asi",
"paramLongName": "actionSetId",
"paramDescription": "action set identifier (name of the orchestrator)",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "graphBasePath",
"paramDescription": "the base path of the raw graph",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "path of the working directory",
"paramRequired": true
},
{
"paramName": "np",
"paramLongName": "numPartitions",
"paramDescription": "number of partitions for the similarity relations intermediate phases",
"paramRequired": false
}
]

View File

@ -17,6 +17,12 @@
"paramDescription": "the url for the lookup service",
"paramRequired": true
},
{
"paramName": "cc",
"paramLongName": "cutConnectedComponent",
"paramDescription": "the number of maximum elements that belongs to a connected components",
"paramRequired": false
},
{
"paramName": "w",
"paramLongName": "workingPath",

View File

@ -22,5 +22,11 @@
"paramLongName": "workingPath",
"paramDescription": "path of the working directory",
"paramRequired": true
},
{
"paramName": "np",
"paramLongName": "numPartitions",
"paramDescription": "number of partitions for the similarity relations intermediate phases",
"paramRequired": false
}
]

View File

@ -20,6 +20,10 @@
<name>dedupGraphPath</name>
<description>path for the output graph</description>
</property>
<property>
<name>cutConnectedComponent</name>
<description>max number of elements in a connected component</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -106,10 +110,11 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--i</arg><arg>${graphBasePath}</arg>
<arg>--la</arg><arg>${isLookUpUrl}</arg>
<arg>--asi</arg><arg>${actionSetId}</arg>
<arg>--w</arg><arg>${workingPath}</arg>
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--numPartitions</arg><arg>8000</arg>
</spark>
<ok to="CreateMergeRel"/>
<error to="Kill"/>
@ -132,10 +137,11 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--i</arg><arg>${graphBasePath}</arg>
<arg>--w</arg><arg>${workingPath}</arg>
<arg>--la</arg><arg>${isLookUpUrl}</arg>
<arg>--asi</arg><arg>${actionSetId}</arg>
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
<arg>--cutConnectedComponent</arg><arg>${cutConnectedComponent}</arg>
</spark>
<ok to="CreateDedupRecord"/>
<error to="Kill"/>
@ -158,10 +164,10 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--i</arg><arg>${graphBasePath}</arg>
<arg>--w</arg><arg>${workingPath}</arg>
<arg>--la</arg><arg>${isLookUpUrl}</arg>
<arg>--asi</arg><arg>${actionSetId}</arg>
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
</spark>
<ok to="UpdateEntity"/>
<error to="Kill"/>
@ -184,9 +190,9 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--i</arg><arg>${graphBasePath}</arg>
<arg>--w</arg><arg>${workingPath}</arg>
<arg>--o</arg><arg>${dedupGraphPath}</arg>
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--dedupGraphPath</arg><arg>${dedupGraphPath}</arg>
</spark>
<ok to="copyRelations"/>
<error to="Kill"/>

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>

View File

@ -0,0 +1,108 @@
<workflow-app name="Create dedup blocks" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>graphBasePath</name>
<description>the raw graph base path</description>
</property>
<property>
<name>isLookUpUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>actionSetId</name>
<description>id of the actionSet</description>
</property>
<property>
<name>numPartitions</name>
<description>number of partitions for the similarity relations intermediate phases</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>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="CreateBlockStats"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="CreateBlockStats">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Create deduplication blocks</name>
<class>eu.dnetlib.dhp.oa.dedup.SparkBlockStats</class>
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
<arg>--workingPath</arg><arg>${workingDir}</arg>
<arg>--numPartitions</arg><arg>${numPartitions}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -1,17 +1,17 @@
[
{
"paramName": "i",
"paramLongName": "graphBasePath",
"paramDescription": "the base path of raw graph",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "the working directory path",
"paramRequired": true
},
{
{
"paramName": "i",
"paramLongName": "graphBasePath",
"paramDescription": "the base path of raw graph",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "the working directory path",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "dedupGraphPath",
"paramDescription": "the path of the dedup graph",

