Merge branch 'master' into przemyslawjacewicz_actionmanager_impl_prototype

dhp-common/pom.xml

@@ -46,6 +46,18 @@
 			<groupId>net.sf.saxon</groupId>
 			<artifactId>Saxon-HE</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>jcl-over-slf4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.cxf</groupId>
+			<artifactId>cxf-rt-transports-http</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>eu.dnetlib</groupId>
+			<artifactId>cnr-rmi-api</artifactId>
+		</dependency>
 	</dependencies>
 
 </project>

dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java

@@ -1,4 +1,4 @@
-package eu.dnetlib.dhp.graph.utils;
+package eu.dnetlib.dhp.utils;
 
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import org.apache.commons.logging.Log;

dhp-schemas/pom.xml

@@ -30,6 +30,12 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
         </dependency>
+        
+         <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>${junit.version}</version>
+        </dependency>
 
         <dependency>
             <groupId>eu.dnetlib.dhp</groupId>

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java

@@ -1,66 +1,83 @@
 package eu.dnetlib.dhp.schema.oaf;
 
+import java.util.ArrayList;
 import java.util.List;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.junit.Assert;
 
 public class Relation extends Oaf {
 
-    private String relType;
+	private String relType;
 
-    private String subRelType;
+	private String subRelType;
 
-    private String relClass;
+	private String relClass;
 
-    private String source;
+	private String source;
 
-    private String target;
+	private String target;
 
-    private List<KeyValue> collectedFrom;
+	private List<KeyValue> collectedFrom = new ArrayList<>();
 
-    public String getRelType() {
+	public String getRelType() {
-        return relType;
+		return relType;
-    }
+	}
 
-    public void setRelType(String relType) {
+	public void setRelType(final String relType) {
-        this.relType = relType;
+		this.relType = relType;
-    }
+	}
 
-    public String getSubRelType() {
+	public String getSubRelType() {
-        return subRelType;
+		return subRelType;
-    }
+	}
 
-    public void setSubRelType(String subRelType) {
+	public void setSubRelType(final String subRelType) {
-        this.subRelType = subRelType;
+		this.subRelType = subRelType;
-    }
+	}
 
-    public String getRelClass() {
+	public String getRelClass() {
-        return relClass;
+		return relClass;
-    }
+	}
 
-    public void setRelClass(String relClass) {
+	public void setRelClass(final String relClass) {
-        this.relClass = relClass;
+		this.relClass = relClass;
-    }
+	}
 
-    public String getSource() {
+	public String getSource() {
-        return source;
+		return source;
-    }
+	}
 
-    public void setSource(String source) {
+	public void setSource(final String source) {
-        this.source = source;
+		this.source = source;
-    }
+	}
 
-    public String getTarget() {
+	public String getTarget() {
-        return target;
+		return target;
-    }
+	}
 
-    public void setTarget(String target) {
+	public void setTarget(final String target) {
-        this.target = target;
+		this.target = target;
-    }
+	}
 
-    public List<KeyValue> getCollectedFrom() {
+	public List<KeyValue> getCollectedFrom() {
-        return collectedFrom;
+		return collectedFrom;
-    }
+	}
+
+	public void setCollectedFrom(final List<KeyValue> collectedFrom) {
+		this.collectedFrom = collectedFrom;
+	}
+
+	public void mergeFrom(final Relation r) {
+		Assert.assertEquals("source ids must be equal", getSource(), r.getSource());
+		Assert.assertEquals("target ids must be equal", getTarget(), r.getTarget());
+		Assert.assertEquals("relType(s) must be equal", getRelType(), r.getRelType());
+		Assert.assertEquals("subRelType(s) must be equal", getSubRelType(), r.getSubRelType());
+		Assert.assertEquals("relClass(es) must be equal", getRelClass(), r.getRelClass());
+		setCollectedFrom(Stream.concat(getCollectedFrom().stream(), r.getCollectedFrom().stream())
+				.distinct() // relies on KeyValue.equals
+				.collect(Collectors.toList()));
+	}
 
-    public void setCollectedFrom(List<KeyValue> collectedFrom) {
-        this.collectedFrom = collectedFrom;
-    }
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMigrationExecutor.java

@@ -227,7 +227,21 @@ public class AbstractMigrationExecutor implements Closeable {
 		final String nsPrefix = StringUtils.substringBefore(originalId, "::");
 		final String rest = StringUtils.substringAfter(originalId, "::");
 		return String.format("%s|%s::%s", prefix, nsPrefix, DHPUtils.md5(rest));
+	}
 
+	public static String createOpenaireId(final String type, final String originalId) {
+		switch (type) {
+		case "datasource":
+			return createOpenaireId(10, originalId);
+		case "organization":
+			return createOpenaireId(20, originalId);
+		case "person":
+			return createOpenaireId(30, originalId);
+		case "project":
+			return createOpenaireId(40, originalId);
+		default:
+			return createOpenaireId(50, originalId);
+		}
 	}
 
 	public static String asString(final Object o) {

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java

@@ -398,6 +398,8 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
 	protected DataInfo prepareDataInfo(final Document doc) {
 		final Node n = doc.selectSingleNode("//oaf:datainfo");
 
+		if (n == null) { return null; }
+
 		final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
 		final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
 		final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/ExtractEntitiesFromHDFSJob.java

@@ -1,56 +1,94 @@
 package eu.dnetlib.dhp.migration;
 
