[graph cleaning] WIP: refactoring of the cleaning stages

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java

@@ -38,6 +38,124 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 
 	public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5;
 
+	public static <T extends Oaf> T cleanContext(T value, String contextId, String verifyParam) {
+		if (ModelSupport.isSubClass(value, Result.class)) {
+			final Result res = (Result) value;
+			if (res
+				.getTitle()
+				.stream()
+				.filter(
+					t -> t
+						.getQualifier()
+						.getClassid()
+						.equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid()))
+				.noneMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) {
+				return (T) res;
+			}
+			res
+				.setContext(
+					res
+						.getContext()
+						.stream()
+						.filter(
+							c -> !c.getId().split("::")[0]
+								.equalsIgnoreCase(contextId))
+						.collect(Collectors.toList()));
+			return (T) res;
+		} else {
+			return value;
+		}
+	}
+
+	public static <T extends Oaf> T cleanCountry(T value, String[] verifyParam, Set<String> hostedBy,
+		String collectedfrom, String country) {
+		if (ModelSupport.isSubClass(value, Result.class)) {
+			final Result res = (Result) value;
+			if (res.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) ||
+				!res.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) {
+				return (T) res;
+			}
+
+			List<StructuredProperty> ids = getPidsAndAltIds(res).collect(Collectors.toList());
+			if (ids
+				.stream()
+				.anyMatch(
+					p -> p
+						.getQualifier()
+						.getClassid()
+						.equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) {
+				res
+					.setCountry(
+						res
+							.getCountry()
+							.stream()
+							.filter(
+								c -> toTakeCountry(c, country))
+							.collect(Collectors.toList()));
+			}
+
+			return (T) res;
+		} else {
+			return value;
+		}
+	}
+
+	private static <T extends Result> Stream<StructuredProperty> getPidsAndAltIds(T r) {
+		final Stream<StructuredProperty> resultPids = Optional
+			.ofNullable(r.getPid())
+			.map(Collection::stream)
+			.orElse(Stream.empty());
+
+		final Stream<StructuredProperty> instancePids = Optional
+			.ofNullable(r.getInstance())
+			.map(
+				instance -> instance
+					.stream()
+					.flatMap(
+						i -> Optional
+							.ofNullable(i.getPid())
+							.map(Collection::stream)
+							.orElse(Stream.empty())))
+			.orElse(Stream.empty());
+
+		final Stream<StructuredProperty> instanceAltIds = Optional
+			.ofNullable(r.getInstance())
+			.map(
+				instance -> instance
+					.stream()
+					.flatMap(
+						i -> Optional
+							.ofNullable(i.getAlternateIdentifier())
+							.map(Collection::stream)
+							.orElse(Stream.empty())))
+			.orElse(Stream.empty());
+
+		return Stream
+			.concat(
+				Stream.concat(resultPids, instancePids),
+				instanceAltIds);
+	}
+
+	private static boolean pidInParam(String value, String[] verifyParam) {
+		for (String s : verifyParam)
+			if (value.startsWith(s))
+				return true;
+		return false;
+	}
+
+	private static boolean toTakeCountry(Country c, String country) {
+		// If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be
+		// inserted via propagation
+		if (!Optional.ofNullable(c.getDataInfo()).isPresent())
+			return true;
+		if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent())
+			return true;
+		return !(c
+			.getClassid()
+			.equalsIgnoreCase(country) &&
+			c.getDataInfo().getInferenceprovenance().equals("propagation"));
+	}
+
 	public static <T extends Oaf> T fixVocabularyNames(T value) {
 		if (value instanceof Datasource) {
 			// nothing to clean here

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java

@@ -3,7 +3,10 @@ package eu.dnetlib.dhp.oa.graph.clean;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
+import java.util.List;
 import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
@@ -17,12 +20,16 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Sets;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.Oaf;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -61,6 +68,24 @@ public class CleanGraphSparkJob {
 		String graphTableClassName = parser.get("graphTableClassName");
 		log.info("graphTableClassName: {}", graphTableClassName);
 
