implementation of the oozie wf to prepare the openorgs input: relations between organizations

This commit is contained in:
miconis 2020-09-25 11:29:51 +02:00
parent 259362ef47
commit 4cf79f32eb
6 changed files with 552 additions and 6 deletions

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@ -0,0 +1,83 @@
package eu.dnetlib.dhp.oa.dedup;
import java.io.Serializable;
public class OrgSimRel implements Serializable {
String local_id;
String oa_original_id;
String oa_name;
String oa_acronym;
String oa_country;
String oa_url;
String oa_collectedfrom;
public OrgSimRel() {
}
public OrgSimRel(String local_id, String oa_original_id, String oa_name, String oa_acronym, String oa_country, String oa_url, String oa_collectedfrom) {
this.local_id = local_id;
this.oa_original_id = oa_original_id;
this.oa_name = oa_name;
this.oa_acronym = oa_acronym;
this.oa_country = oa_country;
this.oa_url = oa_url;
this.oa_collectedfrom = oa_collectedfrom;
}
public String getLocal_id() {
return local_id;
}
public void setLocal_id(String local_id) {
this.local_id = local_id;
}
public String getOa_original_id() {
return oa_original_id;
}
public void setOa_original_id(String oa_original_id) {
this.oa_original_id = oa_original_id;
}
public String getOa_name() {
return oa_name;
}
public void setOa_name(String oa_name) {
this.oa_name = oa_name;
}
public String getOa_acronym() {
return oa_acronym;
}
public void setOa_acronym(String oa_acronym) {
this.oa_acronym = oa_acronym;
}
public String getOa_country() {
return oa_country;
}
public void setOa_country(String oa_country) {
this.oa_country = oa_country;
}
public String getOa_url() {
return oa_url;
}
public void setOa_url(String oa_url) {
this.oa_url = oa_url;
}
public String getOa_collectedfrom() {
return oa_collectedfrom;
}
public void setOa_collectedfrom(String oa_collectedfrom) {
this.oa_collectedfrom = oa_collectedfrom;
}
}

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@ -4,16 +4,20 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; 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.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.config.DedupConfig;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.sql.*; import org.apache.spark.sql.*;
import org.dom4j.DocumentException;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import scala.Tuple2; import scala.Tuple2;
import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Optional; import java.util.Optional;
@ -65,7 +69,7 @@ public class SparkCollectSimRels extends AbstractSparkAction {
} }
@Override @Override
void run(ISLookUpService isLookUpService) { void run(ISLookUpService isLookUpService) throws DocumentException, ISLookUpException, IOException {
// read oozie parameters // read oozie parameters
final String isLookUpUrl = parser.get("isLookUpUrl"); final String isLookUpUrl = parser.get("isLookUpUrl");
@ -126,11 +130,16 @@ public class SparkCollectSimRels extends AbstractSparkAction {
Encoders.bean(Relation.class) Encoders.bean(Relation.class)
).repartition(numPartitions); ).repartition(numPartitions);
for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
switch(dedupConf.getWf().getSubEntityValue()){
case "organization":
savePostgresRelation(organizationRelations, workingPath, actionSetId, "organization"); savePostgresRelation(organizationRelations, workingPath, actionSetId, "organization");
savePostgresRelation(resultRelations, workingPath, actionSetId, "publication"); break;
savePostgresRelation(resultRelations, workingPath, actionSetId, "software"); default:
savePostgresRelation(resultRelations, workingPath, actionSetId, "otherresearchproduct"); savePostgresRelation(resultRelations, workingPath, actionSetId, dedupConf.getWf().getSubEntityValue());
savePostgresRelation(resultRelations, workingPath, actionSetId, "dataset"); break;
}
}
} }

