Merge branch 'beta' into 7096-fileGZip-collector-plugin

dhp-build/dhp-build-assembly-resources/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>eu.dnetlib.dhp</groupId>
         <artifactId>dhp-build</artifactId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
 
     <artifactId>dhp-build-assembly-resources</artifactId>

dhp-build/dhp-build-properties-maven-plugin/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>eu.dnetlib.dhp</groupId>
         <artifactId>dhp-build</artifactId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
 
     <artifactId>dhp-build-properties-maven-plugin</artifactId>

dhp-build/dhp-code-style/pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>eu.dnetlib.dhp</groupId>
     <artifactId>dhp-code-style</artifactId>
-    <version>1.2.4-SNAPSHOT</version>
+    <version>1.2.5-SNAPSHOT</version>
 
     <packaging>jar</packaging>
 
@@ -47,12 +47,16 @@
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-site-plugin</artifactId>
                     <version>3.9.1</version>
+                    <configuration>
+                        <skip>true</skip>
+                    </configuration>
                 </plugin>
             </plugins>
         </pluginManagement>
     </build>
 
     <properties>
+
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <dhp.site.stage.path>sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop</dhp.site.stage.path>
     </properties>

dhp-build/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>eu.dnetlib.dhp</groupId>
 		<artifactId>dhp</artifactId>
-		<version>1.2.4-SNAPSHOT</version>
+		<version>1.2.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>dhp-build</artifactId>
 	<packaging>pom</packaging>

dhp-common/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>eu.dnetlib.dhp</groupId>
 		<artifactId>dhp</artifactId>
-		<version>1.2.4-SNAPSHOT</version>
+		<version>1.2.5-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 
 	</parent>

dhp-workflows/dhp-actionmanager/pom.xml

@@ -4,7 +4,7 @@
     <parent>
         <groupId>eu.dnetlib.dhp</groupId>
         <artifactId>dhp-workflows</artifactId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <artifactId>dhp-actionmanager</artifactId>
 

dhp-workflows/dhp-aggregation/pom.xml

@@ -4,7 +4,7 @@
     <parent>
         <groupId>eu.dnetlib.dhp</groupId>
         <artifactId>dhp-workflows</artifactId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <artifactId>dhp-aggregation</artifactId>
     <build>

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala

@@ -72,7 +72,6 @@ class DataciteToOAFTest extends AbstractVocabularyTest {
 
     spark.read.load(targetPath).printSchema();
 
-
     val result: Dataset[Oaf] = spark.read.load(targetPath).as[Oaf]
 
     result

dhp-workflows/dhp-blacklist/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

dhp-workflows/dhp-broker-events/pom.xml

@@ -1,11 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0"
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<parent>
 		<artifactId>dhp-workflows</artifactId>
 		<groupId>eu.dnetlib.dhp</groupId>
-		<version>1.2.4-SNAPSHOT</version>
+		<version>1.2.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 

dhp-workflows/dhp-dedup-openaire/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>dhp-dedup-openaire</artifactId>

dhp-workflows/dhp-distcp/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

dhp-workflows/dhp-doiboost/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala

@@ -446,16 +446,12 @@ case object Crossref2Oaf {
             case "10.13039/501100000781" =>
               generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
               generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
-            case "10.13039/100000001" =>
+            case "10.13039/100000001"    => generateSimpleRelationFromAward(funder, "nsf_________", a => a)
-              generateSimpleRelationFromAward(funder, "nsf_________", a => a)
+            case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a)
-            case "10.13039/501100001665" =>
+            case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a)
-              generateSimpleRelationFromAward(funder, "anr_________", a => a)
-            case "10.13039/501100002341" =>
-              generateSimpleRelationFromAward(funder, "aka_________", a => a)
             case "10.13039/501100001602" =>
-              generateSimpleRelationFromAward(funder, "aka_________", a => a.replace("SFI", ""))
+              generateSimpleRelationFromAward(funder, "sfi_________", a => a.replace("SFI", ""))
-            case "10.13039/501100000923" =>
+            case "10.13039/501100000923" => generateSimpleRelationFromAward(funder, "arc_________", a => a)
-              generateSimpleRelationFromAward(funder, "arc_________", a => a)
             case "10.13039/501100000038" =>
               val targetId = getProjectId("nserc_______", "1e5e62235d094afd01cd56e65112fc63")
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
@@ -468,14 +464,10 @@ case object Crossref2Oaf {
               val targetId = getProjectId("cihr________", "1e5e62235d094afd01cd56e65112fc63")
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
               queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
-            case "10.13039/501100002848" =>
+            case "10.13039/501100002848" => generateSimpleRelationFromAward(funder, "conicytf____", a => a)
-              generateSimpleRelationFromAward(funder, "conicytf____", a => a)
+            case "10.13039/501100003448" => generateSimpleRelationFromAward(funder, "gsrt________", extractECAward)
-            case "10.13039/501100003448" =>
+            case "10.13039/501100010198" => generateSimpleRelationFromAward(funder, "sgov________", a => a)
-              generateSimpleRelationFromAward(funder, "gsrt________", extractECAward)
+            case "10.13039/501100004564" => generateSimpleRelationFromAward(funder, "mestd_______", extractECAward)
-            case "10.13039/501100010198" =>
-              generateSimpleRelationFromAward(funder, "sgov________", a => a)
-            case "10.13039/501100004564" =>
-              generateSimpleRelationFromAward(funder, "mestd_______", extractECAward)
             case "10.13039/501100003407" =>
               generateSimpleRelationFromAward(funder, "miur________", a => a)
               val targetId = getProjectId("miur________", "1e5e62235d094afd01cd56e65112fc63")
@@ -487,15 +479,11 @@ case object Crossref2Oaf {
                 "irb_hr______",
                 a => a.replaceAll("Project No.", "").replaceAll("HRZZ-", "")
               )
-            case "10.13039/501100006769" =>
+            case "10.13039/501100006769" => generateSimpleRelationFromAward(funder, "rsf_________", a => a)
-              generateSimpleRelationFromAward(funder, "rsf_________", a => a)
+            case "10.13039/501100001711" => generateSimpleRelationFromAward(funder, "snsf________", snsfRule)
-            case "10.13039/501100001711" =>
+            case "10.13039/501100004410" => generateSimpleRelationFromAward(funder, "tubitakf____", a => a)
-              generateSimpleRelationFromAward(funder, "snsf________", snsfRule)
-            case "10.13039/501100004410" =>
-              generateSimpleRelationFromAward(funder, "tubitakf____", a => a)
-            case "10.10.13039/100004440" =>
-              generateSimpleRelationFromAward(funder, "wt__________", a => a)
             case "10.13039/100004440" =>
+              generateSimpleRelationFromAward(funder, "wt__________", a => a)
               val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63")
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
               queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
@@ -516,6 +504,7 @@ case object Crossref2Oaf {
             case "CONICYT, Programa de Formación de Capital Humano Avanzado" =>
               generateSimpleRelationFromAward(funder, "conicytf____", extractECAward)
             case "Wellcome Trust Masters Fellowship" =>
+              generateSimpleRelationFromAward(funder, "wt__________", a => a)
               val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63")
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
               queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)

dhp-workflows/dhp-enrichment/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -51,7 +51,7 @@
         <dependency>
             <groupId>eu.dnetlib.dhp</groupId>
             <artifactId>dhp-aggregation</artifactId>
-            <version>1.2.4-SNAPSHOT</version>
+            <version>1.2.5-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 

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

@@ -274,7 +274,6 @@
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
             <arg>--preparedInfoPath</arg><arg>${workingDir}/publication</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
             <arg>--outputPath</arg><arg>${outputPath}/publication</arg>
         </spark>
@@ -304,7 +303,6 @@
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
             <arg>--preparedInfoPath</arg><arg>${workingDir}/dataset</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
             <arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
         </spark>
@@ -334,7 +332,6 @@
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
             <arg>--preparedInfoPath</arg><arg>${workingDir}/otherresearchproduct</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
             <arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
         </spark>
@@ -364,7 +361,6 @@
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
             <arg>--preparedInfoPath</arg><arg>${workingDir}/software</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
             <arg>--outputPath</arg><arg>${outputPath}/software</arg>
         </spark>