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
 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.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.Text;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.sql.SparkSession;
-import scala.Tuple2;
 
-import java.util.Arrays;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import java.util.List;
+import eu.dnetlib.dhp.schema.oaf.Dataset;
+import eu.dnetlib.dhp.schema.oaf.Datasource;
+import eu.dnetlib.dhp.schema.oaf.Organization;
+import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
+import eu.dnetlib.dhp.schema.oaf.Project;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.Software;
+import scala.Tuple2;
 
 public class ExtractEntitiesFromHDFSJob {
 
+	private static final Log log = LogFactory.getLog(ExtractEntitiesFromHDFSJob.class);
 
-    private static List<String> folderNames = Arrays.asList("db_entities", "oaf_entities", "odf_entities");
+	public static void main(final String[] args) throws Exception {
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+				IOUtils.toString(MigrateMongoMdstoresApplication.class
+						.getResourceAsStream("/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json")));
+		parser.parseArgument(args);
 
-    public static void main(String[] args) throws Exception {
+		final SparkSession spark = SparkSession
-        final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+				.builder()
-                IOUtils.toString(MigrateMongoMdstoresApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json")));
+				.appName(ExtractEntitiesFromHDFSJob.class.getSimpleName())
-        parser.parseArgument(args);
+				.master(parser.get("master"))
+				.getOrCreate();
 
-        final SparkSession spark = SparkSession
+		try (final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext())) {
-                .builder()
-                .appName(ExtractEntitiesFromHDFSJob.class.getSimpleName())
-                .master(parser.get("master"))
-                .getOrCreate();
 
-        final String sourcePath = parser.get("sourcePath");
+			final List<String> sourcePaths = Arrays.stream(parser.get("sourcePaths").split(",")).filter(p -> exists(sc, p)).collect(Collectors.toList());
-        final String targetPath = parser.get("graphRawPath");
+			final String targetPath = parser.get("graphRawPath");
-        final String entity = parser.get("entity");
 
+			processEntity(sc, Publication.class, sourcePaths, targetPath);
+			processEntity(sc, Dataset.class, sourcePaths, targetPath);
+			processEntity(sc, Software.class, sourcePaths, targetPath);
+			processEntity(sc, OtherResearchProduct.class, sourcePaths, targetPath);
+			processEntity(sc, Datasource.class, sourcePaths, targetPath);
+			processEntity(sc, Organization.class, sourcePaths, targetPath);
+			processEntity(sc, Project.class, sourcePaths, targetPath);
+			processEntity(sc, Relation.class, sourcePaths, targetPath);
+		}
+	}
 
-        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+	private static void processEntity(final JavaSparkContext sc, final Class<?> clazz, final List<String> sourcePaths, final String targetPath) {
+		final String type = clazz.getSimpleName().toLowerCase();
 
+		log.info(String.format("Processing entities (%s) in files:", type));
+		sourcePaths.forEach(log::info);
 
-        JavaRDD<String> inputRdd = sc.emptyRDD();
+		JavaRDD<String> inputRdd = sc.emptyRDD();
 
+		for (final String sp : sourcePaths) {
+			inputRdd = inputRdd.union(sc.sequenceFile(sp, Text.class, Text.class)
+					.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
+					.filter(k -> isEntityType(k._1(), type))
+					.map(Tuple2::_2));
+		}
 
-        folderNames.forEach(p -> inputRdd.union(
+		inputRdd.saveAsTextFile(targetPath + "/" + type);
-                sc.sequenceFile(sourcePath+"/"+p, Text.class, Text.class)
-                    .map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
-                        .filter(k -> isEntityType(k._1(), entity))
-                        .map(Tuple2::_2))
-        );
 
-        inputRdd.saveAsTextFile(targetPath+"/"+entity);
+	}
-    }
 
+	private static boolean isEntityType(final String item, final String type) {
+		return StringUtils.substringAfter(item, ":").equalsIgnoreCase(type);
+	}
 
-    private static boolean isEntityType(final String item, final String entity) {
+	private static boolean exists(final JavaSparkContext context, final String pathToFile) {
-        return StringUtils.substringAfter(item, ":").equalsIgnoreCase(entity);
+		try {
-    }
+			final FileSystem hdfs = org.apache.hadoop.fs.FileSystem.get(context.hadoopConfiguration());
+			final Path path = new Path(pathToFile);
+			return hdfs.exists(path);
+		} catch (final IOException e) {
+			throw new RuntimeException(e);
+		}
+	}
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MigrateDbEntitiesApplication.java

@@ -17,15 +17,21 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.oaf.Context;
 import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.Dataset;
 import eu.dnetlib.dhp.schema.oaf.Datasource;
 import eu.dnetlib.dhp.schema.oaf.Field;
 import eu.dnetlib.dhp.schema.oaf.Journal;
 import eu.dnetlib.dhp.schema.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.oaf.Organization;
+import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
 import eu.dnetlib.dhp.schema.oaf.Project;
+import eu.dnetlib.dhp.schema.oaf.Publication;
 import eu.dnetlib.dhp.schema.oaf.Qualifier;
 import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.Software;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 
 public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor implements Closeable {
@@ -53,22 +59,28 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor impl
 		final String hdfsNameNode = parser.get("namenode");
 		final String hdfsUser = parser.get("hdfsUser");
 
