Merge branch 'beta' into dump

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala

@@ -1,4 +1,4 @@
-package eu.dnetllib.dhp.sx.bio
+package eu.dnetlib.dhp.sx.bio
 
 import eu.dnetlib.dhp.schema.common.ModelConstants
 import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, OafMapperUtils}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala

@@ -1,8 +1,8 @@
-package eu.dnetllib.dhp.sx.bio
+package eu.dnetlib.dhp.sx.bio
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.schema.oaf.Oaf
-import eu.dnetllib.dhp.sx.bio.BioDBToOAF.ScholixResolved
+import BioDBToOAF.ScholixResolved
 import org.apache.commons.io.IOUtils
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
@@ -13,7 +13,7 @@ object SparkTransformBioDatabaseToOAF {
   def main(args: Array[String]): Unit = {
     val conf: SparkConf = new SparkConf()
     val log: Logger = LoggerFactory.getLogger(getClass)
-    val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/bio_to_oaf_params.json")))
+    val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json")))
     parser.parseArgument(args)
     val database: String = parser.get("database")
     log.info("database: {}", database)

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala

@@ -1,10 +1,10 @@
-package eu.dnetllib.dhp.sx.bio.ebi
+package eu.dnetlib.dhp.sx.bio.ebi
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
 import eu.dnetlib.dhp.schema.oaf.Result
+import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
 import eu.dnetlib.dhp.utils.ISLookupClientFactory
-import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
 import org.apache.commons.io.IOUtils
 import org.apache.hadoop.conf.Configuration
 import org.apache.hadoop.fs.{FSDataOutputStream, FileSystem, Path}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala

@@ -1,8 +1,9 @@
-package eu.dnetllib.dhp.sx.bio.ebi
+package eu.dnetlib.dhp.sx.bio.ebi
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem
+import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
-import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
+import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
+import eu.dnetlib.dhp.sx.bio.pubmed.PMJournal
 import org.apache.commons.io.IOUtils
 import org.apache.http.client.config.RequestConfig
 import org.apache.http.client.methods.HttpGet

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala

@@ -1,9 +1,10 @@
-package eu.dnetllib.dhp.sx.bio.ebi
+package eu.dnetlib.dhp.sx.bio.ebi
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.schema.oaf.Oaf
-import eu.dnetllib.dhp.sx.bio.BioDBToOAF
+import eu.dnetlib.dhp.sx.bio.BioDBToOAF
-import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem
+import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
+import BioDBToOAF.EBILinkItem
 import org.apache.commons.io.IOUtils
 import org.apache.spark.SparkConf
 import org.apache.spark.sql._

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java

@@ -1,5 +1,5 @@
 
-package eu.dnetllib.dhp.sx.bio.pubmed;
+package eu.dnetlib.dhp.sx.bio.pubmed;
 
 import java.io.Serializable;
 import java.util.ArrayList;

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java

@@ -1,5 +1,5 @@
 
-package eu.dnetllib.dhp.sx.bio.pubmed;
+package eu.dnetlib.dhp.sx.bio.pubmed;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMGrant.java

@@ -1,5 +1,5 @@
 
-package eu.dnetllib.dhp.sx.bio.pubmed;
+package eu.dnetlib.dhp.sx.bio.pubmed;
 
 public class PMGrant {
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMJournal.java

@@ -1,5 +1,5 @@
 
-package eu.dnetllib.dhp.sx.bio.pubmed;
+package eu.dnetlib.dhp.sx.bio.pubmed;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala

@@ -1,4 +1,4 @@
-package eu.dnetllib.dhp.sx.bio.pubmed
+package eu.dnetlib.dhp.sx.bio.pubmed
 
 import scala.xml.MetaData
 import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMSubject.java

@@ -1,5 +1,5 @@
 
-package eu.dnetllib.dhp.sx.bio.pubmed;
+package eu.dnetlib.dhp.sx.bio.pubmed;
 
 public class PMSubject {
 	private String value;

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala

@@ -1,4 +1,4 @@
-package eu.dnetllib.dhp.sx.bio.pubmed
+package eu.dnetlib.dhp.sx.bio.pubmed
 
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
 import eu.dnetlib.dhp.schema.common.ModelConstants