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

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

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

@@ -0,0 +1,113 @@
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Context;
+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.utils.ISLookupClientFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.Serializable;
+import java.util.List;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+public class CleanContextSparkJob implements Serializable {
+    private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    public static void main(String[] args) throws Exception {
+
+        String jsonConfiguration = IOUtils
+                .toString(
+                        CleanContextSparkJob.class
+                                .getResourceAsStream(
+                                        "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json"));
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+        parser.parseArgument(args);
+
+        Boolean isSparkSessionManaged = Optional
+                .ofNullable(parser.get("isSparkSessionManaged"))
+                .map(Boolean::valueOf)
+                .orElse(Boolean.TRUE);
+        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+        String inputPath = parser.get("inputPath");
+        log.info("inputPath: {}", inputPath);
+
+        String workingPath = parser.get("workingPath");
+        log.info("workingPath: {}", workingPath);
+
+        String contextId = parser.get("contextId");
+        log.info("contextId: {}", contextId);
+
+        String verifyParam = parser.get("verifyParam");
+        log.info("verifyParam: {}", verifyParam);
+
+
+        String graphTableClassName = parser.get("graphTableClassName");
+        log.info("graphTableClassName: {}", graphTableClassName);
+
+        Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
+
+
+        SparkConf conf = new SparkConf();
+        runWithSparkSession(
+                conf,
+                isSparkSessionManaged,
+                spark -> {
+
+                    cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath);
+                });
+    }
+
+    private static <T extends Result> void  cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class<T> entityClazz, String workingPath) {
+        Dataset<T> res = spark
+                .read()
+                .textFile(inputPath)
+                .map(
+                        (MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
+                        Encoders.bean(entityClazz));
+
+        res.map((MapFunction<T, T>) r -> {
+            if(!r.getTitle()
+                    .stream()
+                    .filter(t -> t.getQualifier().getClassid()
+                            .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid()))
+                    .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){
+                return r;
+            }
+            r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0]
+                    .equalsIgnoreCase(contextId)).collect(Collectors.toList()));
+            return r;
+        } ,Encoders.bean(entityClazz))
+                .write()
+                .mode(SaveMode.Overwrite)
+                .option("compression","gzip")
+                .json(workingPath);
+
+        spark.read().textFile(workingPath).map((MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
+                Encoders.bean(entityClazz))
+                .write()
+                .mode(SaveMode.Overwrite)
+                .option("compression","gzip")
+                .json(inputPath);
+    }
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java

@@ -4,8 +4,6 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj;
 import java.io.Serializable;
 import java.util.List;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
-
 public class BibJson implements Serializable {
 	private Editorial editorial;
 	private PidScheme pid_scheme;

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

@@ -0,0 +1,37 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "in",
+    "paramLongName": "inputPath",
+    "paramDescription": "the path to the graph data dump to read",
+    "paramRequired": true
+  },
+  {
+    "paramName": "wp",
+    "paramLongName": "workingPath",
+    "paramDescription": "the path to store the output graph",
+    "paramRequired": true
+  },
+  {
+    "paramName": "ci",
+    "paramLongName": "contextId",
+    "paramDescription": "the id of the context to be removed",
+    "paramRequired": true
+  },
+  {
+    "paramName": "class",
+    "paramLongName": "graphTableClassName",
+    "paramDescription": "class name moelling the graph table",
+    "paramRequired": true
+  },{
+  "paramName": "vf",
+  "paramLongName": "verifyParam",
+  "paramDescription": "the parameter to be verified to remove the context",
+  "paramRequired": true
+}
+]