+		final boolean processClaims = parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims");
+
 		try (final MigrateDbEntitiesApplication smdbe = new MigrateDbEntitiesApplication(hdfsPath, hdfsNameNode, hdfsUser, dbUrl, dbUser, dbPassword)) {
-			log.info("Processing datasources...");
+			if (processClaims) {
-			smdbe.execute("queryDatasources.sql", smdbe::processDatasource);
+				log.info("Processing claims...");
+				smdbe.execute("queryClaims.sql", smdbe::processClaims);
+			} else {
+				log.info("Processing datasources...");
+				smdbe.execute("queryDatasources.sql", smdbe::processDatasource);
 
-			log.info("Processing projects...");
+				log.info("Processing projects...");
-			smdbe.execute("queryProjects.sql", smdbe::processProject);
+				smdbe.execute("queryProjects.sql", smdbe::processProject);
 
-			log.info("Processing orgs...");
+				log.info("Processing orgs...");
-			smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
+				smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
 
-			log.info("Processing relations ds <-> orgs ...");
+				log.info("Processing relations ds <-> orgs ...");
-			smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
+				smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
-
-			log.info("Processing projects <-> orgs ...");
-			smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
 
+				log.info("Processing projects <-> orgs ...");
+				smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
+			}
 			log.info("All done.");
 		}
 	}
@@ -377,7 +389,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor impl
 			r2.setTarget(dsId);
 			r2.setCollectedFrom(collectedFrom);
 			r2.setDataInfo(info);
-			r1.setLastupdatetimestamp(lastUpdateTimestamp);
+			r2.setLastupdatetimestamp(lastUpdateTimestamp);
 			emitOaf(r2);
 
 			// rs.getString("datasource");
@@ -426,7 +438,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor impl
 			r2.setTarget(projectId);
 			r2.setCollectedFrom(collectedFrom);
 			r2.setDataInfo(info);
-			r1.setLastupdatetimestamp(lastUpdateTimestamp);
+			r2.setLastupdatetimestamp(lastUpdateTimestamp);
 			emitOaf(r2);
 
 			// rs.getString("project");
@@ -450,6 +462,81 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor impl
 		}
 	}
 
+	public void processClaims(final ResultSet rs) {
+
+		final DataInfo info =
+				dataInfo(false, null, false, false, qualifier("user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"), "0.9");
+
+		try {
+
+			if (rs.getString("source_type").equals("context")) {
+				final Result r;
+
+				if (rs.getString("target_type").equals("dataset")) {
+					r = new Dataset();
+				} else if (rs.getString("target_type").equals("software")) {
+					r = new Software();
+				} else if (rs.getString("target_type").equals("other")) {
+					r = new OtherResearchProduct();
+				} else {
+					r = new Publication();
+				}
+				r.setId(createOpenaireId(50, rs.getString("target_id")));
+				r.setLastupdatetimestamp(lastUpdateTimestamp);
+				r.setContext(prepareContext(rs.getString("source_id"), info));
+				r.setDataInfo(info);
+				emitOaf(r);
+			} else {
+				final String sourceId = createOpenaireId(rs.getString("source_type"), rs.getString("source_id"));
+				final String targetId = createOpenaireId(rs.getString("target_type"), rs.getString("target_id"));
+
+				final Relation r1 = new Relation();
+				final Relation r2 = new Relation();
+
+				if (rs.getString("source_type").equals("project")) {
+					r1.setRelType("resultProject");
+					r1.setSubRelType("outcome");
+					r1.setRelClass("produces");
+
+					r2.setRelType("resultProject");
+					r2.setSubRelType("outcome");
+					r2.setRelClass("isProducedBy");
+				} else {
+					r1.setRelType("resultResult");
+					r1.setSubRelType("relationship");
+					r1.setRelClass("isRelatedTo");
+
+					r2.setRelType("resultResult");
+					r2.setSubRelType("relationship");
+					r2.setRelClass("isRelatedTo");
+				}
+
+				r1.setSource(sourceId);
+				r1.setTarget(targetId);
+				r1.setDataInfo(info);
+				r1.setLastupdatetimestamp(lastUpdateTimestamp);
+				emitOaf(r1);
+
+				r2.setSource(targetId);
+				r2.setTarget(sourceId);
+				r2.setDataInfo(info);
+				r2.setLastupdatetimestamp(lastUpdateTimestamp);
+				emitOaf(r2);
+
+			}
+
+		} catch (final Exception e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	private List<Context> prepareContext(final String id, final DataInfo dataInfo) {
+		final Context context = new Context();
+		context.setId(id);
+		context.setDataInfo(Arrays.asList(dataInfo));
+		return Arrays.asList(context);
+	}
+
 	private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException {
 		final Boolean deletedbyinference = rs.getBoolean("deletedbyinference");
 		final String inferenceprovenance = rs.getString("inferenceprovenance");

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json

@@ -1,8 +1,8 @@
 [
 	{
 		"paramName": "s",
-		"paramLongName": "sourcePath",
+		"paramLongName": "sourcePaths",
-		"paramDescription": "the HDFS  source path which contains the sequential file",
+		"paramDescription": "the HDFS  source paths which contains the sequential file (comma separated)",
 		"paramRequired": true
 	},
 	{
@@ -16,11 +16,5 @@
 		"paramLongName": "graphRawPath",
 		"paramDescription": "the path of the graph Raw in hdfs",
 		"paramRequired": true
-	},
-	{
-		"paramName": "e",
-		"paramLongName": "entity",
-		"paramDescription": "The entity to extract",
-		"paramRequired": true
 	}
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json