View File

@ -3,6 +3,8 @@ package eu.dnetlib.dhp.oa.dedup;
import static java.nio.file.Files.createTempDirectory;
import static org.apache.spark.sql.functions.col;
import static org.apache.spark.sql.functions.count;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.lenient;
@ -11,6 +13,9 @@ import java.io.IOException;
import java.io.Serializable;
import java.net.URISyntaxException;
import java.nio.file.Paths;
import java.util.HashSet;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
@ -18,6 +23,7 @@ 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.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Dataset;
@ -71,11 +77,13 @@ public class SparkDedupTest implements Serializable {
FileUtils.deleteDirectory(new File(testOutputBasePath));
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
final SparkConf conf = new SparkConf();
conf.set("spark.sql.shuffle.partitions", "200");
spark = SparkSession
.builder()
.appName(SparkDedupTest.class.getSimpleName())
.master("local[*]")
.config(new SparkConf())
.config(conf)
.getOrCreate();
jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -152,37 +160,42 @@ public class SparkDedupTest implements Serializable {
parser
.parseArgument(
new String[] {
"-i",
testGraphBasePath,
"-asi",
testActionSetId,
"-la",
"lookupurl",
"-w",
testOutputBasePath
"-i", testGraphBasePath,
"-asi", testActionSetId,
"-la", "lookupurl",
"-w", testOutputBasePath,
"-np", "50"
});
new SparkCreateSimRels(parser, spark).run(isLookUpService);
long orgs_simrel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
.count();
long pubs_simrel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
.count();
long sw_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_simrel").count();
long ds_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/dataset_simrel").count();
long sw_simrel = spark
.read()
.textFile(testOutputBasePath + "/" + testActionSetId + "/software_simrel")
.count();
long ds_simrel = spark
.read()
.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_simrel")
.count();
long orp_simrel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_simrel")
.textFile(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_simrel")
.count();
assertEquals(3432, orgs_simrel);
assertEquals(7054, pubs_simrel);
assertEquals(7152, pubs_simrel);
assertEquals(344, sw_simrel);
assertEquals(458, ds_simrel);
assertEquals(6750, orp_simrel);
@ -190,6 +203,101 @@ public class SparkDedupTest implements Serializable {
@Test
@Order(2)
public void cutMergeRelsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateMergeRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
parser
.parseArgument(
new String[] {
"-i",
testGraphBasePath,
"-asi",
testActionSetId,
"-la",
"lookupurl",
"-w",
testOutputBasePath,
"-cc",
"3"
});
new SparkCreateMergeRels(parser, spark).run(isLookUpService);
long orgs_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
.as(Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
.groupBy("source")
.agg(count("target").alias("cnt"))
.select("source", "cnt")
.where("cnt > 3")
.count();
long pubs_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
.as(Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
.groupBy("source")
.agg(count("target").alias("cnt"))
.select("source", "cnt")
.where("cnt > 3")
.count();
long sw_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
.as(Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
.groupBy("source")
.agg(count("target").alias("cnt"))
.select("source", "cnt")
.where("cnt > 3")
.count();
long ds_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
.as(Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
.groupBy("source")
.agg(count("target").alias("cnt"))
.select("source", "cnt")
.where("cnt > 3")
.count();
long orp_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
.as(Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
.groupBy("source")
.agg(count("target").alias("cnt"))
.select("source", "cnt")
.where("cnt > 3")
.count();
assertEquals(0, orgs_mergerel);
assertEquals(0, pubs_mergerel);
assertEquals(0, sw_mergerel);
assertEquals(0, ds_mergerel);
assertEquals(0, orp_mergerel);
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel"));
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel"));
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/software_mergerel"));
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel"));
FileUtils
.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel"));
}
@Test
@Order(3)
public void createMergeRelsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -225,8 +333,10 @@ public class SparkDedupTest implements Serializable {
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
.count();
long ds_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel").count();
long ds_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
.count();
long orp_mergerel = spark
.read()
@ -234,14 +344,14 @@ public class SparkDedupTest implements Serializable {
.count();
assertEquals(1276, orgs_mergerel);
assertEquals(1440, pubs_mergerel);
assertEquals(1442, pubs_mergerel);
assertEquals(288, sw_mergerel);
assertEquals(472, ds_mergerel);
assertEquals(718, orp_mergerel);
}
@Test
@Order(3)
@Order(4)
public void createDedupRecordTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -288,7 +398,7 @@ public class SparkDedupTest implements Serializable {
}
@Test
@Order(4)
@Order(5)
public void updateEntityTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -404,7 +514,7 @@ public class SparkDedupTest implements Serializable {
}
@Test
@Order(5)
@Order(6)
public void propagateRelationTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -423,7 +533,7 @@ public class SparkDedupTest implements Serializable {
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
assertEquals(4971, relations);
assertEquals(4866, relations);
// check deletedbyinference
final Dataset<Relation> mergeRels = spark
@ -454,7 +564,7 @@ public class SparkDedupTest implements Serializable {
}
@Test
@Order(6)
@Order(7)
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);

