implementation of the workflow for new organizations in openorgs

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPrepareNewOrgs.java

@@ -0,0 +1,145 @@
+
+package eu.dnetlib.dhp.oa.dedup;
+
+import java.io.IOException;
+import java.util.Optional;
+import java.util.Properties;
+
+import org.apache.commons.io.IOUtils;
+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.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.Organization;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import scala.Tuple2;
+
+public class SparkPrepareNewOrgs extends AbstractSparkAction {
+
+	private static final Logger log = LoggerFactory.getLogger(SparkCreateDedupRecord.class);
+
+	public SparkPrepareNewOrgs(ArgumentApplicationParser parser, SparkSession spark) {
+		super(parser, spark);
+	}
+
+	public static void main(String[] args) throws Exception {
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					SparkPrepareNewOrgs.class
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/dedup/prepareNewOrgs_parameters.json")));
+		parser.parseArgument(args);
+
+		SparkConf conf = new SparkConf();
+		conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
+		conf.registerKryoClasses(ModelSupport.getOafModelClasses());
+
+		new SparkPrepareNewOrgs(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 int numConnections = Optional
+			.ofNullable(parser.get("numConnections"))
+			.map(Integer::valueOf)
+			.orElse(NUM_CONNECTIONS);
+
+		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("numPartitions: '{}'", numConnections);
+		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> newOrgs = createNewOrgs(spark, mergeRelPath, entityPath);
+
+		final Properties connectionProperties = new Properties();
+		connectionProperties.put("user", dbUser);
+		connectionProperties.put("password", dbPwd);
+
+		newOrgs
+			.repartition(numConnections)
+			.write()
+			.mode(SaveMode.Overwrite)
+			.jdbc(dbUrl, dbTable, connectionProperties);
+
+	}
+
+	public static Dataset<OrgSimRel> createNewOrgs(
+		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>> mergerels = spark
+			.createDataset(
+				spark
+					.read()
+					.load(mergeRelsPath)
+					.as(Encoders.bean(Relation.class))
+					.where("relClass == 'isMergedIn'")
+					.toJavaRDD()
+					.mapToPair(r -> new Tuple2<>(r.getSource(), r.getTarget()))
+					.rdd(),
+				Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
+
+		return entities
+			.joinWith(mergerels, entities.col("_1").equalTo(mergerels.col("_1")), "left")
+			.filter((FilterFunction<Tuple2<Tuple2<String, Organization>, Tuple2<String, String>>>) t -> t._2() == null)
+			.filter(
+				(FilterFunction<Tuple2<Tuple2<String, Organization>, Tuple2<String, String>>>) t -> !t
+					._1()
+					._1()
+					.contains("openorgs"))
+			.map(
+				(MapFunction<Tuple2<Tuple2<String, Organization>, Tuple2<String, String>>, OrgSimRel>) r -> new OrgSimRel(
+					"",
+					r._1()._2().getOriginalId().get(0),
+					r._1()._2().getLegalname() != null ? r._1()._2().getLegalname().getValue() : "",
+					r._1()._2().getLegalshortname() != null ? r._1()._2().getLegalshortname().getValue() : "",
+					r._1()._2().getCountry() != null ? r._1()._2().getCountry().getClassid() : "",
+					r._1()._2().getWebsiteurl() != null ? r._1()._2().getWebsiteurl().getValue() : "",
+					r._1()._2().getCollectedfrom().get(0).getValue()),
+				Encoders.bean(OrgSimRel.class));
+
+	}
+
+}

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPrepareOrgRels.java

@@ -1,10 +1,11 @@
 
 package eu.dnetlib.dhp.oa.dedup;
 
-import static jdk.nashorn.internal.objects.NativeDebug.map;
-
 import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+import java.util.Properties;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
@@ -12,26 +13,20 @@ 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.FilterFunction;
 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 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.schema.oaf.Organization;
+import eu.dnetlib.dhp.schema.oaf.Relation;
 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 scala.Tuple2;
 
 public class SparkPrepareOrgRels extends AbstractSparkAction {

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

@@ -28,8 +28,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 		SOURCE, TARGET
 	}
 
-	public SparkPropagateRelation(ArgumentApplicationParser parser, SparkSession spark)
-		throws Exception {
+	public SparkPropagateRelation(ArgumentApplicationParser parser, SparkSession spark) throws Exception {
 		super(parser, spark);
 	}
 

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/neworgs/oozie_app/config-default.xml

@@ -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>

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/neworgs/oozie_app/workflow.xml

@@ -0,0 +1,208 @@
+<workflow-app name="Organization Dedup" 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>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="${workingPath}"/>
+        </fs>
+        <ok to="copyRelations"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="copyRelations">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <arg>-pb</arg>
+            <arg>${graphBasePath}/relation</arg>
+            <arg>${workingPath}/${actionSetId}/organization_simrel</arg>
+        </distcp>
+        <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>${workingPath}</arg>
+            <arg>--numPartitions</arg><arg>8000</arg>
+        </spark>
+        <ok to="CreateMergeRel"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="CreateMergeRel">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Create Merge Relations</name>
+            <class>eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels</class>
+            <jar>dhp-dedup-openaire-${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>${cutConnectedComponent}</arg>
+        </spark>
+        <ok to="PrepareNewOrgs"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="PrepareNewOrgs">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Prepare New Organizations</name>
+            <class>eu.dnetlib.dhp.oa.dedup.SparkPrepareNewOrgs</class>
+            <jar>dhp-dedup-openaire-${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>--dbUrl</arg><arg>${dbUrl}</arg>
+            <arg>--dbTable</arg><arg>${dbTable}</arg>
+            <arg>--dbUser</arg><arg>${dbUser}</arg>
+            <arg>--dbPwd</arg><arg>${dbPwd}</arg>
+            <arg>--numConnections</arg><arg>20</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/prepareNewOrgs_parameters.json

@@ -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": "nc",
+    "paramLongName": "numConnections",
+    "paramDescription": "number of connections to the postgres db (for the write operation)",
+    "paramRequired": false
+  },
+  {
+    "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
+  }
+]

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

@@ -223,11 +223,11 @@ public class SparkDedupTest implements Serializable {
 				});
 
 		new SparkCollectSimRels(
-				parser,
-				spark,
-				spark.read().load(testDedupAssertionsBasePath + "/similarity_groups"),
-				spark.read().load(testDedupAssertionsBasePath + "/groups"))
-			.run(isLookUpService);
+			parser,
+			spark,
+			spark.read().load(testDedupAssertionsBasePath + "/similarity_groups"),
+			spark.read().load(testDedupAssertionsBasePath + "/groups"))
+				.run(isLookUpService);
 
 		long orgs_simrel = spark
 			.read()