bulktagging wfs moved into common dhp-enrichment module

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

@@ -16,16 +16,23 @@
             <name>sourcePath</name>
             <description>the source path</description>
         </property>
+        <property>
+            <name>outputPath</name>
+            <description>the graph output path</description>
+        </property>
     </parameters>
-<start to="reset-outputpath"/>
+
+    <start to="reset_outputpath"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
-    <action name="reset-outputpath">
+    <action name="reset_outputpath">
         <fs>
-            <delete path='${workingDir}/blacklist'/>
+            <delete path="${workingDir}/blacklist"/>
+            <delete path="${outputPath}"/>
+            <mkdir path="${outputPath}"/>
         </fs>
         <ok to="read_blacklist"/>
         <error to="Kill"/>
@@ -87,12 +94,14 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/relation</arg>
+            <arg>--outputPath</arg><arg>${outputPath}/relation</arg>
             <arg>--hdfsPath</arg><arg>${workingDir}/blacklist</arg>
             <arg>--mergesPath</arg><arg>${workingDir}/mergesRelation</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>
     </action>
+
     <end name="End"/>
+
 </workflow-app>

dhp-workflows/dhp-bulktag/project-default.properties

@@ -1,7 +0,0 @@
-#sandboxName when not provided explicitly will be generated
-sandboxName=${sandboxName}
-sandboxDir=/user/${dhp.hadoop.frontend.user.name}/${sandboxName}
-workingDir=${sandboxDir}/working_dir
-oozie.wf.application.path = ${nameNode}${sandboxDir}/${oozieAppDir}
-oozieTopWfApplicationPath = ${oozie.wf.application.path}
-

dhp-workflows/dhp-enrichment/pom.xml

@@ -9,7 +9,7 @@
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
-    <artifactId>dhp-bulktag</artifactId>
+    <artifactId>dhp-enrichment</artifactId>
     <dependencies>
 
         <dependency>
@@ -31,6 +31,12 @@
             <artifactId>dhp-schemas</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.spark</groupId>
+            <artifactId>spark-hive_2.11</artifactId>
+            <scope>test</scope>
+        </dependency>
+
         <dependency>
             <groupId>dom4j</groupId>
             <artifactId>dom4j</artifactId>
@@ -43,23 +49,16 @@
             <groupId>com.jayway.jsonpath</groupId>
             <artifactId>json-path</artifactId>
         </dependency>
-        <dependency>
+
-            <groupId>org.reflections</groupId>
-            <artifactId>reflections</artifactId>
-            <version>0.9.11</version>
-            <scope>compile</scope>
-        </dependency>
-        <dependency>
-            <groupId>com.google.guava</groupId>
-            <artifactId>guava</artifactId>
-            <version>23.3-jre</version>
-        </dependency>
         <dependency>
             <groupId>io.github.classgraph</groupId>
             <artifactId>classgraph</artifactId>
             <version>4.8.71</version>
         </dependency>
+
+
     </dependencies>
 
 
+
 </project>

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java

@@ -1,10 +1,11 @@
 
 package eu.dnetlib.dhp.bulktag;
 
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import com.fasterxml.jackson.databind.ObjectMapper;
-
+import com.google.gson.Gson;
-import java.util.Optional;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-
+import eu.dnetlib.dhp.bulktag.community.*;
+import eu.dnetlib.dhp.schema.oaf.Result;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
@@ -15,12 +16,9 @@ import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import java.util.Optional;
-import com.google.gson.Gson;
 
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import eu.dnetlib.dhp.community.*;
-import eu.dnetlib.dhp.schema.oaf.*;
 
 public class SparkBulkTagJob {
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java

@@ -1,15 +1,14 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
+
+import com.google.gson.Gson;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.google.gson.Gson;
-
 /** Created by miriam on 01/08/2018. */
 public class Community implements Serializable {
 
@@ -17,7 +16,7 @@ public class Community implements Serializable {
 
 	private String id;
 	private List<String> subjects = new ArrayList<>();
-	private List<Datasource> datasources = new ArrayList<>();
+	private List<Provider> providers = new ArrayList<>();
 	private List<ZenodoCommunity> zenodoCommunities = new ArrayList<>();
 
 	public String toJson() {
@@ -27,7 +26,7 @@ public class Community implements Serializable {
 
 	public boolean isValid() {
 		return !getSubjects().isEmpty()
-			|| !getDatasources().isEmpty()
+			|| !getProviders().isEmpty()
 			|| !getZenodoCommunities().isEmpty();
 	}
 
@@ -47,12 +46,12 @@ public class Community implements Serializable {
 		this.subjects = subjects;
 	}
 
-	public List<Datasource> getDatasources() {
+	public List<Provider> getProviders() {
-		return datasources;
+		return providers;
 	}
 
-	public void setDatasources(List<Datasource> datasources) {
+	public void setProviders(List<Provider> providers) {
-		this.datasources = datasources;
+		this.providers = providers;
 	}
 
 	public List<ZenodoCommunity> getZenodoCommunities() {

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java

@@ -1,5 +1,14 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
+
+import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import eu.dnetlib.dhp.bulktag.criteria.InterfaceAdapter;
+import eu.dnetlib.dhp.bulktag.criteria.Selection;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 
 import java.io.Serializable;
 import java.util.ArrayList;
@@ -8,17 +17,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.google.common.collect.Lists;
-import com.google.common.collect.Maps;
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
-
-import eu.dnetlib.dhp.selectioncriteria.InterfaceAdapter;
-import eu.dnetlib.dhp.selectioncriteria.Selection;
-
 /** Created by miriam on 02/08/2018. */
 public class CommunityConfiguration implements Serializable {
 
@@ -84,7 +82,7 @@ public class CommunityConfiguration implements Serializable {
 				add(sbj.toLowerCase().trim(), p, subjectMap);
 			}
 			// get datasources
-			for (Datasource d : c.getDatasources()) {
+			for (Provider d : c.getProviders()) {
 
 				add(d.getOpenaireId(), new Pair<>(id, d.getSelectionConstraints()), datasourceMap);
 			}

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java

@@ -1,11 +1,14 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
-
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
 
+import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import eu.dnetlib.dhp.bulktag.criteria.InterfaceAdapter;
+import eu.dnetlib.dhp.bulktag.criteria.Selection;
+import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
+import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -14,15 +17,10 @@ import org.dom4j.DocumentException;
 import org.dom4j.Node;
 import org.dom4j.io.SAXReader;
 
-import com.google.common.collect.Lists;
+import java.io.StringReader;
-import com.google.common.collect.Maps;
+import java.util.ArrayList;
-import com.google.gson.Gson;
+import java.util.List;
-import com.google.gson.GsonBuilder;
+import java.util.Map;
-
-import eu.dnetlib.dhp.selectioncriteria.InterfaceAdapter;
-import eu.dnetlib.dhp.selectioncriteria.Selection;
-import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
-import eu.dnetlib.dhp.selectioncriteria.VerbResolverFactory;
 
 /** Created by miriam on 03/08/2018. */
 public class CommunityConfigurationFactory {
@@ -77,7 +75,7 @@ public class CommunityConfigurationFactory {
 		log.info(String.format("community id: %s", c.getId()));
 
 		c.setSubjects(parseSubjects(node));
-		c.setDatasources(parseDatasources(node));
+		c.setProviders(parseDatasources(node));
 		c.setZenodoCommunities(parseZenodoCommunities(node));
 		return c;
 	}
@@ -96,17 +94,17 @@ public class CommunityConfigurationFactory {
 		return subjects;
 	}
 