@@ -34,5 +34,11 @@
 		"paramLongName": "postgresPassword",
 		"paramDescription": "postgres password",
 		"paramRequired": false
+	},
+	{
+		"paramName": "a",
+		"paramLongName": "action",
+		"paramDescription": "process claims",
+		"paramRequired": false
 	}
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/workflow.xml

@@ -43,8 +43,7 @@
         </property>
     </parameters>
 
-    <start to="ResetWorkingPath"/>
+	<start to="ResetWorkingPath"/>
-
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
@@ -71,7 +70,24 @@
             <arg>-dbuser</arg><arg>${postgresUser}</arg>
             <arg>-dbpasswd</arg><arg>${postgresPassword}</arg>
         </java>
-        <ok to="ImportODFEntitiesFromMongoDB"/>
+        <ok to="ImportClaimsFromPostgres"/>
+        <error to="Kill"/>
+    </action>
+    
+    <action name="ImportClaimsFromPostgres">
+        <java>
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <main-class>eu.dnetlib.dhp.migration.MigrateDbEntitiesApplication</main-class>
+            <arg>-p</arg><arg>${workingPath}/db_claims</arg>
+            <arg>-n</arg><arg>${nameNode}</arg>
+            <arg>-u</arg><arg>${hdfsUser}</arg>
+            <arg>-dburl</arg><arg>${postgresURL}</arg>
+            <arg>-dbuser</arg><arg>${postgresUser}</arg>
+            <arg>-dbpasswd</arg><arg>${postgresPassword}</arg>
+            <arg>-a</arg><arg>claims</arg>
+        </java>
+		<ok to="ImportODFEntitiesFromMongoDB"/>
         <error to="Kill"/>
     </action>
 
@@ -113,170 +129,78 @@
             <arg>-pguser</arg><arg>${postgresUser}</arg>
             <arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
         </java>
-        <ok to="End"/>
+        <ok to="ImportODFClaimsFromMongoDB"/>
+        <error to="Kill"/>
+    </action>
+    
+    <action name="ImportODFClaimsFromMongoDB">
+        <java>
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <main-class>eu.dnetlib.dhp.migration.MigrateMongoMdstoresApplication</main-class>
+            <arg>-p</arg><arg>${workingPath}/odf_claims</arg>
+            <arg>-n</arg><arg>${nameNode}</arg>
+            <arg>-u</arg><arg>${hdfsUser}</arg>
+            <arg>-mongourl</arg><arg>${mongourl}</arg>
+            <arg>-db</arg><arg>${mongoDb}</arg>
+            <arg>-f</arg><arg>ODF</arg>
+            <arg>-l</arg><arg>store</arg>
+            <arg>-i</arg><arg>claim</arg>
+            <arg>-pgurl</arg><arg>${postgresURL}</arg>
+            <arg>-pguser</arg><arg>${postgresUser}</arg>
+            <arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
+        </java>
+        <ok to="ImportOAFClaimsFromMongoDB"/>
         <error to="Kill"/>
     </action>
 
+    <action name="ImportOAFClaimsFromMongoDB">
+        <java>
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <main-class>eu.dnetlib.dhp.migration.MigrateMongoMdstoresApplication</main-class>
+            <arg>-p</arg><arg>${workingPath}/oaf_claims</arg>
+            <arg>-n</arg><arg>${nameNode}</arg>
+            <arg>-u</arg><arg>${hdfsUser}</arg>
+            <arg>-mongourl</arg><arg>${mongourl}</arg>
+            <arg>-db</arg><arg>${mongoDb}</arg>
+            <arg>-f</arg><arg>OAF</arg>
+            <arg>-l</arg><arg>store</arg>
+            <arg>-i</arg><arg>claim</arg>
+            <arg>-pgurl</arg><arg>${postgresURL}</arg>
+            <arg>-pguser</arg><arg>${postgresUser}</arg>
+            <arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
+        </java>
+        <ok to="ResetGraphRawPath"/>
+        <error to="Kill"/>
+    </action>
 