View File

@ -0,0 +1,177 @@
package eu.dnetlib.dhp.oa.dedup;
import static java.nio.file.Files.createTempDirectory;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.lenient;
import java.io.File;
import java.io.IOException;
import java.io.Serializable;
import java.net.URISyntaxException;
import java.nio.file.Paths;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class)
public class SparkStatsTest implements Serializable {
@Mock(serializable = true)
ISLookUpService isLookUpService;
private static SparkSession spark;
private static JavaSparkContext jsc;
private static String testGraphBasePath;
private static String testOutputBasePath;
private static final String testActionSetId = "test-orchestrator";
@BeforeAll
public static void cleanUp() throws IOException, URISyntaxException {
testGraphBasePath = Paths
.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI())
.toFile()
.getAbsolutePath();
testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
.toAbsolutePath()
.toString();
FileUtils.deleteDirectory(new File(testOutputBasePath));
final SparkConf conf = new SparkConf();
conf.set("spark.sql.shuffle.partitions", "200");
spark = SparkSession
.builder()
.appName(SparkDedupTest.class.getSimpleName())
.master("local[*]")
.config(conf)
.getOrCreate();
jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
}
@BeforeEach
public void setUp() throws IOException, ISLookUpException {
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
.thenReturn(
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
.thenReturn(
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
.thenReturn(
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
.thenReturn(
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset")))
.thenReturn(
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct")))
.thenReturn(
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json")));
}
@Test
public void createBlockStatsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateSimRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/createBlockStats_parameters.json")));
parser
.parseArgument(
new String[] {
"-i", testGraphBasePath,
"-asi", testActionSetId,
"-la", "lookupurl",
"-w", testOutputBasePath
});
new SparkBlockStats(parser, spark).run(isLookUpService);
long orgs_blocks = spark
.read()
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_blockstats")
.count();
long pubs_blocks = spark
.read()
.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_blockstats")
.count();
long sw_blocks = spark
.read()
.textFile(testOutputBasePath + "/" + testActionSetId + "/software_blockstats")
.count();
long ds_blocks = spark
.read()
.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_blockstats")
.count();
long orp_blocks = spark
.read()
.textFile(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_blockstats")
.count();
assertEquals(121, orgs_blocks);
assertEquals(110, pubs_blocks);
assertEquals(21, sw_blocks);
assertEquals(67, ds_blocks);
assertEquals(55, orp_blocks);
}
}

View File

@ -6,10 +6,10 @@
"subEntityType" : "resulttype",
"subEntityValue" : "dataset",
"orderField" : "title",
"queueMaxSize" : "800",
"queueMaxSize" : "100",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "80",
"slidingWindowSize" : "100",
"rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true",
"idPath" : "$.id",
@ -17,7 +17,8 @@
},
"pace" : {
"clustering" : [
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree" : {

View File

@ -6,10 +6,10 @@
"subEntityType" : "resulttype",
"subEntityValue" : "otherresearchproduct",
"orderField" : "title",
"queueMaxSize" : "800",
"queueMaxSize" : "100",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "80",
"slidingWindowSize" : "100",
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true",
"idPath" : "$.id",
@ -17,7 +17,8 @@
},
"pace" : {
"clustering" : [
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree" : {

View File

@ -6,10 +6,10 @@
"subEntityType": "resulttype",
"subEntityValue": "publication",
"orderField": "title",
"queueMaxSize": "800",
"queueMaxSize": "100",
"groupMaxSize": "100",
"maxChildren": "100",
"slidingWindowSize": "80",
"slidingWindowSize": "100",
"rootBuilder": [
"result",
"resultProject_outcome_isProducedBy",
@ -29,7 +29,8 @@
},
"pace": {
"clustering" : [
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree": {