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java

@@ -0,0 +1,159 @@
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.oa.graph.dump.Constants;
+import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
+import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
+import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.dump.oaf.Instance;
+import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
+import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.Software;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+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.MapFunction;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+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.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.Locale;
+
+public class CleanContextTest {
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    private static SparkSession spark;
+
+    private static Path workingDir;
+
+    private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class);
+
+    @BeforeAll
+    public static void beforeAll() throws IOException {
+        workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName());
+        log.info("using work dir {}", workingDir);
+
+        SparkConf conf = new SparkConf();
+        conf.setAppName(DumpJobTest.class.getSimpleName());
+
+        conf.setMaster("local[*]");
+        conf.set("spark.driver.host", "localhost");
+        conf.set("hive.metastore.local", "true");
+        conf.set("spark.ui.enabled", "false");
+        conf.set("spark.sql.warehouse.dir", workingDir.toString());
+        conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+        spark = SparkSession
+                .builder()
+                .appName(DumpJobTest.class.getSimpleName())
+                .config(conf)
+                .getOrCreate();
+    }
+
+    @AfterAll
+    public static void afterAll() throws IOException {
+        FileUtils.deleteDirectory(workingDir.toFile());
+        spark.stop();
+    }
+
+    @Test
+    public void testResultClean() throws Exception {
+        final String sourcePath = getClass()
+                .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json")
+                .getPath();
+        final String prefix = "gcube ";
+
+
+        spark.read().textFile(sourcePath).map((MapFunction<String, Publication>)  r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class))
+                        .write().json(workingDir.toString() + "/publication");
+
+
+        CleanContextSparkJob.main(new String[] {
+                        "--isSparkSessionManaged", Boolean.FALSE.toString(),
+                        "--inputPath", workingDir.toString() + "/publication",
+                        "-graphTableClassName", Publication.class.getCanonicalName(),
+                        "-workingPath", workingDir.toString() + "/working",
+                "-contextId","sobigdata",
+                "-verifyParam","gCube "
+                });
+
+        final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+        JavaRDD<Publication> tmp = sc
+                .textFile(workingDir.toString() + "/publication")
+                .map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
+
+        Assertions.assertEquals(7, tmp.count());
+
+        //original result with sobigdata context and gcube as starting string in the main title for the publication
+        Assertions.assertEquals(0,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size());
+
+        //original result with sobigdata context without gcube as starting string in the main title for the publication
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size());
+        Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() );
+
+        //original result with sobigdata context with gcube as starting string in the subtitle
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size());
+        Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() );
+        List<StructuredProperty> titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle();
+        Assertions.assertEquals(1, titles.size());
+        Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
+        Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid());
+
+        //original result with sobigdata context with gcube not as starting string in the main title
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size());
+        Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() );
+        titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle();
+        Assertions.assertEquals(1, titles.size());
+        Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
+        Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) );
+        Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
+
+        //original result with sobigdata in context and also other contexts with gcube as starting string for the main title
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size());
+        Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() );
+        titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle();
+        Assertions.assertEquals(1, titles.size());
+        Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
+        Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
+
+        //original result with multiple main title one of which whith gcube as starting string and with 2 contextes
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size());
+        Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() );
+        titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle();
+        Assertions.assertEquals(2, titles.size());
+        Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) );
+
+
+        //original result without sobigdata in context with gcube as starting string for the main title
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size());
+        Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() );
+        titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle();
+        Assertions.assertEquals(2, titles.size());
+
+        Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)));
+
+
+    }
+}

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

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

dhp-workflows/dhp-stats-promote/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>dhp-stats-promote</artifactId>

dhp-workflows/dhp-stats-update/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>dhp-stats-update</artifactId>

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql

@@ -12,6 +12,8 @@ and (ri.accessright = 'Open Access'
 or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp
 on p.id= tmp.id;
 
+compute stats indi_pub_green_oa;
+
 create table indi_pub_grey_lit stored as parquet as
 select distinct p.id, coalesce(grey_lit, 0) as grey_lit
 from publication p
@@ -22,6 +24,8 @@ join result_classifications rt on rt.id = p.id
 where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and
 not exists (select 1 from result_classifications rc where type ='Other literature type' and rc.id=p.id)) tmp on p.id=tmp.id;
 
+compute stats indi_pub_grey_lit;
+
 create table indi_pub_doi_from_crossref stored as parquet as
 select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref
 from publication p
@@ -31,6 +35,7 @@ join datasource d on d.id = ri.collectedfrom
 where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp
 on tmp.id=p.id;
 
+compute stats indi_pub_doi_from_crossref;
 ---- Sprint 2 ----
 create table indi_result_has_cc_licence stored as parquet as
 select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license
@@ -40,6 +45,8 @@ join result_licenses as license on license.id = r.id
 where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp
 on r.id= tmp.id;
 
+compute stats indi_result_has_cc_licence;
+
 create table indi_result_has_cc_licence_url stored as parquet as
 select distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url
 from result r
@@ -49,16 +56,21 @@ join result_licenses as license on license.id = r.id
 WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp
 on r.id= tmp.id;
 