+		String contextId = parser.get("contextId");
+		log.info("contextId: {}", contextId);
+
+		String verifyParam = parser.get("verifyParam");
+		log.info("verifyParam: {}", verifyParam);
+
+		String datasourcePath = parser.get("hostedBy");
+		log.info("datasourcePath: {}", datasourcePath);
+
+		String country = parser.get("country");
+		log.info("country: {}", country);
+
+		String[] verifyCountryParam = parser.get("verifyCountryParam").split(";");
+		log.info("verifyCountryParam: {}", verifyCountryParam);
+
+		String collectedfrom = parser.get("collectedfrom");
+		log.info("collectedfrom: {}", collectedfrom);
+
 		Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
 
 		final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
@@ -72,7 +97,9 @@ public class CleanGraphSparkJob {
 			isSparkSessionManaged,
 			spark -> {
 				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				cleanGraphTable(spark, vocs, inputPath, entityClazz, outputPath);
+				cleanGraphTable(
+					spark, vocs, inputPath, entityClazz, outputPath, contextId, verifyParam, datasourcePath, country,
+					verifyCountryParam, collectedfrom);
 			});
 	}
 
@@ -81,7 +108,15 @@ public class CleanGraphSparkJob {
 		VocabularyGroup vocs,
 		String inputPath,
 		Class<T> clazz,
-		String outputPath) {
+		String outputPath, String contextId, String verifyParam, String datasourcePath, String country,
+		String[] verifyCountryParam, String collectedfrom) {
+
+		Set<String> hostedBy = Sets
+			.newHashSet(
+				spark
+					.read()
+					.textFile(datasourcePath)
+					.collectAsList());
 
 		final CleaningRuleMap mapping = CleaningRuleMap.create(vocs);
 
@@ -90,6 +125,13 @@ public class CleanGraphSparkJob {
 			.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
 			.map((MapFunction<T, T>) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz))
 			.filter((FilterFunction<T>) GraphCleaningFunctions::filter)
+			.map(
+				(MapFunction<T, T>) value -> GraphCleaningFunctions.cleanContext(value, contextId, verifyParam),
+				Encoders.bean(clazz))
+			.map(
+				(MapFunction<T, T>) value -> GraphCleaningFunctions
+					.cleanCountry(value, verifyCountryParam, hostedBy, collectedfrom, country),
+				Encoders.bean(clazz))
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")

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

@@ -83,12 +83,37 @@
         </property>
     </parameters>
 
-    <start to="fork_clean_graph"/>
+    <start to="select_datasourceId_from_country"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
+    <action name="select_datasourceId_from_country">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Select datasource ID from country</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphOutputPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--country</arg><arg>${country}</arg>
+        </spark>
+        <ok to="fork_clean_graph"/>
+        <error to="Kill"/>
+    </action>
+
     <fork name="fork_clean_graph">
         <path start="clean_publication"/>
         <path start="clean_dataset"/>
@@ -121,6 +146,12 @@
             <arg>--outputPath</arg><arg>${graphOutputPath}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -147,6 +178,12 @@
             <arg>--outputPath</arg><arg>${graphOutputPath}/dataset</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -173,6 +210,12 @@
             <arg>--outputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -199,6 +242,12 @@
             <arg>--outputPath</arg><arg>${graphOutputPath}/software</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -225,6 +274,12 @@
             <arg>--outputPath</arg><arg>${graphOutputPath}/datasource</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -251,6 +306,12 @@
             <arg>--outputPath</arg><arg>${graphOutputPath}/organization</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -277,6 +338,12 @@
             <arg>--outputPath</arg><arg>${graphOutputPath}/project</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
@@ -303,286 +370,18 @@
             <arg>--outputPath</arg><arg>${graphOutputPath}/relation</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
         </spark>
         <ok to="wait_clean"/>
         <error to="Kill"/>
     </action>
 