-    <action name="ExtractPublication">
+	<action name="ResetGraphRawPath">
+        <fs>
+            <delete path='${graphRawPath}'/>
+            <mkdir path='${graphRawPath}'/>
+        </fs>
+        <ok to="ExtractEntitiesInGraphRawPath"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ExtractEntitiesInGraphRawPath">
         <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>ExtractEntities: publication</name>
+            <name>ExtractEntities</name>
             <class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</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>--sourcePath</arg><arg>${workingPath}</arg>
+            <arg>-s</arg><arg>${workingPath}/db_entities,${workingPath}/oaf_entities,${workingPath}/odf_entities</arg>
-            <arg>-g</arg><arg>${graphRawPath}/publication</arg>
+            <arg>-g</arg><arg>${graphRawPath}</arg>
-            <arg>-e</arg><arg>publication</arg>
-        </spark>
-        <ok to="ExtractDataset"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="ExtractDataset">
-        <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>ExtractEntities: dataset</name>
-            <class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</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>--sourcePath</arg><arg>${workingPath}</arg>
-            <arg>-g</arg><arg>${graphRawPath}/dataset</arg>
-            <arg>-e</arg><arg>dataset</arg>
-        </spark>
-        <ok to="ExtractSoftware"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="ExtractSoftware">
-        <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>ExtractEntities: software</name>
-            <class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</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>--sourcePath</arg><arg>${workingPath}</arg>
-            <arg>-g</arg><arg>${graphRawPath}/software</arg>
-            <arg>-e</arg><arg>software</arg>
-        </spark>
-        <ok to="ExtractORP"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="ExtractORP">
-        <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>ExtractEntities: otherresearchproduct</name>
-            <class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</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>--sourcePath</arg><arg>${workingPath}</arg>
-            <arg>-g</arg><arg>${graphRawPath}/otherresearchproduct</arg>
-            <arg>-e</arg><arg>otherresearchproduct</arg>
-        </spark>
-        <ok to="ExtractDatasource"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="ExtractDatasource">
-        <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>ExtractEntities: datasource</name>
-            <class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</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>--sourcePath</arg><arg>${workingPath}</arg>
-            <arg>-g</arg><arg>${graphRawPath}/datasource</arg>
-            <arg>-e</arg><arg>datasource</arg>
-        </spark>
-        <ok to="ExtractOrganization"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="ExtractOrganization">
-        <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>ExtractEntities: organization</name>
-            <class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</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>--sourcePath</arg><arg>${workingPath}</arg>
-            <arg>-g</arg><arg>${graphRawPath}/organization</arg>
-            <arg>-e</arg><arg>organization</arg>
-        </spark>
-        <ok to="ExtractProject"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="ExtractProject">
-        <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>ExtractEntities: project</name>
-            <class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</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>--sourcePath</arg><arg>${workingPath}</arg>
-            <arg>-g</arg><arg>${graphRawPath}/project</arg>
-            <arg>-e</arg><arg>project</arg>
-        </spark>
-        <ok to="ExtractRelation"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="ExtractRelation">
-        <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>ExtractEntities: relation</name>
-            <class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</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>--sourcePath</arg><arg>${workingPath}</arg>
-            <arg>-g</arg><arg>${graphRawPath}/relation</arg>
-            <arg>-e</arg><arg>relation</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>
-    </action>
+    </action>  
-
 
     <end name="End"/>
 </workflow-app>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryClaims.sql

@@ -0,0 +1 @@
+SELECT source_type, source_id, target_type, target_id, semantics FROM claim WHERE approved=TRUE;

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects.sql

@@ -28,15 +28,17 @@ SELECT
                 p.summary                                                                                                  AS summary,
                 p.currency                                                                                                 AS currency,
                 p.totalcost                                                                                                AS totalcost,
-        p.fundedamount                                                                                             AS fundedamount,
+                p.fundedamount                                                                                             AS fundedamount,
                 dc.id                                                                                                      AS collectedfromid,
                 dc.officialname                                                                                            AS collectedfromname,
-                ctc.code || '@@@' || ctc.name || '@@@' || cts.code || '@@@' || cts.name                                    AS contracttype,
+                p.contracttype || '@@@' || p.contracttypename || '@@@' || p.contracttypescheme || '@@@' || p.contracttypescheme     AS contracttype,
-                pac.code || '@@@' || pac.name || '@@@' || pas.code || '@@@' || pas.name                                    AS provenanceaction,
+                pac.code || '@@@' || pac.name || '@@@' || pas.code || '@@@' || pas.name                                             AS provenanceaction,
-                array_agg(DISTINCT i.pid || '###' || i.issuertype)                                                         AS pid,
+                array_agg(DISTINCT i.pid || '###' || i.issuertype)                                                                  AS pid,
-                array_agg(DISTINCT s.name || '###' || sc.code || '@@@' || sc.name || '@@@' || ss.code || '@@@' || ss.name) AS subjects,
+                array_agg(DISTINCT s.name || '###' || sc.code || '@@@' || sc.name || '@@@' || ss.code || '@@@' || ss.name)          AS subjects,
-                array_agg(DISTINCT fp.path)                                                                                AS fundingtree
+                array_agg(DISTINCT fp.path)                                                                                         AS fundingtree
+
         FROM projects p
+
                 LEFT OUTER JOIN class pac ON (pac.code = p.provenanceactionclass)
                 LEFT OUTER JOIN scheme pas ON (pas.code = p.provenanceactionscheme)
 
@@ -54,9 +56,6 @@ SELECT
                 LEFT OUTER JOIN class sc ON (sc.code = s.semanticclass)
                 LEFT OUTER JOIN scheme ss ON (ss.code = s.semanticscheme)
 
-                LEFT OUTER JOIN class ctc ON (ctc.code = p.contracttypeclass)
-                LEFT OUTER JOIN scheme cts ON (cts.code = p.contracttypescheme)
-
         GROUP BY
                 p.id,
                 p.code,
@@ -87,4 +86,4 @@ SELECT
                 dc.id,
                 dc.officialname,
                 pac.code, pac.name, pas.code, pas.name,
-                ctc.code, ctc.name, cts.code, cts.name;
+                p.contracttype , p.contracttypename, p.contracttypescheme;