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml

@@ -0,0 +1,51 @@
+    <workflow-app name="Transform_BioEntity_Workflow" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>sourcePath</name>
+            <description>the PDB Database Working Path</description>
+        </property>
+        <property>
+            <name>database</name>
+            <description>the PDB Database Working Path</description>
+        </property>
+
+        <property>
+            <name>targetPath</name>
+            <description>the Target Working dir path</description>
+        </property>
+    </parameters>
+
+    <start to="ConvertDB"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="ConvertDB">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Convert Bio DB to OAF Dataset</name>
+            <class>eu.dnetlib.dhp.sx.bio.SparkTransformBioDatabaseToOAF</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.shuffle.partitions=2000
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--master</arg><arg>yarn</arg>
+            <arg>--dbPath</arg><arg>${sourcePath}</arg>
+            <arg>--database</arg><arg>${database}</arg>
+            <arg>--targetPath</arg><arg>${targetPath}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+    <end name="End"/>
+
+</workflow-app>

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala

@@ -1,10 +1,10 @@
-package eu.dnetllib.dhp.sx.bio
+package eu.dnetlib.dhp.sx.bio
 
 import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature}
 import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
 import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
-import eu.dnetllib.dhp.sx.bio.BioDBToOAF.ScholixResolved
+import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
-import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf}
+import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf}
 import org.json4s.DefaultFormats
 import org.json4s.JsonAST.{JField, JObject, JString}
 import org.json4s.jackson.JsonMethods.parse

dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java

@@ -91,8 +91,8 @@ public class ReadBlacklistFromDB implements Closeable {
 
 			String encoding = rs.getString("relationship");
 			RelationInverse ri = ModelSupport.relationInverseMap.get(encoding);
-			direct.setRelClass(ri.getRelation());
+			direct.setRelClass(ri.getRelClass());
-			inverse.setRelClass(ri.getInverse());
+			inverse.setRelClass(ri.getInverseRelClass());
 			direct.setRelType(ri.getRelType());
 			inverse.setRelType(ri.getRelType());
 			direct.setSubRelType(ri.getSubReltype());

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java

@@ -0,0 +1,134 @@
+
+package eu.dnetlib.dhp.oa.graph.raw;
+
+import com.clearspring.analytics.util.Lists;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
+import eu.dnetlib.dhp.schema.common.EntityType;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.FlatMapFunction;
+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 java.util.*;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+public class CopyHdfsOafApplication extends AbstractMigrationApplication {
+
+	private static final Logger log = LoggerFactory.getLogger(CopyHdfsOafApplication.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static void main(final String[] args) throws Exception {
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					CopyHdfsOafApplication.class
+						.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json")));
+		parser.parseArgument(args);
+
+		final Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String mdstoreManagerUrl = parser.get("mdstoreManagerUrl");
+		log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl);
+
+		final String mdFormat = parser.get("mdFormat");
+		log.info("mdFormat: {}", mdFormat);
+
+		final String mdLayout = parser.get("mdLayout");
+		log.info("mdLayout: {}", mdLayout);
+
+		final String mdInterpretation = parser.get("mdInterpretation");
+		log.info("mdInterpretation: {}", mdInterpretation);
+
+		final String hdfsPath = parser.get("hdfsPath");
+		log.info("hdfsPath: {}", hdfsPath);
+
+		final String isLookupUrl = parser.get("isLookupUrl");
+		log.info("isLookupUrl: {}", isLookupUrl);
+
+		final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
+		final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
+
+		final Set<String> paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation);
+
+		final SparkConf conf = new SparkConf();
+		runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, vocs, hdfsPath, paths));
+	}
+
+	public static void processPaths(final SparkSession spark,
+		final VocabularyGroup vocs,
+		final String outputPath,
+		final Set<String> paths) {
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		log.info("Found {} mdstores", paths.size());
+		paths.forEach(log::info);
+
+		final String[] validPaths = paths
+			.stream()
+			.filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()))
+			.toArray(String[]::new);
+		log.info("Non empty mdstores {}", validPaths.length);
+
+		if (validPaths.length > 0) {
+			// load the dataset
+			Dataset<Oaf> oaf = spark
+					.read()
+					.load(validPaths)
+					.as(Encoders.kryo(Oaf.class));
+
+			// dispatch each entity type individually in the respective graph subdirectory in append mode
+			for(Map.Entry<String, Class> e : ModelSupport.oafTypes.entrySet()) {
+				oaf
+					.filter((FilterFunction<Oaf>) o -> o.getClass().getSimpleName().toLowerCase().equals(e.getKey()))
+					.map((MapFunction<Oaf, String>) OBJECT_MAPPER::writeValueAsString, Encoders.bean(e.getValue()))
+					.write()
+					.option("compression", "gzip")
+					.mode(SaveMode.Append)
+					.text(outputPath + "/" + e.getKey());
+			}
+		}
+	}
+
+	private static Relation getInverse(Relation rel, VocabularyGroup vocs) {
+		final Relation inverse = new Relation();
+
+		inverse.setProperties(rel.getProperties());
+		inverse.setValidated(rel.getValidated());
+		inverse.setValidationDate(rel.getValidationDate());
+		inverse.setCollectedfrom(rel.getCollectedfrom());
+		inverse.setDataInfo(rel.getDataInfo());
+		inverse.setLastupdatetimestamp(rel.getLastupdatetimestamp());
+
+		inverse.setSource(rel.getTarget());
+		inverse.setTarget(rel.getSource());
+		inverse.setRelType(rel.getRelType());
+		inverse.setSubRelType(rel.getSubRelType());
+
+		return inverse;
+	}
+
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java

