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dnet-hadoop
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merge upstream

This commit is contained in:
Miriam Baglioni 2020-07-06 13:58:02 +02:00
parent c133a23cf0 edf6c6c4dc
commit d22240c0ba
8 changed files with 201 additions and 233 deletions
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2
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java
View File

@ -15,7 +15,7 @@ public class EnrichMissingProject extends UpdateMatcher<OaBrokerProject> {
super(20,
prj -> Topic.ENRICH_MISSING_PROJECT,
(p, prj) -> p.getProjects().add(prj),
prj -> prj.getFunder() + "::" + prj.getFundingProgram() + prj.getCode());
prj -> prj.getOpenaireId());
}
@Override

14
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java
View File

@ -18,31 +18,25 @@ public class EnrichMoreProject extends UpdateMatcher<OaBrokerProject> {
super(20,
prj -> Topic.ENRICH_MORE_PROJECT,
(p, prj) -> p.getProjects().add(prj),
prj -> projectAsString(prj));
}
private static String projectAsString(final OaBrokerProject prj) {
return prj.getFunder() + "::" + prj.getFundingProgram() + "::" + prj.getCode();
prj -> prj.getOpenaireId());
}
@Override
protected List<OaBrokerProject> findDifferences(final OaBrokerMainEntity source,
final OaBrokerMainEntity target) {
if (target.getProjects().size() >= BrokerConstants.MAX_LIST_SIZE) {
return new ArrayList<>();
}
if (target.getProjects().size() >= BrokerConstants.MAX_LIST_SIZE) { return new ArrayList<>(); }
final Set<String> existingProjects = target
.getProjects()
.stream()
.map(EnrichMoreProject::projectAsString)
.map(p -> p.getOpenaireId())
.collect(Collectors.toSet());
return source
.getProjects()
.stream()
.filter(p -> !existingProjects.contains(projectAsString(p)))
.filter(p -> !existingProjects.contains(p.getOpenaireId()))
.collect(Collectors.toList());
}

61
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java
View File

@ -44,9 +44,7 @@ public class ConversionUtils {
private static final Logger log = LoggerFactory.getLogger(ConversionUtils.class);
public static List<OaBrokerInstance> oafInstanceToBrokerInstances(final Instance i) {
if (i == null) {
return new ArrayList<>();
}
if (i == null) { return new ArrayList<>(); }
return mappedList(i.getUrl(), url -> {
final OaBrokerInstance res = new OaBrokerInstance();
@ -67,9 +65,7 @@ public class ConversionUtils {
}
public static final OaBrokerRelatedDataset oafDatasetToBrokerDataset(final Dataset d) {
if (d == null) {
return null;
}
if (d == null) { return null; }
final OaBrokerRelatedDataset res = new OaBrokerRelatedDataset();
res.setOpenaireId(d.getId());
@ -82,9 +78,7 @@ public class ConversionUtils {
}
public static OaBrokerRelatedPublication oafPublicationToBrokerPublication(final Publication p) {
if (p == null) {
return null;
}
if (p == null) { return null; }
final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication();
res.setOpenaireId(p.getId());
@ -98,9 +92,7 @@ public class ConversionUtils {
}
public static final OaBrokerMainEntity oafResultToBrokerResult(final Result result) {
if (result == null) {
return null;
}
if (result == null) { return null; }
final OaBrokerMainEntity res = new OaBrokerMainEntity();
@ -117,8 +109,7 @@ public class ConversionUtils {
res.setEmbargoenddate(fieldValue(result.getEmbargoenddate()));
res.setContributor(fieldList(result.getContributor()));
res
.setJournal(
result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null);
.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));
@ -130,9 +121,7 @@ public class ConversionUtils {
}
private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) {
if (author == null) {
return null;
}
if (author == null) { return null; }
final String pids = author.getPid() != null ? author
.getPid()
@ -142,6 +131,7 @@ public class ConversionUtils {
.filter(pid -> pid.getQualifier().getClassid() != null)
.filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid"))
.map(pid -> pid.getValue())
.map(pid -> cleanOrcid(pid))
.filter(StringUtils::isNotBlank)
.findFirst()
.orElse(null) : null;
@ -149,10 +139,13 @@ public class ConversionUtils {
return new OaBrokerAuthor(author.getFullname(), pids);
}
private static String cleanOrcid(final String s) {
final String match = "//orcid.org/";
return s.contains(match) ? StringUtils.substringAfter(s, match) : s;
}
private static OaBrokerJournal oafJournalToBrokerJournal(final Journal journal) {
if (journal == null) {
return null;
}
if (journal == null) { return null; }
final OaBrokerJournal res = new OaBrokerJournal();
res.setName(journal.getName());
@ -164,9 +157,7 @@ public class ConversionUtils {
}
private static OaBrokerExternalReference oafExtRefToBrokerExtRef(final ExternalReference ref) {
if (ref == null) {
return null;
}
if (ref == null) { return null; }
final OaBrokerExternalReference res = new OaBrokerExternalReference();
res.setRefidentifier(ref.getRefidentifier());
@ -177,9 +168,7 @@ public class ConversionUtils {
}
public static final OaBrokerProject oafProjectToBrokerProject(final Project p) {
if (p == null) {
return null;
}
if (p == null) { return null; }
final OaBrokerProject res = new OaBrokerProject();
res.setOpenaireId(p.getId());
@ -203,9 +192,7 @@ public class ConversionUtils {
}
public static final OaBrokerRelatedSoftware oafSoftwareToBrokerSoftware(final Software sw) {
if (sw == null) {
return null;
}
if (sw == null) { return null; }
final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware();
res.setOpenaireId(sw.getId());
@ -268,9 +255,7 @@ public class ConversionUtils {
}
private static List<OaBrokerTypedValue> structPropTypedList(final List<StructuredProperty> list) {
if (list == null) {
return new ArrayList<>();
}
if (list == null) { return new ArrayList<>(); }
return list
.stream()
@ -280,9 +265,7 @@ public class ConversionUtils {
}
private static <F, T> List<T> mappedList(final List<F> list, final Function<F, T> func) {
if (list == null) {
return new ArrayList<>();
}
if (list == null) { return new ArrayList<>(); }
return list
.stream()
@ -293,9 +276,7 @@ public class ConversionUtils {
}
private static <F, T> List<T> flatMappedList(final List<F> list, final Function<F, List<T>> func) {
if (list == null) {
return new ArrayList<>();
}
if (list == null) { return new ArrayList<>(); }
return list
.stream()
@ -307,9 +288,7 @@ public class ConversionUtils {
}
private static <F, T> T mappedFirst(final List<F> list, final Function<F, T> func) {
if (list == null) {
return null;
}
if (list == null) { return null; }
return list
.stream()