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects_production.sql

@@ -0,0 +1,90 @@
+SELECT
+                p.id                                                                                                       AS projectid,
+                p.code                                                                                                     AS code,
+                p.websiteurl                                                                                               AS websiteurl,
+                p.acronym                                                                                                  AS acronym,
+                p.title                                                                                                    AS title,
+                p.startdate                                                                                                AS startdate,
+                p.enddate                                                                                                  AS enddate,
+                p.call_identifier                                                                                          AS callidentifier,
+                p.keywords                                                                                                 AS keywords,
+                p.duration                                                                                                 AS duration,
+                p.ec_sc39                                                                                                  AS ecsc39,
+                p.oa_mandate_for_publications                                                                              AS oamandatepublications,
+                p.ec_article29_3                                                                                           AS ecarticle29_3,
+                p.dateofcollection                                                                                         AS dateofcollection,
+                p.lastupdate                                                                                               AS dateoftransformation,
+                p.inferred                                                                                                 AS inferred,
+                p.deletedbyinference                                                                                       AS deletedbyinference,
+                p.trust                                                                                                    AS trust,
+                p.inferenceprovenance                                                                                      AS inferenceprovenance,
+                p.optional1                                                                                                AS optional1,
+                p.optional2                                                                                                AS optional2,
+                p.jsonextrainfo                                                                                            AS jsonextrainfo,
+                p.contactfullname                                                                                          AS contactfullname,
+                p.contactfax                                                                                               AS contactfax,
+                p.contactphone                                                                                             AS contactphone,
+                p.contactemail                                                                                             AS contactemail,
+                p.summary                                                                                                  AS summary,
+                p.currency                                                                                                 AS currency,
+                p.totalcost                                                                                                AS totalcost,
+        p.fundedamount                                                                                             AS fundedamount,
+                dc.id                                                                                                      AS collectedfromid,
+                dc.officialname                                                                                            AS collectedfromname,
+                ctc.code || '@@@' || ctc.name || '@@@' || cts.code || '@@@' || cts.name                                    AS contracttype,
+                pac.code || '@@@' || pac.name || '@@@' || pas.code || '@@@' || pas.name                                    AS provenanceaction,
+                array_agg(DISTINCT i.pid || '###' || i.issuertype)                                                         AS pid,
+                array_agg(DISTINCT s.name || '###' || sc.code || '@@@' || sc.name || '@@@' || ss.code || '@@@' || ss.name) AS subjects,
+                array_agg(DISTINCT fp.path)                                                                                AS fundingtree
+        FROM projects p
+                LEFT OUTER JOIN class pac ON (pac.code = p.provenanceactionclass)
+                LEFT OUTER JOIN scheme pas ON (pas.code = p.provenanceactionscheme)
+
+                LEFT OUTER JOIN projectpids pp ON (pp.project = p.id)
+                LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid)
+
+                LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom)
+
+                LEFT OUTER JOIN project_fundingpath pf ON (pf.project = p.id)
+                LEFT OUTER JOIN fundingpaths fp ON (fp.id = pf.funding)
+
+                LEFT OUTER JOIN project_subject ps ON (ps.project = p.id)
+                LEFT OUTER JOIN subjects s ON (s.id = ps.subject)
+
+                LEFT OUTER JOIN class sc ON (sc.code = s.semanticclass)
+                LEFT OUTER JOIN scheme ss ON (ss.code = s.semanticscheme)
+
+                LEFT OUTER JOIN class ctc ON (ctc.code = p.contracttypeclass)
+                LEFT OUTER JOIN scheme cts ON (cts.code = p.contracttypescheme)
+
+        GROUP BY
+                p.id,
+                p.code,
+                p.websiteurl,
+                p.acronym,
+                p.title,
+                p.startdate,
+                p.enddate,
+                p.call_identifier,
+                p.keywords,
+                p.duration,
+                p.ec_sc39,
+                p.oa_mandate_for_publications,
+                p.ec_article29_3,
+                p.dateofcollection,
+                p.inferred,
+                p.deletedbyinference,
+                p.trust,
+                p.inferenceprovenance,
+                p.contactfullname,
+                p.contactfax,
+                p.contactphone,
+                p.contactemail,
+                p.summary,
+                p.currency,
+                p.totalcost,
+                p.fundedamount,
+                dc.id,
+                dc.officialname,
+                pac.code, pac.name, pas.code, pas.name,
+                ctc.code, ctc.name, cts.code, cts.name;

dhp-workflows/dhp-graph-provision/pom.xml

@@ -66,14 +66,6 @@
             <artifactId>zookeeper</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>org.apache.cxf</groupId>
-            <artifactId>cxf-rt-transports-http</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib</groupId>
-            <artifactId>cnr-rmi-api</artifactId>
-        </dependency>
 
         <dependency>
             <groupId>eu.dnetlib.dhp</groupId>

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlIndexingJob.java

@@ -2,8 +2,8 @@ package eu.dnetlib.dhp.graph;
 
 import com.lucidworks.spark.util.SolrSupport;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.graph.utils.ISLookupClientFactory;
 import eu.dnetlib.dhp.graph.utils.StreamingInputDocumentFactory;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpDocumentNotFoundException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ContextMapper.java

@@ -1,6 +1,7 @@
 package eu.dnetlib.dhp.graph.utils;
 
 import com.google.common.base.Joiner;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import org.dom4j.Document;

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/XmlRecordFactory.java

@@ -43,8 +43,6 @@ public class XmlRecordFactory implements Serializable {
 
     private String schemaLocation;
 