-	private static List<Datasource> parseDatasources(final Node node) {
+	private static List<Provider> parseDatasources(final Node node) {
 		final List<Node> list = node.selectNodes("./datasources/datasource");
-		final List<Datasource> datasourceList = new ArrayList<>();
+		final List<Provider> providerList = new ArrayList<>();
 		for (Node n : list) {
-			Datasource d = new Datasource();
+			Provider d = new Provider();
 			d.setOpenaireId(n.selectSingleNode("./openaireId").getText());
 			d.setSelCriteria(n.selectSingleNode("./selcriteria"), resolver);
-			datasourceList.add(d);
+			providerList.add(d);
 		}
-		log.info("size of the datasource list " + datasourceList.size());
+		log.info("size of the datasource list " + providerList.size());
-		return datasourceList;
+		return providerList;
 	}
 
 	private static List<ZenodoCommunity> parseZenodoCommunities(final Node node) {

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java

@@ -1,12 +1,12 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
+
+import eu.dnetlib.dhp.bulktag.criteria.Selection;
+import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
 
 import java.io.Serializable;
 import java.lang.reflect.InvocationTargetException;
 
-import eu.dnetlib.dhp.selectioncriteria.Selection;
-import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
-
 public class Constraint implements Serializable {
 	private String verb;
 	private String field;

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraints.java

@@ -1,5 +1,11 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
+
+import com.google.gson.Gson;
+import com.google.gson.reflect.TypeToken;
+import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 
 import java.io.Serializable;
 import java.lang.reflect.InvocationTargetException;
@@ -8,14 +14,6 @@ import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.google.gson.Gson;
-import com.google.gson.reflect.TypeToken;
-
-import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
-
 /** Created by miriam on 02/08/2018. */
 public class Constraints implements Serializable {
 	private static final Log log = LogFactory.getLog(Constraints.class);

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Pair.java

@@ -1,10 +1,10 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
-
-import java.io.Serializable;
 
 import com.google.gson.Gson;
 
+import java.io.Serializable;
+
 /** Created by miriam on 03/08/2018. */
 public class Pair<A, B> implements Serializable {
 	private A fst;

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
 
 import java.io.Serializable;
 import java.util.HashMap;

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Provider.java

@@ -1,19 +1,17 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
-
-import java.io.Serializable;
 
+import com.google.gson.Gson;
+import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.dom4j.Node;
 
-import com.google.gson.Gson;
+import java.io.Serializable;
-
-import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
 
 /** Created by miriam on 01/08/2018. */
-public class Datasource implements Serializable {
+public class Provider implements Serializable {
-	private static final Log log = LogFactory.getLog(Datasource.class);
+	private static final Log log = LogFactory.getLog(Provider.class);
 
 	private String openaireId;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java

@@ -1,15 +1,13 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
-
-import java.util.List;
-
-import org.dom4j.DocumentException;
 
 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.DocumentException;
+
+import java.util.List;
 
 public class QueryInformationSystem {
 	private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java

@@ -1,20 +1,19 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
 
-import static eu.dnetlib.dhp.community.TagginConstants.*;
+import com.google.gson.Gson;
+import com.jayway.jsonpath.DocumentContext;
+import com.jayway.jsonpath.JsonPath;
+import eu.dnetlib.dhp.schema.oaf.*;
+import org.apache.commons.lang3.StringUtils;
 
 import java.io.Serializable;
 import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import org.apache.commons.lang3.StringUtils;
+import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*;
-
+import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
-import com.google.gson.Gson;
-import com.jayway.jsonpath.DocumentContext;
-import com.jayway.jsonpath.JsonPath;
-
-import eu.dnetlib.dhp.schema.oaf.*;
 
 /** Created by miriam on 02/08/2018. */
 public class ResultTagger implements Serializable {
@@ -239,8 +238,8 @@ public class ResultTagger implements Serializable {
 		Qualifier pa = new Qualifier();
 		pa.setClassid(inference_class_id);
 		pa.setClassname(inference_class_name);
-		pa.setSchemeid(DNET_SCHEMA_ID);
+		pa.setSchemeid(DNET_PROVENANCE_ACTIONS);
-		pa.setSchemename(DNET_SCHEMA_NAME);
+		pa.setSchemename(DNET_PROVENANCE_ACTIONS);
 		return pa;
 	}
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java

@@ -1,5 +1,9 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
+
+import com.google.gson.Gson;
+import com.google.gson.reflect.TypeToken;
+import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
 
 import java.io.Serializable;
 import java.lang.reflect.Type;
@@ -7,11 +11,6 @@ import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 
-import com.google.gson.Gson;
-import com.google.gson.reflect.TypeToken;
-
-import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
-
 public class SelectionConstraints implements Serializable {
 	private List<Constraints> criteria;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java

@@ -1,20 +1,14 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
 
-public class TagginConstants {
+public class TaggingConstants {
 
 	public static final String BULKTAG_DATA_INFO_TYPE = "bulktagging";
 
-	public static final String DNET_SCHEMA_NAME = "dnet:provenanceActions";
-	public static final String DNET_SCHEMA_ID = "dnet:provenanceActions";
-
 	public static final String CLASS_ID_SUBJECT = "community:subject";
 	public static final String CLASS_ID_DATASOURCE = "community:datasource";
 	public static final String CLASS_ID_CZENODO = "community:zenodocommunity";
 
-	public static final String SCHEMA_ID = "dnet:provenanceActions";
-	public static final String COUNTER_GROUP = "Bulk Tagging";
-
 	public static final String ZENODO_COMMUNITY_INDICATOR = "zenodo.org/communities/";
 
 	public static final String CLASS_NAME_BULKTAG_SUBJECT = "Bulktagging for Community - Subject";

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ZenodoCommunity.java

@@ -1,11 +1,10 @@
 
-package eu.dnetlib.dhp.community;
+package eu.dnetlib.dhp.bulktag.community;
-
-import java.io.Serializable;
-
-import org.dom4j.Node;
 
 import com.google.gson.Gson;
+import org.dom4j.Node;
+
+import java.io.Serializable;
 
 /** Created by miriam on 01/08/2018. */
 public class ZenodoCommunity implements Serializable {

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/ContainsVerb.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/ContainsVerbIgnoreCase.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/EqualVerb.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/EqualVerbIgnoreCase.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/InterfaceAdapter.java

@@ -1,10 +1,10 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
-
-import java.lang.reflect.Type;
 
 import com.google.gson.*;
 
+import java.lang.reflect.Type;
+
 public class InterfaceAdapter implements JsonSerializer, JsonDeserializer {
 
 	private static final String CLASSNAME = "CLASSNAME";

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotContainsVerb.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotContainsVerbIgnoreCase.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotEqualVerb.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotEqualVerbIgnoreCase.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/Selection.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
 
 public interface Selection {
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbClass.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
 
 import java.lang.annotation.ElementType;
 import java.lang.annotation.Retention;

