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dnet-hadoop
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Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop

This commit is contained in:
Sandro La Bruzzo 2020-12-07 19:59:39 +01:00
parent 302baab67b d6934f370e
commit 7f8b93de72
5 changed files with 43 additions and 91 deletions
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28
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java
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@ -4,8 +4,13 @@ package eu.dnetlib.dhp.broker.oa;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.codec.digest.DigestUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.conf.Configuration;
@ -29,15 +34,14 @@ import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
public class PartitionEventsByDsIdJob {
private static final Logger log = LoggerFactory.getLogger(PartitionEventsByDsIdJob.class);
private static final String OPENDOAR_NSPREFIX = "opendoar____::";
private static final String OPENDOAR_NSPREFIX = "10|opendoar____::";
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
PartitionEventsByDsIdJob.class
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json")));
.toString(PartitionEventsByDsIdJob.class
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/od_partitions_params.json")));
parser.parseArgument(args);
final Boolean isSparkSessionManaged = Optional
@ -54,13 +58,25 @@ public class PartitionEventsByDsIdJob {
final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId";
log.info("partitionPath: {}", partitionPath);
final String opendoarIds = parser.get("opendoarIds");
log.info("opendoarIds: {}", opendoarIds);
final Set<String> validOpendoarIds = new HashSet<>();
if (!opendoarIds.trim().equals("-")) {
validOpendoarIds.addAll(Arrays.stream(opendoarIds.split(","))
.map(String::trim)
.filter(StringUtils::isNotBlank)
.map(s -> OPENDOAR_NSPREFIX + DigestUtils.md5Hex(s))
.collect(Collectors.toSet()));
}
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
ClusterUtils
.readPath(spark, eventsPath, Event.class)
.filter(e -> StringUtils.isNotBlank(e.getMap().getTargetDatasourceId()))
.filter(e -> e.getMap().getTargetDatasourceId().contains(OPENDOAR_NSPREFIX))
.limit(10000)
.filter(e -> e.getMap().getTargetDatasourceId().startsWith(OPENDOAR_NSPREFIX))
.filter(e -> validOpendoarIds.contains(e.getMap().getTargetDatasourceId()))
.map(e -> messageFromNotification(e), Encoders.bean(ShortEventMessageWithGroupId.class))
.coalesce(1)
.write()

14
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/od_partitions_params.json Normal file
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@ -0,0 +1,14 @@
[
{
"paramName": "o",
"paramLongName": "workingPath",
"paramDescription": "the path where the temporary data will be stored",
"paramRequired": true
},
{
"paramName": "list",
"paramLongName": "opendoarIds",
"paramDescription": "the opendoar IDs whitelist (comma separated)",
"paramRequired": true
}
]

0
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/config-default.xml → dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/config-default.xml
View File

59
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml → dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml
View File

@ -1,60 +1,13 @@
<workflow-app name="create broker events - partial" xmlns="uri:oozie:workflow:0.5">
<workflow-app name="partitionEventsByOpendoarIds" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>graphInputPath</name>
<description>the path where the graph is stored</description>
<name>opendoarIds</name>
<description>the opendoar IDs whitelist (comma separated)</description>
</property>
<property>
<name>workingPath</name>
<description>the path where the the generated data will be stored</description>
</property>
<property>
<name>datasourceIdWhitelist</name>
<value>-</value>
<description>a white list (comma separeted, - for empty list) of datasource ids</description>
</property>
<property>
<name>datasourceTypeWhitelist</name>
<value>-</value>
<description>a white list (comma separeted, - for empty list) of datasource types</description>
</property>
<property>
<name>datasourceIdBlacklist</name>
<value>-</value>
<description>a black list (comma separeted, - for empty list) of datasource ids</description>
</property>
<property>
<name>esEventIndexName</name>
<description>the elasticsearch index name for events</description>
</property>
<property>
<name>esNotificationsIndexName</name>
<description>the elasticsearch index name for notifications</description>
</property>
<property>
<name>esIndexHost</name>
<description>the elasticsearch host</description>
</property>
<property>
<name>maxIndexedEventsForDsAndTopic</name>
<description>the max number of events for each couple (ds/topic)</description>
</property>
<property>
<name>brokerApiBaseUrl</name>
<description>the url of the broker service api</description>
</property>
<property>
<name>brokerDbUrl</name>
<description>the url of the broker database</description>
</property>
<property>
<name>brokerDbUser</name>
<description>the user of the broker database</description>
</property>
<property>
<name>brokerDbPassword</name>
<description>the password of the broker database</description>
</property>
<property>
<name>sparkDriverMemory</name>
@ -111,13 +64,13 @@
</configuration>
</global>
<start to="partition"/>
<start to="opendoarPartition"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="partition">
<action name="opendoarPartition">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
@ -134,8 +87,8 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--opendoarIds</arg><arg>${opendoarIds}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

33
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
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@ -5,31 +5,23 @@ import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
import java.io.StringReader;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.io.SAXReader;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.mockito.Mock;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.OafMapperUtils;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
//TODO to enable it we need to update the joined_entity.json test file
//@Disabled
@Disabled
public class XmlRecordFactoryTest {
private static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource";
@ -43,27 +35,6 @@ public class XmlRecordFactoryTest {
JoinedEntity je = new ObjectMapper().readValue(json, JoinedEntity.class);
assertNotNull(je);
Document doc = buildXml(je);
//// TODO specific test assertion on doc
}
@Test
void testBologna() throws IOException, DocumentException {
final String json = IOUtils.toString(getClass().getResourceAsStream("oaf-bologna.json"));
Publication oaf = new ObjectMapper().readValue(json, Publication.class);
assertNotNull(oaf);
JoinedEntity je = new JoinedEntity();
je.setEntity(oaf);
assertNotNull(je);
Document doc = buildXml(je);
// TODO specific test assertion on doc
System.out.println(doc.asXML());
}
private Document buildXml(JoinedEntity je) throws DocumentException {
ContextMapper contextMapper = new ContextMapper();
XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation,
@ -78,7 +49,5 @@ public class XmlRecordFactoryTest {
assertNotNull(doc);
// TODO add assertions based of values extracted from the XML record
return doc;
}
}