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@ -0,0 +1,168 @@
package eu.dnetlib.dhp.oa.dedup;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
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 org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Properties;
public class SparkPrepareOrgRels extends AbstractSparkAction {
private static final Logger log = LoggerFactory.getLogger(SparkCreateDedupRecord.class);
public static final String ROOT_TRUST = "0.8";
public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
public static final String PROVENANCE_ACTIONS = "dnet:provenanceActions";
public SparkPrepareOrgRels(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
}
public static void main(String[] args) throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateSimRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/prepareOrgRels_parameters.json")));
parser.parseArgument(args);
SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
new SparkCreateDedupRecord(parser, getSparkSession(conf))
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
}
@Override
public void run(ISLookUpService isLookUpService) throws IOException {
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 String apiUrl = parser.get("apiUrl");
final String dbUrl = parser.get("dbUrl");
final String dbTable = parser.get("dbTable");
final String dbUser = parser.get("dbUser");
final String dbPwd = parser.get("dbPwd");
log.info("graphBasePath: '{}'", graphBasePath);
log.info("isLookUpUrl: '{}'", isLookUpUrl);
log.info("actionSetId: '{}'", actionSetId);
log.info("workingPath: '{}'", workingPath);
log.info("apiUrl: '{}'", apiUrl);
log.info("dbUrl: '{}'", dbUrl);
log.info("dbUser: '{}'", dbUser);
log.info("table: '{}'", dbTable);
log.info("dbPwd: '{}'", "xxx");
final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, "organization");
final String entityPath = DedupUtility.createEntityPath(graphBasePath, "organization");
Dataset<OrgSimRel> relations = createRelations(spark, mergeRelPath, entityPath);
final Properties connectionProperties = new Properties();
connectionProperties.put("user", dbUser);
connectionProperties.put("password", dbPwd);
relations.write().mode(SaveMode.Overwrite).jdbc(dbUrl, dbTable, connectionProperties);
if (!apiUrl.isEmpty())
updateSimRels(apiUrl);
}
public static Dataset<OrgSimRel> createRelations(
final SparkSession spark,
final String mergeRelsPath,
final String entitiesPath) {
// <id, json_entity>
Dataset<Tuple2<String, Organization>> entities = spark
.read()
.textFile(entitiesPath)
.map(
(MapFunction<String, Tuple2<String, Organization>>) it -> {
Organization entity = OBJECT_MAPPER.readValue(it, Organization.class);
return new Tuple2<>(entity.getId(), entity);
},
Encoders.tuple(Encoders.STRING(), Encoders.kryo(Organization.class)));
Dataset<Tuple2<String, String>> relations = spark.createDataset(
spark
.read()
.load(mergeRelsPath)
.as(Encoders.bean(Relation.class))
.where("relClass == 'merges'")
.toJavaRDD()
.mapToPair(r -> new Tuple2<>(r.getSource(), r.getTarget()))
.groupByKey()
.flatMap(g -> {
List<Tuple2<String, String>> rels = new ArrayList<>();
for (String id1 : g._2()) {
for (String id2 : g._2()) {
if (!id1.equals(id2))
if (id1.contains("openorgs"))
rels.add(new Tuple2<>(id1, id2));
}
}
return rels.iterator();
}).rdd(),
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
return relations
.joinWith(entities, relations.col("_2").equalTo(entities.col("_1")), "inner")
.map(
(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, Organization>>, OrgSimRel>)r ->
new OrgSimRel(
r._1()._2(),
r._2()._2().getOriginalId().get(0),
r._2()._2().getLegalname().getValue(),
r._2()._2().getLegalshortname().getValue(),
r._2()._2().getCountry().getClassid(),
r._2()._2().getWebsiteurl().getValue(),
r._2()._2().getCollectedfrom().get(0).getValue()
),
Encoders.bean(OrgSimRel.class)
);
}
private static String updateSimRels(final String apiUrl) throws IOException {
final HttpGet req = new HttpGet(apiUrl);
try (final CloseableHttpClient client = HttpClients.createDefault()) {
try (final CloseableHttpResponse response = client.execute(req)) {
return IOUtils.toString(response.getEntity().getContent());
}
}
}
}

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@ -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>

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@ -0,0 +1,212 @@
<workflow-app name="Duplicate Scan" 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>workingPath</name>
<description>path for the working directory</description>
</property>
<property>
<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>apiUrl</name>
<description>the url for the APIs of the openorgs service</description>
</property>
<property>
<name>dbUrl</name>
<description>the url of the database</description>
</property>
<property>
<name>dbUser</name>
<description>the user of the database</description>
</property>
<property>
<name>dbTable</name>
<description>the name of the table in the database</description>
</property>
<property>
<name>dbPwd</name>
<description>the passowrd of the user of the 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>
<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>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="resetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="resetWorkingPath">
<fs>
<delete path="${workingPath}"/>
</fs>
<ok to="CreateSimRel"/>
<error to="Kill"/>
</action>
<action name="CreateSimRel">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Create Similarity Relations</name>
<class>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</class>
<jar>dhp-dedup-openaire-${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>${actionSetId}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--numPartitions</arg><arg>8000</arg>
</spark>
<ok to="copyRelations"/>
<error to="Kill"/>
</action>
<action name="copyRelations">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>-pb</arg>
<arg>${graphBasePath}/relation</arg>
<arg>${workingPath}/organization_simrel</arg>
</distcp>
<ok to="CreateMergeRel"/>
<error to="Kill"/>
</action>
<action name="CreateMergeRel">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Create Merge Relations</name>
<class>eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels</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>--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="PrepareOrgRels"/>
<error to="Kill"/>
</action>
<action name="PrepareOrgRels">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Prepare Organization Relations</name>
<class>eu.dnetlib.dhp.oa.dedup.SparkPrepareOrgRels</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>--workingPath</arg><arg>${workingPath}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
<arg>--apiUrl</arg><arg>${apiUrl}</arg>
<arg>--dbUrl</arg><arg>${dbUrl}</arg>
<arg>--dbTable</arg><arg>${dbTable}</arg>
<arg>--dbUser</arg><arg>${dbUser}</arg>
<arg>--dbPwd</arg><arg>${dbPwd}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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@ -0,0 +1,56 @@
[
{
"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": "la",
"paramLongName": "isLookUpUrl",
"paramDescription": "the url of the lookup service",
"paramRequired": true
},
{
"paramName": "asi",
"paramLongName": "actionSetId",
"paramDescription": "the id of the actionset (orchestrator)",
"paramRequired": true
},
{
"paramName": "au",
"paramLongName": "apiUrl",
"paramDescription": "the url for the APIs of the openorgs service",
"paramRequired": true
},
{
"paramName": "du",
"paramLongName": "dbUrl",
"paramDescription": "the url of the database",
"paramRequired": true
},
{
"paramName": "dusr",
"paramLongName": "dbUser",
"paramDescription": "the user of the database",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "dbTable",
"paramDescription": "the name of the table in the database",
"paramRequired": true
},
{
"paramName": "dpwd",
"paramLongName": "dbPwd",
"paramDescription": "the password for the user of the database",
"paramRequired": true
}
]