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbResolver.java

@@ -1,16 +1,16 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
-
-import java.io.Serializable;
-import java.lang.reflect.InvocationTargetException;
-import java.util.Map;
-import java.util.stream.Collectors;
 
 import io.github.classgraph.ClassGraph;
 import io.github.classgraph.ClassInfo;
 import io.github.classgraph.ClassInfoList;
 import io.github.classgraph.ScanResult;
 
+import java.io.Serializable;
+import java.lang.reflect.InvocationTargetException;
+import java.util.Map;
+import java.util.stream.Collectors;
+
 public class VerbResolver implements Serializable {
 	private Map<String, Class<Selection>> map = null; // = new HashMap<>();
 	private final ClassGraph classgraph = new ClassGraph();

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbResolverFactory.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.selectioncriteria;
+package eu.dnetlib.dhp.bulktag.criteria;
 
 public class VerbResolverFactory {
 

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java

@@ -1,13 +1,13 @@
 
-package eu.dnetlib.dhp;
+package eu.dnetlib.dhp.bulktag;
-
-import static eu.dnetlib.dhp.community.TagginConstants.ZENODO_COMMUNITY_INDICATOR;
-
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.schema.oaf.Dataset;
+import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.Software;
 import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
@@ -18,37 +18,44 @@ import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
-import org.mortbay.util.IO;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 
-import eu.dnetlib.dhp.bulktag.SparkBulkTagJob;
+import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR;
-import eu.dnetlib.dhp.schema.oaf.Dataset;
-import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.oaf.Software;
 
 public class BulkTagJobTest {
+
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	private static final ClassLoader cl = eu.dnetlib.dhp.BulkTagJobTest.class.getClassLoader();
+	public static final String MOCK_IS_LOOK_UP_URL = "BASEURL:8280/is/services/isLookUp";
+
+	public static final String pathMap =
+			"{ \"author\" : \"$['author'][*]['fullname']\","
+			+ "  \"title\" : \"$['title'][*]['value']\","
+			+ "  \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+			+ "  \"contributor\" : \"$['contributor'][*]['value']\","
+			+ "  \"description\" : \"$['description'][*]['value']\"}";
 
 	private static SparkSession spark;
 
 	private static Path workingDir;
-	private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.BulkTagJobTest.class);
+
+	private static final Logger log = LoggerFactory.getLogger(BulkTagJobTest.class);
 
 	private static String taggingConf = "";
 
 	static {
 		try {
-			taggingConf = IO
+			taggingConf = IOUtils
 				.toString(
 					BulkTagJobTest.class
 						.getResourceAsStream(
-							"/eu/dnetlib/dhp/communityconfiguration/tagging_conf.xml"));
+							"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml"));
 		} catch (IOException e) {
 			e.printStackTrace();
 		}
@@ -56,11 +63,11 @@ public class BulkTagJobTest {
 
 	@BeforeAll
 	public static void beforeAll() throws IOException {
-		workingDir = Files.createTempDirectory(eu.dnetlib.dhp.BulkTagJobTest.class.getSimpleName());
+		workingDir = Files.createTempDirectory(BulkTagJobTest.class.getSimpleName());
 		log.info("using work dir {}", workingDir);
 
 		SparkConf conf = new SparkConf();
-		conf.setAppName(eu.dnetlib.dhp.BulkTagJobTest.class.getSimpleName());
+		conf.setAppName(BulkTagJobTest.class.getSimpleName());
 
 		conf.setMaster("local[*]");
 		conf.set("spark.driver.host", "localhost");
@@ -84,34 +91,21 @@ public class BulkTagJobTest {
 
 	@Test
 	public void noUpdatesTest() throws Exception {
+		final String pathMap = BulkTagJobTest.pathMap;
 		SparkBulkTagJob
 			.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(),
-					Boolean.FALSE.toString(),
+					"-taggingConf", taggingConf,
-					"-sourcePath",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
-					getClass().getResource("/eu/dnetlib/dhp/sample/dataset/no_updates").getPath(),
+					"-outputPath", workingDir.toString() + "/dataset",
-					"-taggingConf",
+					"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
-					taggingConf,
+					"-pathMap", pathMap
-					"-resultTableName",
-					"eu.dnetlib.dhp.schema.oaf.Dataset",
-					"-outputPath",
-					workingDir.toString() + "/dataset",
-					"-isLookUpUrl",
-					"http://beta.services.openaire.eu:8280/is/services/isLookUp",
-					"-pathMap",
-					"{ \"author\" : \"$['author'][*]['fullname']\","
-						+ "  \"title\" : \"$['title'][*]['value']\","
-						+ "  \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
-						+ "  \"contributor\" : \"$['contributor'][*]['value']\","
-						+ "  \"description\" : \"$['description'][*]['value']\"}"
-				// "-preparedInfoPath",
-				// getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/preparedInfo").getPath()
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Dataset> tmp = sc
 			.textFile(workingDir.toString() + "/dataset")
@@ -134,34 +128,24 @@ public class BulkTagJobTest {
 
 	@Test
 	public void bulktagBySubjectNoPreviousContextTest() throws Exception {
+		final String sourcePath = getClass()
+				.getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext")
+				.getPath();
+		final String pathMap = BulkTagJobTest.pathMap;
 		SparkBulkTagJob
 			.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", sourcePath,
-					Boolean.FALSE.toString(),
+					"-taggingConf", taggingConf,
-					"-sourcePath",
+					"-resultTableName",	"eu.dnetlib.dhp.schema.oaf.Dataset",
-					getClass()
+					"-outputPath", workingDir.toString() + "/dataset",
-						.getResource("/eu/dnetlib/dhp/sample/dataset/update_subject/nocontext")
+					"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
-						.getPath(),
+					"-pathMap", pathMap
-					"-taggingConf",
-					taggingConf,
-					"-resultTableName",
-					"eu.dnetlib.dhp.schema.oaf.Dataset",
-					"-outputPath",
-					workingDir.toString() + "/dataset",
-					"-isLookUpUrl",
-					"http://beta.services.openaire.eu:8280/is/services/isLookUp",
-					"-pathMap",
-					"{ \"author\" : \"$['author'][*]['fullname']\","
-						+ "  \"title\" : \"$['title'][*]['value']\","
-						+ "  \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
-						+ "  \"contributor\" : \"$['contributor'][*]['value']\","
-						+ "  \"description\" : \"$['description'][*]['value']\"}"
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Dataset> tmp = sc
 			.textFile(workingDir.toString() + "/dataset")
@@ -240,32 +224,22 @@ public class BulkTagJobTest {
 
 	@Test
 	public void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception {
+		final String sourcePath = getClass()
+				.getResource(
+						"/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance")
+				.getPath();
+		final String pathMap = BulkTagJobTest.pathMap;
 		SparkBulkTagJob
 			.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", sourcePath,
-					Boolean.FALSE.toString(),
+					"-taggingConf", taggingConf,
-					"-sourcePath",
+					"-resultTableName",	"eu.dnetlib.dhp.schema.oaf.Dataset",
-					getClass()
+					"-outputPath", workingDir.toString() + "/dataset",
-						.getResource(
+					"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
-							"/eu/dnetlib/dhp/sample/dataset/update_subject/contextnoprovenance")
+					"-pathMap", pathMap
-						.getPath(),
-					"-taggingConf",
-					taggingConf,
-					"-resultTableName",
-					"eu.dnetlib.dhp.schema.oaf.Dataset",
-					"-outputPath",
-					workingDir.toString() + "/dataset",
-					"-isLookUpUrl",
-					"http://beta.services.openaire.eu:8280/is/services/isLookUp",
-					"-pathMap",
-					"{ \"author\" : \"$['author'][*]['fullname']\","
-						+ "  \"title\" : \"$['title'][*]['value']\","
-						+ "  \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
-						+ "  \"contributor\" : \"$['contributor'][*]['value']\","
-						+ "  \"description\" : \"$['description'][*]['value']\"}"
 				});
 