2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java
View File

@ -37,7 +37,7 @@ public class Deduper implements Serializable {
public static JavaPairRDD<String, Block> createSortedBlocks(
JavaPairRDD<String, MapDocument> mapDocs, DedupConfig config) {
final String of = config.getWf().getOrderField();
final int maxQueueSize = config.getWf().getGroupMaxSize();
final int maxQueueSize = config.getWf().getQueueMaxSize();
return mapDocs
// the reduce is just to be sure that we haven't document with same id

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/config-default.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/oozie_app/config-default.xml
View File

157
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/oozie_app/workflow.xml Normal file
View File

@ -0,0 +1,157 @@
<workflow-app name="import Claims as Graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>reuseContent</name>
<value>false</value>
<description>should import content from the aggregator or reuse a previous version</description>
</property>
<property>
<name>contentPath</name>
<description>path location to store (or reuse) content from the aggregator</description>
</property>
<property>
<name>postgresURL</name>
<description>the postgres URL to access to the database</description>
</property>
<property>
<name>postgresUser</name>
<description>the user postgres</description>
</property>
<property>
<name>postgresPassword</name>
<description>the password postgres</description>
</property>
<property>
<name>dbSchema</name>
<value>beta</value>
<description>the database schema according to the D-Net infrastructure (beta or production)</description>
</property>
<property>
<name>mongoURL</name>
<description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
</property>
<property>
<name>mongoDb</name>
<description>mongo database</description>
</property>
<property>
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<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>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="ImportDB_claims"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ImportDB_claims">
<java>
<prepare>
<delete path="${contentPath}/db_claims"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication</main-class>
<arg>--hdfsPath</arg><arg>${contentPath}/db_claims</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--action</arg><arg>claims</arg>
<arg>--dbschema</arg><arg>${dbSchema}</arg>
</java>
<ok to="ImportODF_claims"/>
<error to="Kill"/>
</action>
<action name="ImportODF_claims">
<java>
<prepare>
<delete path="${contentPath}/odf_claims"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${contentPath}/odf_claims</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>claim</arg>
</java>
<ok to="ImportOAF_claims"/>
<error to="Kill"/>
</action>
<action name="ImportOAF_claims">
<java>
<prepare>
<delete path="${contentPath}/oaf_claims"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${contentPath}/oaf_claims</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>claim</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