+compute stats indi_result_has_cc_licence_url;
+
 create table indi_pub_has_abstract stored as parquet as
 select distinct publication.id, coalesce(abstract, 1) has_abstract
 from publication;
 
+compute stats indi_pub_has_abstract;
+
 create table indi_result_with_orcid stored as parquet as
 select distinct r.id, coalesce(has_orcid, 0) as has_orcid
 from result r
 left outer join (select id, 1 as has_orcid from result_orcid) tmp
 on r.id= tmp.id;
 
+compute stats indi_result_with_orcid;
 
 ---- Sprint 3 ----
 create table indi_funded_result_with_fundref stored as parquet as
@@ -68,6 +80,8 @@ left outer join (select distinct id, 1 as fundref from project_results
 where provenance='Harvested') tmp
 on r.id= tmp.id;
 
+compute stats indi_funded_result_with_fundref;
+
 create table indi_result_org_country_collab stored as parquet as
 with tmp as
 (select o.id as id, o.country , ro.id as result,r.type  from organization o
@@ -79,6 +93,8 @@ join tmp as o2 on o1.result=o2.result
 where o1.id<>o2.id and o1.country<>o2.country
 group by o1.id, o1.type,o2.country;
 
+compute stats indi_result_org_country_collab;
+
 create table indi_result_org_collab stored as parquet as
 with tmp as
 (select o.id, ro.id as result,r.type  from organization o
@@ -90,6 +106,8 @@ join tmp as o2 on o1.result=o2.result
 where o1.id<>o2.id
 group by o1.id, o2.id, o1.type;
 
+compute stats indi_result_org_collab;
+
 create table indi_funder_country_collab stored as parquet as
 with tmp as (select funder, project, country from organization_projects op
 join organization o on o.id=op.id
@@ -101,6 +119,8 @@ join tmp as f2 on f1.project=f2.project
 where f1.country<>f2.country
 group by f1.funder, f2.country, f1.country;
 
+compute stats indi_funder_country_collab;
+
 create table indi_result_country_collab stored as parquet as
 with tmp as
 (select country, ro.id as result,r.type  from organization o
@@ -112,6 +132,8 @@ join tmp as o2 on o1.result=o2.result
 where o1.country<>o2.country
 group by o1.country, o2.country, o1.type;
 
+compute stats indi_result_country_collab;
+
 ---- Sprint 4 ----
 create table indi_pub_diamond stored as parquet as
 select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal
@@ -123,6 +145,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli
 and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp
 on pd.id=tmp.id;
 
+compute stats indi_pub_diamond;
+
 create table indi_pub_hybrid stored as parquet as
 select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid
 from publication_datasources pd
@@ -133,6 +157,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli
 and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp
 on pd.id=tmp.id;
 
+compute stats indi_pub_hybrid;
+
 create table indi_pub_in_transformative stored as parquet as
 select distinct pd.id, coalesce(is_transformative, 0) as is_transformative
 from publication pd
@@ -143,6 +169,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli
 and ps.is_transformative_journal=true) tmp
 on pd.id=tmp.id;
 
+compute stats indi_pub_in_transformative;
+
 create table indi_pub_closed_other_open stored as parquet as
 select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from result_instance ri
 left outer join
@@ -153,11 +181,12 @@ where d.type like '%Journal%' and ri.accessright='Closed Access' and
 (p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp
 on tmp.id=ri.id;
 
-
+compute stats indi_pub_closed_other_open;
 ---- Sprint 5 ----
 create table indi_result_no_of_copies stored as parquet as
 select id, count(id) as number_of_copies from result_instance group by id;
 
+compute stats indi_result_no_of_copies;
 ---- Sprint 6 ----
 create table indi_pub_gold_oa stored as parquet as
 WITH gold_oa AS (
@@ -183,6 +212,8 @@ LEFT OUTER JOIN (
     JOIN issn on issn.id=pd.datasource
     JOIN gold_oa  on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id;
 
+compute stats indi_pub_gold_oa;
+
 create table indi_datasets_gold_oa stored as parquet as
 WITH gold_oa AS (
     SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn
@@ -210,6 +241,8 @@ LEFT OUTER JOIN (
     JOIN issn on issn.id=pd.datasource
     JOIN gold_oa  on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id;
 