 		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
@@ -332,34 +306,23 @@ public class BulkTagJobTest {
 
 	@Test
 	public void bulktagByDatasourceTest() throws Exception {
+		final String sourcePath = getClass()
+				.getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource")
+				.getPath();
 		SparkBulkTagJob
 			.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", sourcePath,
-					Boolean.FALSE.toString(),
+					"-taggingConf", taggingConf,
-					"-sourcePath",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
-					getClass()
+					"-outputPath", workingDir.toString() + "/publication",
-						.getResource("/eu/dnetlib/dhp/sample/publication/update_datasource")
+					"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
-						.getPath(),
+					"-pathMap", pathMap
-					"-taggingConf",
-					taggingConf,
-					"-resultTableName",
-					"eu.dnetlib.dhp.schema.oaf.Publication",
-					"-outputPath",
-					workingDir.toString() + "/publication",
-					"-isLookUpUrl",
-					"http://beta.services.openaire.eu:8280/is/services/isLookUp",
-					"-pathMap",
-					"{ \"author\" : \"$['author'][*]['fullname']\","
-						+ "  \"title\" : \"$['title'][*]['value']\","
-						+ "  \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
-						+ "  \"contributor\" : \"$['contributor'][*]['value']\","
-						+ "  \"description\" : \"$['description'][*]['value']\"}"
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Publication> tmp = sc
 			.textFile(workingDir.toString() + "/publication")
@@ -415,35 +378,24 @@ public class BulkTagJobTest {
 
 	@Test
 	public void bulktagByZenodoCommunityTest() throws Exception {
+		final String sourcePath = getClass()
+				.getResource(
+						"/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity")
+				.getPath();
 		SparkBulkTagJob
 			.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", sourcePath,
-					Boolean.FALSE.toString(),
+					"-taggingConf", taggingConf,
-					"-sourcePath",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
-					getClass()
+					"-outputPath", workingDir.toString() + "/orp",
-						.getResource(
+					"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
-							"/eu/dnetlib/dhp/sample/otherresearchproduct/update_zenodocommunity")
+					"-pathMap", pathMap
-						.getPath(),
-					"-taggingConf",
-					taggingConf,
-					"-resultTableName",
-					"eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
-					"-outputPath",
-					workingDir.toString() + "/orp",
-					"-isLookUpUrl",
-					"http://beta.services.openaire.eu:8280/is/services/isLookUp",
-					"-pathMap",
-					"{ \"author\" : \"$['author'][*]['fullname']\","
-						+ "  \"title\" : \"$['title'][*]['value']\","
-						+ "  \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
-						+ "  \"contributor\" : \"$['contributor'][*]['value']\","
-						+ "  \"description\" : \"$['description'][*]['value']\"}"
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<OtherResearchProduct> tmp = sc
 			.textFile(workingDir.toString() + "/orp")
@@ -548,34 +500,23 @@ public class BulkTagJobTest {
 
 	@Test
 	public void bulktagBySubjectDatasourceTest() throws Exception {
+		final String sourcePath = getClass()
+				.getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource")
+				.getPath();
 		SparkBulkTagJob
 			.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", sourcePath,
-					Boolean.FALSE.toString(),
+					"-taggingConf", taggingConf,
-					"-sourcePath",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
-					getClass()
+					"-outputPath", workingDir.toString() + "/dataset",
-						.getResource("/eu/dnetlib/dhp/sample/dataset/update_subject_datasource")
+					"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
-						.getPath(),
+					"-pathMap", pathMap
-					"-taggingConf",
-					taggingConf,
-					"-resultTableName",
-					"eu.dnetlib.dhp.schema.oaf.Dataset",
-					"-outputPath",
-					workingDir.toString() + "/dataset",
-					"-isLookUpUrl",
-					"http://beta.services.openaire.eu:8280/is/services/isLookUp",
-					"-pathMap",
-					"{ \"author\" : \"$['author'][*]['fullname']\","
-						+ "  \"title\" : \"$['title'][*]['value']\","
-						+ "  \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
-						+ "  \"contributor\" : \"$['contributor'][*]['value']\","
-						+ "  \"description\" : \"$['description'][*]['value']\"}"
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Dataset> tmp = sc
 			.textFile(workingDir.toString() + "/dataset")
@@ -691,29 +632,17 @@ public class BulkTagJobTest {
 		SparkBulkTagJob
 			.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/").getPath(),
-					Boolean.FALSE.toString(),
+					"-taggingConf", taggingConf,
-					"-sourcePath",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
-					getClass().getResource("/eu/dnetlib/dhp/sample/software/").getPath(),
+					"-outputPath", workingDir.toString() + "/software",
-					"-taggingConf",
+					"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
-					taggingConf,
+					"-pathMap", pathMap
-					"-resultTableName",
-					"eu.dnetlib.dhp.schema.oaf.Software",
-					"-outputPath",
-					workingDir.toString() + "/software",
-					"-isLookUpUrl",
-					"http://beta.services.openaire.eu:8280/is/services/isLookUp",
-					"-pathMap",
-					"{ \"author\" : \"$['author'][*]['fullname']\","
-						+ "  \"title\" : \"$['title'][*]['value']\","
-						+ "  \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
-						+ "  \"contributor\" : \"$['contributor'][*]['value']\","
-						+ "  \"description\" : \"$['description'][*]['value']\"}"
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Software> tmp = sc
 			.textFile(workingDir.toString() + "/software")
@@ -796,35 +725,24 @@ public class BulkTagJobTest {
 	@Test
 	public void bulktagDatasourcewithConstraintsTest() throws Exception {
 
+		final String sourcePath = getClass()
+				.getResource(
+						"/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints")
+				.getPath();
 		SparkBulkTagJob
 			.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", sourcePath,
-					Boolean.FALSE.toString(),
+					"-taggingConf", taggingConf,
-					"-sourcePath",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
-					getClass()
+					"-outputPath", workingDir.toString() + "/dataset",
-						.getResource(
+					"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
-							"/eu/dnetlib/dhp/sample/dataset/update_datasourcewithconstraints")
+					"-pathMap", pathMap
-						.getPath(),
-					"-taggingConf",
-					taggingConf,
-					"-resultTableName",
-					"eu.dnetlib.dhp.schema.oaf.Dataset",
-					"-outputPath",
-					workingDir.toString() + "/dataset",
-					"-isLookUpUrl",
-					"http://beta.services.openaire.eu:8280/is/services/isLookUp",
-					"-pathMap",
-					"{ \"author\" : \"$['author'][*]['fullname']\","
-						+ "  \"title\" : \"$['title'][*]['value']\","
-						+ "  \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
-						+ "  \"contributor\" : \"$['contributor'][*]['value']\","
-						+ "  \"description\" : \"$['description'][*]['value']\"}"
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Dataset> tmp = sc
 			.textFile(workingDir.toString() + "/dataset")