169
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/workflow.xml
View File

@ -1,169 +0,0 @@
<workflow-app name="import Claims as Graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>migrationClaimsPathStep1</name>
<description>the base path to store hdfs file</description>
</property>
<property>
<name>migrationClaimsPathStep2</name>
<description>the temporary path to store entities before dispatching</description>
</property>
<property>
<name>migrationClaimsPathStep3</name>
<description>the graph Raw base path</description>
</property>
<property>
<name>postgresURL</name>
<description>the postgres URL to access to the database</description>
</property>
<property>
<name>postgresUser</name>
<description>the user postgres</description>
</property>
<property>
<name>postgresPassword</name>
<description>the password postgres</description>
</property>
<property>
<name>mongoURL</name>
<description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
</property>
<property>
<name>mongoDb</name>
<description>mongo database</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>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${migrationClaimsPathStep1}'/>
<mkdir path='${migrationClaimsPathStep1}'/>
</fs>
<ok to="ImportDBClaims"/>
<error to="Kill"/>
</action>
<action name="ImportDBClaims">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${migrationClaimsPathStep1}/db_claims</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
<arg>-a</arg><arg>claims</arg>
</java>
<ok to="ImportODFClaims"/>
<error to="Kill"/>
</action>
<action name="ImportODFClaims">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationClaimsPathStep1}/odf_claims</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>claim</arg>
</java>
<ok to="ImportOAFClaims"/>
<error to="Kill"/>
</action>
<action name="ImportOAFClaims">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationClaimsPathStep1}/oaf_claims</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>claim</arg>
</java>
<ok to="ResetClaimEntities"/>
<error to="Kill"/>
</action>
<action name="ResetClaimEntities">
<fs>
<delete path='${migrationClaimsPathStep2}'/>
<mkdir path='${migrationClaimsPathStep2}'/>
</fs>
<ok to="GenerateClaimEntities"/>
<error to="Kill"/>
</action>
<action name="GenerateClaimEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>GenerateClaimEntities</name>
<class>eu.dnetlib.dhp.migration.step2.GenerateEntitiesApplication</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>-s</arg><arg>${migrationClaimsPathStep1}/db_claims,${migrationClaimsPathStep1}/oaf_claims,${migrationClaimsPathStep1}/odf_claims</arg>
<arg>-t</arg><arg>${migrationClaimsPathStep2}/claim_entities</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</spark>
<ok to="ResetClaimGraph"/>
<error to="Kill"/>
</action>
<action name="ResetClaimGraph">
<fs>
<delete path='${migrationClaimsPathStep3}'/>
<mkdir path='${migrationClaimsPathStep3}'/>
</fs>
<ok to="GenerateClaimGraph"/>
<error to="Kill"/>
</action>
<action name="GenerateClaimGraph">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>GenerateClaimGraph</name>
<class>eu.dnetlib.dhp.migration.step3.DispatchEntitiesApplication</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>-s</arg><arg>${migrationClaimsPathStep2}/claim_entities</arg>
<arg>-g</arg><arg>${migrationClaimsPathStep3}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

29
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJobTest.java
View File

@ -1,9 +1,10 @@
package eu.dnetlib.dhp.oa.provision;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
import eu.dnetlib.dhp.schema.oaf.Relation;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -19,9 +20,10 @@ import org.junit.jupiter.api.io.TempDir;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class PrepareRelationsJobTest {
@ -74,14 +76,19 @@ public class PrepareRelationsJobTest {
"-maxRelations", String.valueOf(maxRelations)
});
Dataset<Relation> out = spark.read()
.parquet(testPath.toString())
.as(Encoders.bean(Relation.class))
.cache();
Dataset<Relation> out = spark
.read()
.parquet(testPath.toString())
.as(Encoders.bean(Relation.class))
.cache();
Assertions.assertEquals(10, out.count());
Dataset<Row> freq = out.toDF().cube(SUBRELTYPE).count().filter((FilterFunction<Row>) value -> !value.isNullAt(0));
Dataset<Row> freq = out
.toDF()
.cube(SUBRELTYPE)
.count()
.filter((FilterFunction<Row>) value -> !value.isNullAt(0));
long outcome = freq.filter(freq.col(SUBRELTYPE).equalTo(OUTCOME)).collectAsList().get(0).getAs("count");
long supplement = freq.filter(freq.col(SUBRELTYPE).equalTo(SUPPLEMENT)).collectAsList().get(0).getAs("count");