@@ -135,30 +135,4 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication
 		}
 	}
 
-	private static Set<String> mdstorePaths(final String mdstoreManagerUrl,
-		final String format,
-		final String layout,
-		final String interpretation) throws IOException {
-		final String url = mdstoreManagerUrl + "/mdstores/";
-		final ObjectMapper objectMapper = new ObjectMapper();
-
-		final HttpGet req = new HttpGet(url);
-
-		try (final CloseableHttpClient client = HttpClients.createDefault()) {
-			try (final CloseableHttpResponse response = client.execute(req)) {
-				final String json = IOUtils.toString(response.getEntity().getContent());
-				final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class);
-				return Arrays
-					.stream(mdstores)
-					.filter(md -> md.getFormat().equalsIgnoreCase(format))
-					.filter(md -> md.getLayout().equalsIgnoreCase(layout))
-					.filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation))
-					.filter(md -> StringUtils.isNotBlank(md.getHdfsPath()))
-					.filter(md -> StringUtils.isNotBlank(md.getCurrentVersion()))
-					.filter(md -> md.getSize() > 0)
-					.map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store")
-					.collect(Collectors.toSet());
-			}
-		}
-	}
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java

@@ -3,8 +3,14 @@ package eu.dnetlib.dhp.oa.graph.raw.common;
 
 import java.io.Closeable;
 import java.io.IOException;
+import java.util.Arrays;
+import java.util.Set;
 import java.util.concurrent.atomic.AtomicInteger;
+import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.apache.hadoop.conf.Configuration;
@@ -16,6 +22,10 @@ import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.schema.oaf.Oaf;
+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;
 
 public class AbstractMigrationApplication implements Closeable {
 
@@ -47,6 +57,43 @@ public class AbstractMigrationApplication implements Closeable {
 				SequenceFile.Writer.valueClass(Text.class));
 	}
 
+	/**
+	 * Retrieves from the metadata store manager application the list of paths associated with mdstores characterized
+	 * by he given format, layout, interpretation
+	 * @param mdstoreManagerUrl the URL of the mdstore manager service
+	 * @param format the mdstore format
+	 * @param layout the mdstore layout
+	 * @param interpretation the mdstore interpretation
+	 * @return the set of hdfs paths
+	 * @throws IOException in case of HTTP communication issues
+	 */
+	protected static Set<String> mdstorePaths(final String mdstoreManagerUrl,
+											final String format,
+											final String layout,
+											final String interpretation) throws IOException {
+		final String url = mdstoreManagerUrl + "/mdstores/";
+		final ObjectMapper objectMapper = new ObjectMapper();
+
+		final HttpGet req = new HttpGet(url);
+
+		try (final CloseableHttpClient client = HttpClients.createDefault()) {
+			try (final CloseableHttpResponse response = client.execute(req)) {
+				final String json = IOUtils.toString(response.getEntity().getContent());
+				final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class);
+				return Arrays
+						.stream(mdstores)
+						.filter(md -> md.getFormat().equalsIgnoreCase(format))
+						.filter(md -> md.getLayout().equalsIgnoreCase(layout))
+						.filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation))
+						.filter(md -> StringUtils.isNotBlank(md.getHdfsPath()))
+						.filter(md -> StringUtils.isNotBlank(md.getCurrentVersion()))
+						.filter(md -> md.getSize() > 0)
+						.map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store")
+						.collect(Collectors.toSet());
+			}
+		}
+	}
+
 	private Configuration getConf() {
 		return new Configuration();
 		/*