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java

@@ -1,23 +1,21 @@
 
-package eu.dnetlib.dhp;
+package eu.dnetlib.dhp.bulktag;
-
-import java.io.IOException;
-import java.lang.reflect.InvocationTargetException;
-import java.util.*;
 
+import com.google.gson.Gson;
+import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration;
+import eu.dnetlib.dhp.bulktag.community.CommunityConfigurationFactory;
+import eu.dnetlib.dhp.bulktag.community.Constraint;
+import eu.dnetlib.dhp.bulktag.community.SelectionConstraints;
+import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.DocumentException;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
-import com.google.gson.Gson;
+import java.io.IOException;
-
+import java.lang.reflect.InvocationTargetException;
-import eu.dnetlib.dhp.community.CommunityConfiguration;
+import java.util.*;
-import eu.dnetlib.dhp.community.CommunityConfigurationFactory;
-import eu.dnetlib.dhp.community.Constraint;
-import eu.dnetlib.dhp.community.SelectionConstraints;
-import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
 
 /** Created by miriam on 03/08/2018. */
 public class CommunityConfigurationFactoryTest {

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java

@@ -5,12 +5,15 @@ import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.*;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Assertions;
@@ -26,12 +29,11 @@ import eu.dnetlib.dhp.schema.oaf.Software;
 import scala.Tuple2;
 
 public class CountryPropagationJobTest {
+
 	private static final Logger log = LoggerFactory.getLogger(CountryPropagationJobTest.class);
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	private static final ClassLoader cl = CountryPropagationJobTest.class.getClassLoader();
-
 	private static SparkSession spark;
 
 	private static Path workingDir;
@@ -101,8 +103,8 @@ public class CountryPropagationJobTest {
 		Assertions.assertEquals(0, verificationDs.filter("size(country) > 2").count());
 
 		Dataset<String> countryExploded = verificationDs
-			.flatMap(row -> row.getCountry().iterator(), Encoders.bean(Country.class))
+			.flatMap((FlatMapFunction<Software, Country>) row -> row.getCountry().iterator(), Encoders.bean(Country.class))
-			.map(c -> c.getClassid(), Encoders.STRING());
+			.map((MapFunction<Country, String>) c -> c.getClassid(), Encoders.STRING());
 
 		Assertions.assertEquals(9, countryExploded.count());
 
@@ -115,8 +117,7 @@ public class CountryPropagationJobTest {
 		Assertions.assertEquals(2, countryExploded.filter("value = 'JP'").count());
 
 		Dataset<Tuple2<String, String>> countryExplodedWithCountryclassid = verificationDs
-			.flatMap(
+			.flatMap((FlatMapFunction<Software, Tuple2<String, String>>) row -> {
-				row -> {
 				List<Tuple2<String, String>> prova = new ArrayList();
 				List<Country> country_list = row.getCountry();
 				country_list
@@ -127,8 +128,7 @@ public class CountryPropagationJobTest {
 									new Tuple2<>(
 										row.getId(), c.getClassid())));
 				return prova.iterator();
-				},
+			}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
-				Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
 
 		Assertions.assertEquals(9, countryExplodedWithCountryclassid.count());
 
@@ -178,7 +178,7 @@ public class CountryPropagationJobTest {
 
 		Dataset<Tuple2<String, String>> countryExplodedWithCountryclassname = verificationDs
 			.flatMap(
-				row -> {
+					(FlatMapFunction<Software, Tuple2<String, String>>) row -> {
 						List<Tuple2<String, String>> prova = new ArrayList();
 						List<Country> country_list = row.getCountry();
 						country_list
@@ -239,7 +239,7 @@ public class CountryPropagationJobTest {
 
 		Dataset<Tuple2<String, String>> countryExplodedWithCountryProvenance = verificationDs
 			.flatMap(
-				row -> {
+					(FlatMapFunction<Software, Tuple2<String, String>>) row -> {
 						List<Tuple2<String, String>> prova = new ArrayList();
 						List<Country> country_list = row.getCountry();
 						country_list

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java

@@ -29,8 +29,6 @@ public class OrcidPropagationJobTest {
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	private static final ClassLoader cl = OrcidPropagationJobTest.class.getClassLoader();
-
 	private static SparkSession spark;
 
 	private static Path workingDir;

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/projecttoresult/ProjectPropagationJobTest.java

@@ -9,6 +9,7 @@ import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
@@ -29,8 +30,6 @@ public class ProjectPropagationJobTest {
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	private static final ClassLoader cl = ProjectPropagationJobTest.class.getClassLoader();
-
 	private static SparkSession spark;
 
 	private static Path workingDir;
@@ -72,34 +71,26 @@ public class ProjectPropagationJobTest {
 	@Test
 	public void NoUpdateTest() throws Exception {
 
-		SparkResultToProjectThroughSemRelJob
+		final String potentialUpdateDate = getClass()
-			.main(
-				new String[] {
-					"-isTest",
-					Boolean.TRUE.toString(),
-					"-isSparkSessionManaged",
-					Boolean.FALSE.toString(),
-					// "-sourcePath",
-					// getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/relation").getPath(),
-					"-hive_metastore_uris",
-					"",
-					"-saveGraph",
-					"true",
-					"-outputPath",
-					workingDir.toString() + "/relation",
-					"-potentialUpdatePath",
-					getClass()
 				.getResource(
 						"/eu/dnetlib/dhp/projecttoresult/preparedInfo/noupdates/potentialUpdates")
-						.getPath(),
+				.getPath();
-					"-alreadyLinkedPath",
+		final String alreadyLinkedPath = getClass()
-					getClass()
 				.getResource(
 						"/eu/dnetlib/dhp/projecttoresult/preparedInfo/alreadyLinked")
-						.getPath(),
+				.getPath();
+		SparkResultToProjectThroughSemRelJob.main(
+				new String[] {
+					"-isTest", Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-hive_metastore_uris", "",
+					"-saveGraph", "true",
+					"-outputPath", workingDir.toString() + "/relation",
+					"-potentialUpdatePath", potentialUpdateDate,
+					"-alreadyLinkedPath", alreadyLinkedPath,
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Relation> tmp = sc
 			.textFile(workingDir.toString() + "/relation")
@@ -115,34 +106,26 @@ public class ProjectPropagationJobTest {
 	 */
 	@Test
 	public void UpdateTenTest() throws Exception {
-		SparkResultToProjectThroughSemRelJob
+		final String potentialUpdatePath = getClass()
-			.main(
-				new String[] {
-					"-isTest",
-					Boolean.TRUE.toString(),
-					"-isSparkSessionManaged",
-					Boolean.FALSE.toString(),
-					// "-sourcePath",
-					// getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/relation").getPath(),
-					"-hive_metastore_uris",
-					"",
-					"-saveGraph",
-					"true",
-					"-outputPath",
-					workingDir.toString() + "/relation",
-					"-potentialUpdatePath",
-					getClass()
 				.getResource(
 						"/eu/dnetlib/dhp/projecttoresult/preparedInfo/tenupdates/potentialUpdates")
-						.getPath(),
+				.getPath();
-					"-alreadyLinkedPath",
+		final String alreadyLinkedPath = getClass()
-					getClass()
 				.getResource(
 						"/eu/dnetlib/dhp/projecttoresult/preparedInfo/alreadyLinked")
-						.getPath(),
+				.getPath();
+		SparkResultToProjectThroughSemRelJob.main(
+				new String[] {
+					"-isTest", Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-hive_metastore_uris", "",
+					"-saveGraph", "true",
+					"-outputPath", workingDir.toString() + "/relation",
+					"-potentialUpdatePath", potentialUpdatePath,
+					"-alreadyLinkedPath", alreadyLinkedPath,
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Relation> tmp = sc
 			.textFile(workingDir.toString() + "/relation")
@@ -160,18 +143,18 @@ public class ProjectPropagationJobTest {
 			.assertEquals(
 				5,
 				verificationDs
-					.filter(
+					.filter((FilterFunction<Relation>) r ->
-						r -> r.getSource().substring(0, 2).equals("50")
+							r.getSource().startsWith("50")
-							&& r.getTarget().substring(0, 2).equals("40")
+							&& r.getTarget().startsWith("40")
 							&& r.getRelClass().equals("isProducedBy"))
 					.count());
 		Assertions
 			.assertEquals(
 				5,
 				verificationDs
-					.filter(
+					.filter((FilterFunction<Relation>) r ->
-						r -> r.getSource().substring(0, 2).equals("40")
+							r.getSource().startsWith("40")
-							&& r.getTarget().substring(0, 2).equals("50")
+							&& r.getTarget().startsWith("50")
 							&& r.getRelClass().equals("produces"))
 					.count());
 