-    private Set<String> contextes = Sets.newHashSet();
-
     private boolean indent = false;
 
     public XmlRecordFactory(
@@ -59,15 +57,18 @@ public class XmlRecordFactory implements Serializable {
     }
 
     public String build(final JoinedEntity je) {
+
+        final Set<String> contexts = Sets.newHashSet();
+
         final OafEntity entity = je.getEntity();
         TemplateFactory templateFactory = new TemplateFactory();
         try {
-            final List<String> metadata = metadata(je.getType(), entity);
+            final List<String> metadata = metadata(je.getType(), entity, contexts);
 
             // rels has to be processed before the contexts because they enrich the contextMap with the funding info.
-            final List<String> relations = listRelations(je, templateFactory);
+            final List<String> relations = listRelations(je, templateFactory, contexts);
 
-            metadata.addAll(buildContexts(getMainType(je.getType())));
+            metadata.addAll(buildContexts(getMainType(je.getType()), contexts));
             metadata.add(parseDataInfo(entity.getDataInfo()));
 
             final String body = templateFactory.buildBody(
@@ -97,10 +98,11 @@ public class XmlRecordFactory implements Serializable {
         }
     }
 
-    private List<String> metadata(final String type, final OafEntity entity) {
+    private List<String> metadata(final String type, final OafEntity entity, final Set<String> contexts) {
 
         final List<String> metadata = Lists.newArrayList();
 
+
         if (entity.getCollectedfrom() != null) {
             metadata.addAll(entity.getCollectedfrom()
                 .stream()
@@ -123,6 +125,17 @@ public class XmlRecordFactory implements Serializable {
         if (GraphMappingUtils.isResult(type)) {
             final Result r = (Result) entity;
 
+            if (r.getContext() != null) {
+                contexts.addAll(r.getContext()
+                        .stream()
+                        .map(c -> c.getId())
+                        .collect(Collectors.toList()));
+                /* FIXME: Workaround for CLARIN mining issue: #3670#note-29 */
+                if (contexts.contains("dh-ch::subcommunity::2")) {
+                    contexts.add("clarin");
+                }
+            }
+
             if (r.getTitle() != null) {
                 metadata.addAll(r.getTitle()
                     .stream()
@@ -235,16 +248,6 @@ public class XmlRecordFactory implements Serializable {
             }
 
             metadata.add(mapQualifier("bestaccessright", getBestAccessright(r)));
-
-            if (r.getContext() != null) {
-                contextes.addAll(r.getContext()
-                    .stream()
-                    .map(c -> c.getId())
-                    .collect(Collectors.toList()));
-                if (contextes.contains("dh-ch::subcommunity::2")) {
-                    contextes.add("clarin");
-                }
-            }
         }
 
         switch (EntityType.valueOf(type)) {
@@ -618,7 +621,7 @@ public class XmlRecordFactory implements Serializable {
         return bestAccessRight;
     }
 
-    private List<String> listRelations(final JoinedEntity je, TemplateFactory templateFactory) {
+    private List<String> listRelations(final JoinedEntity je, TemplateFactory templateFactory, final Set<String> contexts) {
         final List<String> rels = Lists.newArrayList();
 
         for (final Tuple2 link : je.getLinks()) {
@@ -699,7 +702,7 @@ public class XmlRecordFactory implements Serializable {
                     if (re.getFundingtree() != null) {
                         metadata.addAll(re.getFundingtree()
                                 .stream()
-                                .peek(ft -> fillContextMap(ft))
+                                .peek(ft -> fillContextMap(ft, contexts))
                                 .map(ft -> getRelFundingTree(ft))
                                 .collect(Collectors.toList()));
                     }
@@ -807,14 +810,14 @@ public class XmlRecordFactory implements Serializable {
                 .collect(Collectors.toList()) : Lists.newArrayList();
     }
 
-    private List<String> buildContexts(final String type) {
+    private List<String> buildContexts(final String type, final Set<String> contexts) {
         final List<String> res = Lists.newArrayList();
 
         if ((contextMapper != null) && !contextMapper.isEmpty() && MainEntityType.result.toString().equals(type)) {
 
             XMLTag document = XMLDoc.newDocument(true).addRoot("contextRoot");
 
-            for (final String context : contextes) {
+            for (final String context : contexts) {
 
                 String id = "";
                 for (final String token : Splitter.on("::").split(context)) {
@@ -882,7 +885,7 @@ public class XmlRecordFactory implements Serializable {
         return buffer.toString();
     }
 
-    private void fillContextMap(final String xmlTree) {
+    private void fillContextMap(final String xmlTree, final Set<String> contexts) {
 
         Document fundingPath;
         try {
@@ -896,7 +899,7 @@ public class XmlRecordFactory implements Serializable {
             if (funder != null) {
 
                 final String funderShortName = funder.valueOf("./shortname");
-                contextes.add(funderShortName);
+                contexts.add(funderShortName);
 
                 contextMapper.put(funderShortName, new ContextDef(funderShortName, funder.valueOf("./name"), "context", "funding"));
                 final Node level0 = fundingPath.selectSingleNode("//funding_level_0");
@@ -905,17 +908,17 @@ public class XmlRecordFactory implements Serializable {
                     contextMapper.put(level0Id, new ContextDef(level0Id, level0.valueOf("./description"), "category", ""));
                     final Node level1 = fundingPath.selectSingleNode("//funding_level_1");
                     if (level1 == null) {
-                        contextes.add(level0Id);
+                        contexts.add(level0Id);
                     } else {
                         final String level1Id = Joiner.on("::").join(level0Id, level1.valueOf("./name"));
                         contextMapper.put(level1Id, new ContextDef(level1Id, level1.valueOf("./description"), "concept", ""));
                         final Node level2 = fundingPath.selectSingleNode("//funding_level_2");
                         if (level2 == null) {
-                            contextes.add(level1Id);
+                            contexts.add(level1Id);
                         } else {
                             final String level2Id = Joiner.on("::").join(level1Id, level2.valueOf("./name"));
                             contextMapper.put(level2Id, new ContextDef(level2Id, level2.valueOf("./description"), "concept", ""));
-                            contextes.add(level2Id);
+                            contexts.add(level2Id);
                         }
                     }
                 }