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json

@@ -0,0 +1,38 @@
+[
+	{
+		"paramName": "p",
+		"paramLongName": "hdfsPath",
+		"paramDescription": "the path where storing the sequential file",
+		"paramRequired": true
+	},
+	{
+		"paramName": "u",
+		"paramLongName": "mdstoreManagerUrl",
+		"paramDescription": "the MdstoreManager url",
+		"paramRequired": true
+	},
+	{
+		"paramName": "f",
+		"paramLongName": "mdFormat",
+		"paramDescription": "metadata format",
+		"paramRequired": true
+	},
+	{
+		"paramName": "l",
+		"paramLongName": "mdLayout",
+		"paramDescription": "metadata layout",
+		"paramRequired": true
+	},
+	{
+		"paramName": "i",
+		"paramLongName": "mdInterpretation",
+		"paramDescription": "metadata interpretation",
+		"paramRequired": true
+	},
+	{
+		"paramName": "isu",
+		"paramLongName": "isLookupUrl",
+		"paramDescription": "the url of the ISLookupService",
+		"paramRequired": true
+	}
+]

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml

@@ -544,6 +544,33 @@
             <arg>--sourcePath</arg><arg>${workingDir}/entities</arg>
             <arg>--graphRawPath</arg><arg>${workingDir}/graph_raw</arg>
         </spark>
+        <ok to="Import_oaf_store_graph"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="Import_oaf_store_graph">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>ImportOAF_hdfs_graph</name>
+            <class>eu.dnetlib.dhp.oa.graph.raw.CopyHdfsOafApplication</class>
+            <jar>dhp-graph-mapper-${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}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--hdfsPath</arg><arg>${workingDir}/graph_raw</arg>
+            <arg>--mdstoreManagerUrl</arg><arg>${mdstoreManagerUrl}</arg>
+            <arg>--mdFormat</arg><arg>OAF</arg>
+            <arg>--mdLayout</arg><arg>store</arg>
+            <arg>--mdInterpretation</arg><arg>graph</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+        </spark>
         <ok to="wait_graphs"/>
         <error to="Kill"/>
     </action>

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/workflow.xml

@@ -1,177 +0,0 @@
-    <workflow-app name="Transform_BioEntity_Workflow" xmlns="uri:oozie:workflow:0.5">
-    <parameters>
-        <property>
-            <name>PDBPath</name>
-            <description>the PDB Database Working Path</description>
-        </property>
-
-        <property>
-            <name>UNIPROTDBPath</name>
-            <description>the UNIPROT Database Working Path</description>
-        </property>
-
-        <property>
-            <name>EBIDataset</name>
-            <description>the EBI Links Dataset  Path</description>
-        </property>
-
-        <property>
-            <name>ScholixResolvedDBPath</name>
-            <description>the Scholix Resolved Dataset  Path</description>
-        </property>
-
-        <property>
-            <name>CrossrefLinksPath</name>
-            <description>the CrossrefLinks Path</description>
-        </property>
-        <property>
-            <name>targetPath</name>
-            <description>the Target Working dir path</description>
-        </property>
-    </parameters>
-
-    <start to="ConvertPDB"/>
-
-    <kill name="Kill">
-        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
-    </kill>
-
-    <action name="ConvertPDB">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Convert PDB to OAF Dataset</name>
-            <class>eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.shuffle.partitions=2000
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-            </spark-opts>
-            <arg>--master</arg><arg>yarn</arg>
-            <arg>--dbPath</arg><arg>${PDBPath}</arg>
-            <arg>--database</arg><arg>PDB</arg>
-            <arg>--targetPath</arg><arg>${targetPath}/pdb_OAF</arg>
-        </spark>
-        <ok to="ConvertUNIPROT"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="ConvertUNIPROT">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Convert UNIPROT to OAF Dataset</name>
-            <class>eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.shuffle.partitions=2000
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-            </spark-opts>
-            <arg>--master</arg><arg>yarn</arg>
-            <arg>--dbPath</arg><arg>${UNIPROTDBPath}</arg>
-            <arg>--database</arg><arg>UNIPROT</arg>
-            <arg>--targetPath</arg><arg>${targetPath}/uniprot_OAF</arg>
-        </spark>
-        <ok to="ConvertEBILinks"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="ConvertEBILinks">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Convert EBI Links to OAF Dataset</name>
-            <class>eu.dnetlib.dhp.sx.graph.ebi.SparkEBILinksToOaf</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.shuffle.partitions=2000
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-            </spark-opts>
-            <arg>--master</arg><arg>yarn</arg>
-            <arg>--sourcePath</arg><arg>${EBIDataset}</arg>
-            <arg>--targetPath</arg><arg>${targetPath}/ebi_OAF</arg>
-        </spark>
-        <ok to="ConvertScholixResolved"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="ConvertScholixResolved">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Convert Scholix to OAF Dataset</name>
-            <class>eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.shuffle.partitions=2000
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-            </spark-opts>
-            <arg>--master</arg><arg>yarn</arg>
-            <arg>--dbPath</arg><arg>${ScholixResolvedDBPath}</arg>
-            <arg>--database</arg><arg>SCHOLIX</arg>
-            <arg>--targetPath</arg><arg>${targetPath}/scholix_resolved_OAF</arg>
-        </spark>
-        <ok to="ConvertCrossrefLinks"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="ConvertCrossrefLinks">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Convert Crossref Links to OAF Dataset</name>
-            <class>eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.shuffle.partitions=2000
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-            </spark-opts>
-            <arg>--master</arg><arg>yarn</arg>
-            <arg>--dbPath</arg><arg>${CrossrefLinksPath}</arg>
-            <arg>--database</arg><arg>CROSSREF_LINKS</arg>
-            <arg>--targetPath</arg><arg>${targetPath}/crossref_unresolved_relation_OAF</arg>
-        </spark>
-        <ok to="End"/>
-        <error to="Kill"/>
-    </action>
-
-
-
-
-    <end name="End"/>
-
-</workflow-app>