@@ -194,34 +177,26 @@ public class ProjectPropagationJobTest {
 	 */
 	@Test
 	public void UpdateMixTest() throws Exception {
-		SparkResultToProjectThroughSemRelJob
+		final String potentialUpdatepath = getClass()
-			.main(
-				new String[] {
-					"-isTest",
-					Boolean.TRUE.toString(),
-					"-isSparkSessionManaged",
-					Boolean.FALSE.toString(),
-					// "-sourcePath",
-					// getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/relation").getPath(),
-					"-hive_metastore_uris",
-					"",
-					"-saveGraph",
-					"true",
-					"-outputPath",
-					workingDir.toString() + "/relation",
-					"-potentialUpdatePath",
-					getClass()
 				.getResource(
 						"/eu/dnetlib/dhp/projecttoresult/preparedInfo/updatesmixed/potentialUpdates")
-						.getPath(),
+				.getPath();
-					"-alreadyLinkedPath",
+		final String alreadyLinkedPath = getClass()
-					getClass()
 				.getResource(
 						"/eu/dnetlib/dhp/projecttoresult/preparedInfo/alreadyLinked")
-						.getPath(),
+				.getPath();
+		SparkResultToProjectThroughSemRelJob.main(
+				new String[] {
+					"-isTest", Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-hive_metastore_uris", "",
+					"-saveGraph", "true",
+					"-outputPath", workingDir.toString() + "/relation",
+					"-potentialUpdatePath", potentialUpdatepath,
+					"-alreadyLinkedPath", alreadyLinkedPath,
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Relation> tmp = sc
 			.textFile(workingDir.toString() + "/relation")
@@ -242,18 +217,18 @@ public class ProjectPropagationJobTest {
 			.assertEquals(
 				4,
 				verificationDs
-					.filter(
+					.filter((FilterFunction<Relation>) r ->
-						r -> r.getSource().substring(0, 2).equals("50")
+							r.getSource().startsWith("50")
-							&& r.getTarget().substring(0, 2).equals("40")
+							&& r.getTarget().startsWith("40")
 							&& r.getRelClass().equals("isProducedBy"))
 					.count());
 		Assertions
 			.assertEquals(
 				4,
 				verificationDs
-					.filter(
+					.filter((FilterFunction<Relation>) r ->
-						r -> r.getSource().substring(0, 2).equals("40")
+							r.getSource().startsWith("40")
-							&& r.getTarget().substring(0, 2).equals("50")
+							&& r.getTarget().startsWith("50")
 							&& r.getRelClass().equals("produces"))
 					.count());
 

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java

@@ -32,8 +32,6 @@ public class ResultToCommunityJobTest {
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	private static final ClassLoader cl = ResultToCommunityJobTest.class.getClassLoader();
-
 	private static SparkSession spark;
 
 	private static Path workingDir;
@@ -68,33 +66,24 @@ public class ResultToCommunityJobTest {
 
 	@Test
 	public void testSparkResultToCommunityFromOrganizationJob() throws Exception {
-		SparkResultToCommunityFromOrganizationJob
+		final String preparedInfoPath = getClass()
-			.main(
+				.getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/preparedInfo")
+				.getPath();
+		SparkResultToCommunityFromOrganizationJob.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", getClass()
-					Boolean.FALSE.toString(),
-					"-sourcePath",
-					getClass()
 						.getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/sample")
 						.getPath(),
-					"-hive_metastore_uris",
+					"-hive_metastore_uris", "",
-					"",
+					"-saveGraph", "true",
-					"-saveGraph",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
-					"true",
+					"-outputPath", workingDir.toString() + "/dataset",
-					"-resultTableName",
+					"-preparedInfoPath", preparedInfoPath
-					"eu.dnetlib.dhp.schema.oaf.Dataset",
-					"-outputPath",
-					workingDir.toString() + "/dataset",
-					"-preparedInfoPath",
-					getClass()
-						.getResource(
-							"/eu/dnetlib/dhp/resulttocommunityfromorganization/preparedInfo")
-						.getPath()
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Dataset> tmp = sc
 			.textFile(workingDir.toString() + "/dataset")
@@ -217,13 +206,6 @@ public class ResultToCommunityJobTest {
 					.get(0)
 					.getString(0));
 
-		/*
-		 * {"communityList":["euromarine","mes"],"resultId":"50|doajarticles::8d817039a63710fcf97e30f14662c6c8"}
-		 * "context" ["id": euromarine] updates = 1
-		 * {"communityList":["euromarine","mes"],"resultId":"50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6"} context
-		 * = [ni, euromarine] updates = 1
-		 */
-
 		query = "select id, MyT.id community "
 			+ "from dataset "
 			+ "lateral view explode(context) c as MyT "

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java

@@ -29,32 +29,21 @@ import eu.dnetlib.dhp.schema.oaf.Dataset;
 
 public class ResultToCommunityJobTest {
 
-	private static final Logger log = LoggerFactory
+	private static final Logger log = LoggerFactory.getLogger(ResultToCommunityJobTest.class);
-		.getLogger(
-			eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.class);
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	private static final ClassLoader cl = eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.class
-		.getClassLoader();
-
 	private static SparkSession spark;
 
 	private static Path workingDir;
 
 	@BeforeAll
 	public static void beforeAll() throws IOException {
-		workingDir = Files
+		workingDir = Files.createTempDirectory(ResultToCommunityJobTest.class.getSimpleName());
-			.createTempDirectory(
-				eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.class
-					.getSimpleName());
 		log.info("using work dir {}", workingDir);
 