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

@@ -1,66 +0,0 @@
-package eu.dnetlib.dhp.graph;
-
-import eu.dnetlib.dhp.graph.model.EntityRelEntity;
-import eu.dnetlib.dhp.graph.model.RelatedEntity;
-import eu.dnetlib.dhp.graph.utils.GraphMappingUtils;
-import org.codehaus.jackson.map.ObjectMapper;
-import org.junit.Before;
-import org.junit.Test;
-
-import java.io.IOException;
-import java.io.InputStreamReader;
-
-public class MappingUtilsTest {
-
-    private GraphMappingUtils utils;
-
-    @Before
-    public void setUp() {
-        utils = new GraphMappingUtils();
-    }
-
-    @Test
-    public void testOafMappingDatasource() throws IOException {
-
-        final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("datasource.json"));
-        final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class);
-        e.getSource().setType("datasource");
-
-        final EntityRelEntity out = utils.asRelatedEntity(e);
-        System.out.println(out);
-
-    }
-
-    //@Test
-    public void testOafMappingResult() throws IOException {
-
-        final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("result.json"));
-        final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class);
-
-        final EntityRelEntity out = utils.asRelatedEntity(e);
-        System.out.println(out);
-
-    }
-
-    @Test
-    public void testOafMappingSoftware() throws IOException {
-
-        final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("software.json"));
-        final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class);
-
-        final EntityRelEntity out = utils.asRelatedEntity(e);
-        System.out.println(out);
-
-    }
-
-
-    @Test
-    public void testParseRelatedEntity() throws IOException {
-
-        final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("related_entity.json"));
-        final RelatedEntity e = new ObjectMapper().readValue(in, RelatedEntity.class);
-
-        System.out.println(e);
-
-    }
-}

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

@@ -1,55 +0,0 @@
-package eu.dnetlib.dhp.graph;
-
-import eu.dnetlib.dhp.graph.utils.ContextMapper;
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.apache.spark.sql.SparkSession;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-
-public class XmlRecordFactoryTest {
-
-    private static final Log log = LogFactory.getLog(XmlRecordFactoryTest.class);
-
-    private Path testDir;
-
-    @Before
-    public void setup() throws IOException {
-        testDir = Files.createTempDirectory(getClass().getSimpleName());
-        log.info("created test directory " + testDir.toString());
-    }
-
-    @After
-    public void tearDown() throws IOException {
-        FileUtils.deleteDirectory(testDir.toFile());
-        log.info("deleted test directory " + testDir.toString());
-    }
-
-    @Test
-    public void  testXmlSerialization() throws Exception {
-
-        final SparkSession spark = SparkSession
-                .builder()
-                .appName(SparkXmlRecordBuilderJob.class.getSimpleName())
-                .master("local[*]")
-                .getOrCreate();
-
-        final String inputDir = testDir.toString() + "/3_joined_entities";
-        FileUtils.forceMkdir(new File(inputDir));
-        FileUtils.copyFile(new File("/Users/claudio/Downloads/joined_entities-part-00000"), new File(inputDir + "/joined_entities-part-00000"));
-
-        final ContextMapper ctx = ContextMapper.fromIS("https://dev-openaire.d4science.org:443/is/services/isLookUp");
-
-        final GraphJoiner g = new GraphJoiner(spark, ctx, inputDir, testDir.toString());
-
-        g.asXML();
-    }
-
-}

dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/related_entity.json

@@ -1,5 +0,0 @@
-{
-  "id": "20|nih_________::6b8108b6d6399f7163a6a7ccdd0efc2d",
-  "type": "organization",
-  "legalname": "MCGILL UNIVERSITY"
-}

pom.xml

@@ -76,7 +76,7 @@
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
-			<version>4.12</version>
+			<version>${junit.version}</version>
 			<scope>test</scope>
 		</dependency>
 
@@ -129,6 +129,13 @@
 				<scope>provided</scope>
 			</dependency>
 
+			<dependency>
+				<groupId>org.slf4j</groupId>
+				<artifactId>jcl-over-slf4j</artifactId>
+				<version>1.7.25</version>
+				<scope>provided</scope>
+			</dependency>
+
 			<dependency>
 				<groupId>org.apache.commons</groupId>
 				<artifactId>commons-lang3</artifactId>
@@ -474,6 +481,7 @@
 		<dhp.jackson.version>2.9.6</dhp.jackson.version>
 		<dhp.commons.lang.version>3.5</dhp.commons.lang.version>
 		<scala.version>2.11.12</scala.version>
+		<junit.version>4.12</junit.version>
 		<mongodb.driver.version>3.4.2</mongodb.driver.version>
 	</properties>
 </project>