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java

@@ -74,7 +74,6 @@ public class SolrConfigExploreTest extends SolrExploreTest {
 			.config(conf)
 			.getOrCreate();
 
-
 	}
 
 	@AfterAll
@@ -87,7 +86,8 @@ public class SolrConfigExploreTest extends SolrExploreTest {
 
 		String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
 
-        new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null).run(isLookupClient);
+		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null)
+			.run(isLookupClient);
 		Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
 
 		String[] queryStrings = {
@@ -108,7 +108,8 @@ public class SolrConfigExploreTest extends SolrExploreTest {
 //            System.out.println(rsp.getExplainMap());
 
 			for (SolrDocument doc : rsp.getResults()) {
-                System.out.println(
+				System.out
+					.println(
 						doc.get("score") + "\t" +
 							doc.get("__indexrecordidentifier") + "\t" +
 							doc.get("resultidentifier") + "\t" +
@@ -118,8 +119,7 @@ public class SolrConfigExploreTest extends SolrExploreTest {
 							doc.get("resulttitle") + "\t" +
 							doc.get("relprojectname") + "\t" +
 							doc.get("resultdescription") + "\t" +
-                        doc.get("__all") + "\t"
+							doc.get("__all") + "\t");
-                );
 			}
 		}
 	}

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java

@@ -83,7 +83,6 @@ public class SolrConfigTest extends SolrTest {
 			.config(conf)
 			.getOrCreate();
 
-
 	}
 
 	@AfterAll
@@ -96,7 +95,8 @@ public class SolrConfigTest extends SolrTest {
 
 		String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
 
-        new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null).run(isLookupClient);
+		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null)
+			.run(isLookupClient);
 		Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
 
 		String[] queryStrings = {
@@ -113,7 +113,8 @@ public class SolrConfigTest extends SolrTest {
 			QueryResponse rsp = miniCluster.getSolrClient().query(query);
 
 			for (SolrDocument doc : rsp.getResults()) {
-                System.out.println(
+				System.out
+					.println(
 						doc.get("score") + "\t" +
 							doc.get("__indexrecordidentifier") + "\t" +
 							doc.get("resultidentifier") + "\t" +
@@ -123,8 +124,7 @@ public class SolrConfigTest extends SolrTest {
 							doc.get("resulttitle") + "\t" +
 							doc.get("relprojectname") + "\t" +
 							doc.get("resultdescription") + "\t" +
-                        doc.get("__all") + "\t"
+							doc.get("__all") + "\t");
-                );
 			}
 		}
 	}

pom.xml

@@ -753,7 +753,7 @@
 		<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>
-		<dhp-schemas.version>[2.8.20]</dhp-schemas.version>
+		<dhp-schemas.version>[2.8.21]</dhp-schemas.version>
 		<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
 		<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
 		<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>