 		SparkConf conf = new SparkConf();
-		conf
+		conf.setAppName(ResultToCommunityJobTest.class.getSimpleName());
-			.setAppName(
-				eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.class
-					.getSimpleName());
 
 		conf.setMaster("local[*]");
 		conf.set("spark.driver.host", "localhost");
@@ -65,7 +54,7 @@ public class ResultToCommunityJobTest {
 
 		spark = SparkSession
 			.builder()
-			.appName(OrcidPropagationJobTest.class.getSimpleName())
+			.appName(ResultToCommunityJobTest.class.getSimpleName())
 			.config(conf)
 			.getOrCreate();
 	}
@@ -83,22 +72,18 @@ public class ResultToCommunityJobTest {
 				new String[] {
 					"-isTest", Boolean.TRUE.toString(),
 					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-sourcePath",
+					"-sourcePath", getClass()
-					getClass()
+						.getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/sample")
-						.getResource(
-							"/eu/dnetlib/dhp/resulttocommunityfromsemrel/sample")
 						.getPath(),
 					"-hive_metastore_uris", "",
 					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
 					"-outputPath", workingDir.toString() + "/dataset",
-					"-preparedInfoPath",
+					"-preparedInfoPath", getClass()
-					getClass()
+						.getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/preparedInfo")
-						.getResource(
-							"/eu/dnetlib/dhp/resulttocommunityfromsemrel/preparedInfo")
 						.getPath()
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Dataset> tmp = sc
 			.textFile(workingDir.toString() + "/dataset")

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/ResultToOrganizationJobTest.java

@@ -23,23 +23,19 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.schema.oaf.Relation;
 
-public class Result2OrganizationJobTest {
+public class ResultToOrganizationJobTest {
 
-	private static final Logger log = LoggerFactory.getLogger(Result2OrganizationJobTest.class);
+	private static final Logger log = LoggerFactory.getLogger(ResultToOrganizationJobTest.class);
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	private static final ClassLoader cl = Result2OrganizationJobTest.class.getClassLoader();
-
 	private static SparkSession spark;
 
 	private static Path workingDir;
 
 	@BeforeAll
 	public static void beforeAll() throws IOException {
-		workingDir = Files
+		workingDir = Files.createTempDirectory(SparkResultToOrganizationFromIstRepoJob.class.getSimpleName());
-			.createTempDirectory(
-				SparkResultToOrganizationFromIstRepoJob.class.getSimpleName());
 		log.info("using work dir {}", workingDir);
 
 		SparkConf conf = new SparkConf();
@@ -72,40 +68,29 @@ public class Result2OrganizationJobTest {
 	 */
 	@Test
 	public void NoUpdateTest() throws Exception {
-		SparkResultToOrganizationFromIstRepoJob
+		final String sourcePath = getClass()
-			.main(
+				.getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix")
+				.getPath();
+		final String datasourceOrganizationPath = getClass()
+				.getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/datasourceOrganization")
+				.getPath();
+		final String alreadyLinkedPath = getClass()
+				.getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/alreadyLinked")
+				.getPath();
+		SparkResultToOrganizationFromIstRepoJob.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", sourcePath,
-					Boolean.FALSE.toString(),
+					"-hive_metastore_uris", "",
-					"-sourcePath",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
-					getClass()
+					"-saveGraph", "true",
-						.getResource(
+					"-outputPath", workingDir.toString() + "/relation",
-							"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix")
+					"-datasourceOrganizationPath", datasourceOrganizationPath,
-						.getPath(),
+					"-alreadyLinkedPath", alreadyLinkedPath,
-					"-hive_metastore_uris",
-					"",
-					"-resultTableName",
-					"eu.dnetlib.dhp.schema.oaf.Software",
-
-					"-saveGraph",
-					"true",
-					"-outputPath",
-					workingDir.toString() + "/relation",
-					"-datasourceOrganizationPath",
-					getClass()
-						.getResource(
-							"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/datasourceOrganization")
-						.getPath(),
-					"-alreadyLinkedPath",
-					getClass()
-						.getResource(
-							"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/alreadyLinked")
-						.getPath(),
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Relation> tmp = sc
 			.textFile(workingDir.toString() + "/relation")
@@ -123,40 +108,29 @@ public class Result2OrganizationJobTest {
 	 */
 	@Test
 	public void UpdateNoMixTest() throws Exception {
-		SparkResultToOrganizationFromIstRepoJob
+		final String sourcePath = getClass()
-			.main(
+				.getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix")
+				.getPath();
+		final String datasourceOrganizationPath = getClass()
+				.getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/datasourceOrganization")
+				.getPath();
+		final String alreadyLinkedPath = getClass()
+				.getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/alreadyLinked")
+				.getPath();
+		SparkResultToOrganizationFromIstRepoJob.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", sourcePath,
-					Boolean.FALSE.toString(),
+					"-hive_metastore_uris", "",
-					"-sourcePath",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
-					getClass()
+					"-saveGraph", "true",
-						.getResource(
+					"-outputPath", workingDir.toString() + "/relation",
-							"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix")
+					"-datasourceOrganizationPath", datasourceOrganizationPath,
-						.getPath(),
+					"-alreadyLinkedPath", alreadyLinkedPath,
-					"-hive_metastore_uris",
-					"",
-					"-resultTableName",
-					"eu.dnetlib.dhp.schema.oaf.Software",
-
-					"-saveGraph",
-					"true",
-					"-outputPath",
-					workingDir.toString() + "/relation",
-					"-datasourceOrganizationPath",
-					getClass()
-						.getResource(
-							"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/datasourceOrganization")
-						.getPath(),
-					"-alreadyLinkedPath",
-					getClass()
-						.getResource(
-							"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/alreadyLinked")
-						.getPath(),
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Relation> tmp = sc
 			.textFile(workingDir.toString() + "/relation")
@@ -197,40 +171,29 @@ public class Result2OrganizationJobTest {
 
 	@Test
 	public void UpdateMixTest() throws Exception {
-		SparkResultToOrganizationFromIstRepoJob
+		final String sourcePath = getClass()
-			.main(
+				.getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/updatemix")
+				.getPath();
+		final String datasourceOrganizationPath = getClass()
+				.getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/datasourceOrganization")
+				.getPath();
+		final String alreadyLinkedPath = getClass()
+				.getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/alreadyLinked")
+				.getPath();
+		SparkResultToOrganizationFromIstRepoJob.main(
 				new String[] {
-					"-isTest",
+					"-isTest", Boolean.TRUE.toString(),
-					Boolean.TRUE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-isSparkSessionManaged",
+					"-sourcePath", sourcePath,
-					Boolean.FALSE.toString(),
+					"-hive_metastore_uris", "",
-					"-sourcePath",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
-					getClass()
+					"-saveGraph", "true",
-						.getResource(
+					"-outputPath", workingDir.toString() + "/relation",
-							"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/updatemix")
+					"-datasourceOrganizationPath", datasourceOrganizationPath,
-						.getPath(),
+					"-alreadyLinkedPath", alreadyLinkedPath,
-					"-hive_metastore_uris",
-					"",
-					"-resultTableName",
-					"eu.dnetlib.dhp.schema.oaf.Software",
-
-					"-saveGraph",
-					"true",
-					"-outputPath",
-					workingDir.toString() + "/relation",
-					"-datasourceOrganizationPath",
-					getClass()
-						.getResource(
-							"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/datasourceOrganization")
-						.getPath(),
-					"-alreadyLinkedPath",
-					getClass()
-						.getResource(
-							"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/alreadyLinked")
-						.getPath(),
 				});
 