-    <join name="wait_clean" to="clean_context"/>
+    <join name="wait_clean" to="should_patch_datasource_ids"/>
-
-    <decision name="clean_context">
-        <switch>
-            <case to="fork_clean_context">${wf:conf('shouldClean') eq true}</case>
-            <default to="End"/>
-        </switch>
-    </decision>
-
-    <fork name="fork_clean_context">
-        <path start="clean_publication_context"/>
-        <path start="clean_dataset_context"/>
-        <path start="clean_otherresearchproduct_context"/>
-        <path start="clean_software_context"/>
-    </fork>
-
-    <action name="clean_publication_context">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean publications context</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/publication</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/publication</arg>
-            <arg>--contextId</arg><arg>${contextId}</arg>
-            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
-        </spark>
-        <ok to="wait_clean_context"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_dataset_context">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean datasets Context</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/dataset</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/dataset</arg>
-            <arg>--contextId</arg><arg>${contextId}</arg>
-            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
-        </spark>
-        <ok to="wait_clean_context"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_otherresearchproduct_context">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean otherresearchproducts context</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/otherresearchproduct</arg>
-            <arg>--contextId</arg><arg>${contextId}</arg>
-            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
-        </spark>
-        <ok to="wait_clean_context"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_software_context">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean softwares context</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/software</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/software</arg>
-            <arg>--contextId</arg><arg>${contextId}</arg>
-            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
-        </spark>
-        <ok to="wait_clean_context"/>
-        <error to="Kill"/>
-    </action>
-
-    <join name="wait_clean_context" to="select_datasourceId_from_country"/>
-
-    <action name="select_datasourceId_from_country">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Select datasource ID from country</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/hostedby</arg>
-            <arg>--country</arg><arg>${country}</arg>
-        </spark>
-        <ok to="fork_clean_country"/>
-        <error to="Kill"/>
-    </action>
-
-    <fork name="fork_clean_country">
-        <path start="clean_publication_country"/>
-        <path start="clean_dataset_country"/>
-        <path start="clean_otherresearchproduct_country"/>
-        <path start="clean_software_country"/>
-    </fork>
-
-    <action name="clean_publication_country">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean publication country</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/publication</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/publication</arg>
-            <arg>--country</arg><arg>${country}</arg>
-            <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
-            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
-            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
-        </spark>
-        <ok to="wait_clean_country"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_dataset_country">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean dataset country</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/dataset</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/dataset</arg>
-            <arg>--country</arg><arg>${country}</arg>
-            <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
-            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
-            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
-        </spark>
-        <ok to="wait_clean_country"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_otherresearchproduct_country">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean otherresearchproduct country</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/otherresearchproduct</arg>
-            <arg>--country</arg><arg>${country}</arg>
-            <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
-            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
-            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
-        </spark>
-        <ok to="wait_clean_country"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="clean_software_country">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean software country</name>
-            <class>eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${graphOutputPath}/software</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/working/software</arg>
-            <arg>--country</arg><arg>${country}</arg>
-            <arg>--verifyParam</arg><arg>${verifyCountryParam}</arg>
-            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
-            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
-        </spark>
-        <ok to="wait_clean_country"/>
-        <error to="Kill"/>
-    </action>
-
-    <join name="wait_clean_country" to="should_patch_datasource_ids"/>
 
     <decision name="should_patch_datasource_ids">
         <switch>

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

@@ -28,5 +28,35 @@
     "paramLongName": "graphTableClassName",
     "paramDescription": "class name moelling the graph table",
     "paramRequired": true
+  },
+  {
+    "paramName": "ci",
+    "paramLongName": "contextId",
+    "paramDescription": "the id of the context to be removed",
+    "paramRequired": true
+  },
+  {
+    "paramName": "c",
+    "paramLongName": "country",
+    "paramDescription": "the id of the context to be removed",
+    "paramRequired": true
+  },
+  {
+    "paramName": "vfc",
+    "paramLongName": "verifyCountryParam",
+    "paramDescription": "the parameter to be verified to remove the country",
+    "paramRequired": true
+  },
+  {
+    "paramName": "cf",
+    "paramLongName": "collectedfrom",
+    "paramDescription": "the collectedfrom value for which we should apply the cleaning",
+    "paramRequired": true
+  },
+  {
+    "paramName": "hb",
+    "paramLongName": "hostedBy",
+    "paramDescription": "the set of datasources having the specified country in the graph searched for in the hostedby of the results",
+    "paramRequired": true
   }
 ]

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

@@ -56,7 +56,7 @@ public class XmlRecordFactoryTest {
 
 		assertNotNull(doc);
 
-		//System.out.println(doc.asXML());
+		// System.out.println(doc.asXML());
 
 		assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid"));
 		assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending"));