+compute stats indi_datasets_gold_oa;
+
 create table indi_software_gold_oa stored as parquet as
 WITH gold_oa AS (
     SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn
@@ -237,6 +270,8 @@ LEFT OUTER JOIN (
     JOIN issn on issn.id=pd.datasource
     JOIN gold_oa  on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id;
 
+compute stats indi_software_gold_oa;
+
 create table indi_org_findable stored as parquet as
 with result_with_pid as (
     select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro
@@ -263,6 +298,8 @@ join result_with_pid_share on result_with_pid_share.organization=allresults.orga
 left outer join (
     select organization, abstract_share from result_with_abstract_share) tmp on tmp.organization=allresults.organization;
 
+compute stats indi_org_findable;
+
 create table indi_org_openess stored as parquet as
 WITH datasets_oa as (
     SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa dg
@@ -313,6 +350,8 @@ left outer join (
 left outer join (
     select organization,s from allsoftwaresshare) tmp1 on tmp1.organization=allpubsshare.organization;
 
+compute stats indi_org_openess;
+
 create table indi_pub_hybrid_oa_with_cc stored as parquet as
 WITH hybrid_oa AS (
     SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn
@@ -343,6 +382,8 @@ LEFT OUTER JOIN (
     JOIN indi_result_has_cc_licence cc on pd.id=cc.id
     where cc.has_cc_license=1) tmp on pd.id=tmp.id;
 
+compute stats indi_pub_hybrid_oa_with_cc;
+
 create table indi_pub_downloads stored as parquet as
 SELECT result_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats
 join publication on result_id=id
@@ -350,6 +391,8 @@ where downloads>0
 GROUP BY result_id
 order by no_dowloads desc;
 
+compute stats indi_pub_downloads;
+
 create table indi_pub_downloads_datasource stored as parquet as
 SELECT result_id, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats
 join publication on result_id=id
@@ -357,15 +400,21 @@ where downloads>0
 GROUP BY result_id, repository_id
 order by result_id;
 
+compute stats indi_pub_downloads_datasource;
+
 create table indi_pub_downloads_year stored as parquet as
 SELECT result_id, substring(us.`date`, 1,4) as `year`, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us
 join publication on result_id=id where downloads>0
 GROUP BY result_id, `year`
 order by `year` asc;
 
+compute stats indi_pub_downloads_year;
+
 create table indi_pub_downloads_datasource_year stored as parquet as
 SELECT result_id, substring(us.`date`, 1,4) as `year`, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us
 join publication on result_id=id
 where downloads>0
 GROUP BY result_id, repository_id, `year`
 order by `year` asc, result_id;
+
+compute stats indi_pub_downloads_datasource_year;

dhp-workflows/dhp-usage-raw-data-update/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>dhp-usage-raw-data-update</artifactId>

dhp-workflows/dhp-usage-stats-build/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>dhp-usage-stats-build</artifactId>

dhp-workflows/dhp-workflow-profiles/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>dhp-workflows</artifactId>
         <groupId>eu.dnetlib.dhp</groupId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

dhp-workflows/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>eu.dnetlib.dhp</groupId>
         <artifactId>dhp</artifactId>
-        <version>1.2.4-SNAPSHOT</version>
+        <version>1.2.5-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>eu.dnetlib.dhp</groupId>
 	<artifactId>dhp</artifactId>
-	<version>1.2.4-SNAPSHOT</version>
+	<version>1.2.5-SNAPSHOT</version>
 	<packaging>pom</packaging>
 
 	<licenses>
@@ -551,6 +551,9 @@
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-site-plugin</artifactId>
 					<version>3.9.1</version>
+					<configuration>
+						<skip>${dhp.site.skip}</skip>
+					</configuration>
 				</plugin>
 
 				<plugin>
@@ -791,6 +794,7 @@
 		<dhp.spark.version>2.4.0.cloudera2</dhp.spark.version>
 		<dhp.jackson.version>2.9.6</dhp.jackson.version>
 		<dhp.commons.lang.version>3.5</dhp.commons.lang.version>
+		<dhp.site.skip>true</dhp.site.skip>
 		<dhp.guava.version>11.0.2</dhp.guava.version>
 		<scala.version>2.11.12</scala.version>
 		<junit-jupiter.version>5.6.1</junit-jupiter.version>