-		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Relation> tmp = sc
 			.textFile(workingDir.toString() + "/relation")

dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/community_configuration.xml

@@ -2,17 +2,17 @@
     <community id="fet-fp7">
         <oacommunity/>
         <subjects/>
-        <datasources/>
+        <providers/>
         <zenodocommunities/>
     </community>
     <community id="fet-h2020">
         <subjects/>
-        <datasources/>
+        <providers/>
         <zenodocommunities/>
     </community>
     <community id="oa-pg">
         <subjects/>
-        <datasources/>
+        <providers/>
         <zenodocommunities/>
     </community>
     <community id="ee">
@@ -35,7 +35,7 @@
             <subject>SDG9 - Industry innovation and infrastructure</subject>
             <subject>SDG16 - Peace justice and strong institutions</subject>
         </subjects>
-        <datasources/>
+        <providers/>
         <zenodocommunities>
             <zenodocommunity>
                 <zenodoid>123</zenodoid>
@@ -45,12 +45,12 @@
     </community>
     <community id="dh-ch">
         <subjects/>
-        <datasources/>
+        <providers/>
         <zenodocommunities/>
     </community>
     <community id="fam">
         <subjects/>
-        <datasources/>
+        <providers/>
         <zenodocommunities/>
     </community>
     <community id="ni">
@@ -74,7 +74,7 @@
             <subject>brain magnetic resonance imaging</subject>
             <subject>brain abnormalities</subject>
         </subjects>
-        <datasources>
+        <providers>
             <datasource>
                 <openaireId>re3data_____::5b9bf9171d92df854cf3c520692e9122</openaireId>
                 <selcriteria/>
@@ -95,7 +95,7 @@
                 <openaireId>doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a</openaireId>
                 <selcriteria/>
             </datasource>
-        </datasources>
+        </providers>
         <zenodocommunities/>
     </community>
     <community id="mes">
@@ -106,12 +106,12 @@
             <subject>aqua</subject>
             <subject>sea</subject>
         </subjects>
-        <datasources>
+        <providers>
             <datasource>
                 <openaireId>re3data_____::9633d1e8c4309c833c2c442abeb0cfeb</openaireId>
                 <selcriteria/>
             </datasource>
-        </datasources>
+        </providers>
         <zenodocommunities/>
     </community>
     <community id="aginfra">
@@ -134,7 +134,7 @@
             <subject>food distribution</subject>
             <subject>forestry</subject>
         </subjects>
-        <datasources>
+        <providers>
             <datasource>
                 <openaireId>opendoar____::1a551829d50f1400b0dab21fdd969c04</openaireId>
                 <selcriteria/>
@@ -159,18 +159,18 @@
                 <openaireId>opendoar____::87ae6fb631f7c8a627e8e28785d9992d</openaireId>
                 <selcriteria/>
             </datasource>
-        </datasources>
+        </providers>
         <zenodocommunities/>
     </community>
     <community id="clarin">
         <oacommunity>oac_clarin</oacommunity>
         <subjects/>
-        <datasources>
+        <providers>
             <datasource>
                 <openaireId>re3data_____::a507cdacc5bbcc08761c92185dee5cab</openaireId>
                 <selcriteria/>
             </datasource>
-        </datasources>
+        </providers>
         <zenodocommunities/>
     </community>
 </communities>

dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/community_configuration_selcrit.xml

@@ -2,17 +2,17 @@
     <community id="fet-fp7">
         <oacommunity/>
         <subjects/>
-        <datasources/>
+        <providers/>
         <zenodocommunities/>
     </community>
     <community id="fet-h2020">
         <subjects/>
-        <datasources/>
+        <providers/>
         <zenodocommunities/>
     </community>
     <community id="oa-pg">
         <subjects/>
-        <datasources/>
+        <providers/>
         <zenodocommunities/>
     </community>
     <community id="ee">
@@ -35,7 +35,7 @@
             <subject>SDG9 - Industry innovation and infrastructure</subject>
             <subject>SDG16 - Peace justice and strong institutions</subject>
         </subjects>
-        <datasources/>
+        <providers/>
         <zenodocommunities>
             <zenodocommunity>
                 <zenodoid>123</zenodoid>
@@ -45,12 +45,12 @@
     </community>
     <community id="dh-ch">
         <subjects/>
-        <datasources/>
+        <providers/>
         <zenodocommunities/>
     </community>
     <community id="fam">
         <subjects/>
-        <datasources/>
+        <providers/>
         <zenodocommunities/>
     </community>
     <community id="ni">
@@ -74,7 +74,7 @@
             <subject>brain magnetic resonance imaging</subject>
             <subject>brain abnormalities</subject>
         </subjects>
-        <datasources>
+        <providers>
             <datasource>
                 <openaireId>re3data_____::5b9bf9171d92df854cf3c520692e9122</openaireId>
                 <selcriteria/>
@@ -95,7 +95,7 @@
                 <openaireId>doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a</openaireId>
                 <selcriteria/>
             </datasource>
-        </datasources>
+        </providers>
         <zenodocommunities/>
     </community>
     <community id="mes">
@@ -106,12 +106,12 @@
             <subject>aqua</subject>
             <subject>sea</subject>
         </subjects>
-        <datasources>
+        <providers>
             <datasource>
                 <openaireId>re3data_____::9633d1e8c4309c833c2c442abeb0cfeb</openaireId>
                 <selcriteria/>
             </datasource>
-        </datasources>
+        </providers>
         <zenodocommunities/>
     </community>
     <community id="aginfra">
@@ -134,7 +134,7 @@
             <subject>food distribution</subject>
             <subject>forestry</subject>
         </subjects>
-        <datasources>
+        <providers>
             <datasource>
                 <openaireId>opendoar____::1a551829d50f1400b0dab21fdd969c04</openaireId>
                 <selcriteria/>
@@ -159,30 +159,30 @@
                 <openaireId>opendoar____::87ae6fb631f7c8a627e8e28785d9992d</openaireId>
                 <selcriteria/>
             </datasource>
-        </datasources>
+        </providers>
         <zenodocommunities/>
     </community>
     <community id="clarin">
         <oacommunity>oac_clarin</oacommunity>
         <subjects/>
-        <datasources>
+        <providers>
             <datasource>
                 <openaireId>re3data_____::a507cdacc5bbcc08761c92185dee5cab</openaireId>
                 <selcriteria/>
             </datasource>
-        </datasources>
+        </providers>
         <zenodocommunities/>
     </community>
     <community id="dariah">
         <oacommunity>oaa_dariah</oacommunity>
         <subjects/>
-        <datasources>
+        <providers>
             <datasource>
                 <openaireId>openaire____::1cfdb2e14977f31a98e0118283401f32</openaireId>
                 <selcriteria>{"criteria":[{"constraint":[{"verb":"contains","field":"contributor","value":"DARIAH"}]}]}
                 </selcriteria>
             </datasource>
-        </datasources>
+        </providers>
         <zenodocommunities>
             <zenodocommunity>
                 <zenodoid>dimpo</zenodoid>