View File

@ -6,10 +6,10 @@
"subEntityType" : "resulttype",
"subEntityValue" : "software",
"orderField" : "title",
"queueMaxSize" : "800",
"queueMaxSize" : "100",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "80",
"slidingWindowSize" : "100",
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true",
"idPath" : "$.id",
@ -17,8 +17,9 @@
},
"pace" : {
"clustering" : [
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi", "url" ], "params" : { } }
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree": {
"start": {

View File

@ -116,23 +116,10 @@ public class CreateRelatedEntitiesJob_phase1 {
Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class)))
.cache();
final String relatedEntityPath = outputPath + "_relatedEntity";
readPathEntity(spark, inputEntityPath, clazz)
Dataset<Tuple2<String, RelatedEntity>> entities = readPathEntity(spark, inputEntityPath, clazz)
.filter("dataInfo.invisible == false")
.map(
(MapFunction<E, RelatedEntity>) value -> asRelatedEntity(value, clazz),
Encoders.kryo(RelatedEntity.class))
.repartition(5000)
.write()
.mode(SaveMode.Overwrite)
.parquet(relatedEntityPath);
Dataset<Tuple2<String, RelatedEntity>> entities = spark
.read()
.load(relatedEntityPath)
.as(Encoders.kryo(RelatedEntity.class))
.map(
(MapFunction<RelatedEntity, Tuple2<String, RelatedEntity>>) e -> new Tuple2<>(e.getId(), e),
(MapFunction<E, Tuple2<String, RelatedEntity>>) e -> new Tuple2<>(e.getId(), asRelatedEntity(e, clazz)),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(RelatedEntity.class)))
.cache();
@ -184,13 +171,16 @@ public class CreateRelatedEntitiesJob_phase1 {
re.setDateofacceptance(getValue(result.getDateofacceptance()));
re.setPublisher(getValue(result.getPublisher()));
re.setResulttype(result.getResulttype());
re
.setInstances(
result
.getInstance()
.stream()
.limit(ProvisionConstants.MAX_INSTANCES)
.collect(Collectors.toList()));
if (Objects.nonNull(result.getInstance())) {
re
.setInstances(
result
.getInstance()
.stream()
.filter(Objects::nonNull)
.limit(ProvisionConstants.MAX_INSTANCES)
.collect(Collectors.toList()));
}
// TODO still to be mapped
// re.setCodeRepositoryUrl(j.read("$.coderepositoryurl"));

View File

@ -329,7 +329,7 @@ public class XmlRecordFactory implements Serializable {
.stream()
.filter(Objects::nonNull)
.map(c -> XmlSerializationUtils.asXmlElement("description", c.getValue()))
.collect(Collectors.toList()));
.collect(Collectors.toCollection(HashSet::new)));
}
if (r.getEmbargoenddate() != null) {
metadata
@ -370,7 +370,7 @@ public class XmlRecordFactory implements Serializable {
.stream()
.filter(Objects::nonNull)
.map(c -> XmlSerializationUtils.asXmlElement("source", c.getValue()))
.collect(Collectors.toList()));
.collect(Collectors.toCollection(HashSet::new)));
}
if (r.getFormat() != null) {
metadata

View File

@ -578,10 +578,18 @@
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--otherDsTypeId</arg><arg>${otherDsTypeId}</arg>
</spark>
<ok to="to_solr_index"/>
<ok to="should_index"/>
<error to="Kill"/>
</action>
<decision name="should_index">
<switch>
<case to="to_solr_index">${wf:conf('shouldIndex') eq 'true'}</case>
<case to="End">${wf:conf('shouldIndex') eq 'false'}</case>
<default to="to_solr_index"/>
</switch>
</decision>
<action name="to_solr_index">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>

View File

@ -324,6 +324,12 @@
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dnet-openaire-broker-common</artifactId>
<version>${dnet.openaire.broker.common}</version>
</dependency>
<dependency>
<groupId>org.apache.cxf</groupId>
<artifactId>cxf-rt-transports-http</artifactId>
<version>3.1.5</version>
@ -618,5 +624,6 @@
<mockito-core.version>3.3.3</mockito-core.version>
<mongodb.driver.version>3.4.2</mongodb.driver.version>
<vtd.version>[2.12,3.0)</vtd.version>
<dnet.openaire.broker.common>3.1.0</dnet.openaire.broker.common>
</properties>
</project>