merged

dhp-workflows/dhp-actionmanager/pom.xml

@@ -47,6 +47,16 @@
             <artifactId>jaxen</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>org.apache.hadoop</groupId>
+            <artifactId>hadoop-distcp</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>eu.dnetlib</groupId>
+            <artifactId>dnet-openaire-data-protos</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>eu.dnetlib.dhp</groupId>
             <artifactId>dhp-schemas</artifactId>
@@ -57,6 +67,44 @@
             <groupId>eu.dnetlib</groupId>
             <artifactId>dnet-actionmanager-api</artifactId>
         </dependency>
+        <dependency>
+            <groupId>eu.dnetlib</groupId>
+            <artifactId>dnet-actionmanager-common</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>eu.dnetlib</groupId>
+                    <artifactId>dnet-openaireplus-mapping-utils</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>saxonica</groupId>
+                    <artifactId>saxon</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>saxonica</groupId>
+                    <artifactId>saxon-dom</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>jgrapht</groupId>
+                    <artifactId>jgrapht</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>net.sf.ehcache</groupId>
+                    <artifactId>ehcache</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.springframework</groupId>
+                    <artifactId>spring-test</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.apache.*</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>apache</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
 
     </dependencies>
 </project>

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/LicenseComparator.java

@@ -1,4 +1,4 @@
-package eu.dnetlib.dhp.migration.actions;
+package eu.dnetlib.dhp.actionmanager.migration;
 
 import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
 import java.util.Comparator;

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java

@@ -1,4 +1,4 @@
-package eu.dnetlib.dhp.migration.actions;
+package eu.dnetlib.dhp.actionmanager.migration;
 
 import com.google.common.base.Splitter;
 import com.google.common.collect.Lists;
@@ -9,35 +9,36 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.OutputStream;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Properties;
 import java.util.stream.Collectors;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.tools.DistCp;
 import org.apache.hadoop.tools.DistCpOptions;
 import org.apache.hadoop.util.ToolRunner;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class MigrateActionSet {
 
-    private static final Log log = LogFactory.getLog(MigrateActionSet.class);
+    private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class);
 
     private static final String SEPARATOR = "/";
     private static final String TARGET_PATHS = "target_paths";
     private static final String RAWSET_PREFIX = "rawset_";
 
-    private static Boolean DEFAULT_TRANSFORM_ONLY = false;
-
     public static void main(String[] args) throws Exception {
         final ArgumentApplicationParser parser =
                 new ArgumentApplicationParser(
                         IOUtils.toString(
                                 MigrateActionSet.class.getResourceAsStream(
-                                        "/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json")));
+                                        "/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json")));
         parser.parseArgument(args);
 
         new MigrateActionSet().run(parser);
@@ -56,11 +57,11 @@ public class MigrateActionSet {
 
         final String transform_only_s = parser.get("transform_only");
 
-        log.info("transform only param: " + transform_only_s);
+        log.info("transform only param: {}", transform_only_s);
 
         final Boolean transformOnly = Boolean.valueOf(parser.get("transform_only"));
 
-        log.info("transform only: " + transformOnly);
+        log.info("transform only: {}", transformOnly);
 
         ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
 
@@ -79,22 +80,19 @@ public class MigrateActionSet {
 
         final List<Path> sourcePaths = getSourcePaths(sourceNN, isLookUp);
         log.info(
-                String.format(
-                        "paths to process:\n%s",
-                        sourcePaths.stream()
-                                .map(p -> p.toString())
-                                .collect(Collectors.joining("\n"))));
+                "paths to process:\n{}",
+                sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n")));
         for (Path source : sourcePaths) {
 
             if (!sourceFS.exists(source)) {
-                log.warn(String.format("skipping unexisting path: %s", source));
+                log.warn("skipping unexisting path: {}", source);
             } else {
 
                 LinkedList<String> pathQ =
                         Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath()));
 
                 final String rawSet = pathQ.pollLast();
-                log.info(String.format("got RAWSET: %s", rawSet));
+                log.info("got RAWSET: {}", rawSet);
 
                 if (StringUtils.isNotBlank(rawSet) && rawSet.startsWith(RAWSET_PREFIX)) {
 
@@ -109,7 +107,7 @@ public class MigrateActionSet {
                                             + SEPARATOR
                                             + rawSet);
 
-                    log.info(String.format("using TARGET PATH: %s", targetPath));
+                    log.info("using TARGET PATH: {}", targetPath);
 
                     if (!transformOnly) {
                         if (targetFS.exists(targetPath)) {

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java

@@ -1,4 +1,9 @@
-package eu.dnetlib.dhp.migration.actions;
+package eu.dnetlib.dhp.actionmanager.migration;
+
+import static eu.dnetlib.data.proto.KindProtos.Kind.entity;
+import static eu.dnetlib.data.proto.KindProtos.Kind.relation;
+import static eu.dnetlib.data.proto.TypeProtos.*;
+import static eu.dnetlib.data.proto.TypeProtos.Type.*;
 
 import com.google.common.collect.Lists;
 import com.googlecode.protobuf.format.JsonFormat;

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java

@@ -0,0 +1,179 @@
+package eu.dnetlib.dhp.actionmanager.migration;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.base.Splitter;
+import com.google.common.collect.Lists;
+import com.google.protobuf.InvalidProtocolBufferException;
+import eu.dnetlib.data.proto.OafProtos;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.LinkedList;
+import java.util.Objects;
+import java.util.Optional;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import scala.Tuple2;
+
+public class TransformActions implements Serializable {
+
+    private static final Logger log = LoggerFactory.getLogger(TransformActions.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    private static final String SEPARATOR = "/";
+
+    public static void main(String[] args) throws Exception {
+        final ArgumentApplicationParser parser =
+                new ArgumentApplicationParser(
+                        IOUtils.toString(
+                                MigrateActionSet.class.getResourceAsStream(
+                                        "/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json")));
+        parser.parseArgument(args);
+
+        Boolean isSparkSessionManaged =
+                Optional.ofNullable(parser.get("isSparkSessionManaged"))
+                        .map(Boolean::valueOf)
+                        .orElse(Boolean.TRUE);
+        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+        final String isLookupUrl = parser.get("isLookupUrl");
+        log.info("isLookupUrl: {}", isLookupUrl);
+
+        final String inputPaths = parser.get("inputPaths");
+
+        if (StringUtils.isBlank(inputPaths)) {
+            throw new RuntimeException("empty inputPaths");
+        }
+        log.info("inputPaths: {}", inputPaths);
+
+        final String targetBaseDir = getTargetBaseDir(isLookupUrl);
+
+        SparkConf conf = new SparkConf();
+
+        runWithSparkSession(
+                conf,
+                isSparkSessionManaged,
+                spark -> transformActions(inputPaths, targetBaseDir, spark));
+    }
+
+    private static void transformActions(
+            String inputPaths, String targetBaseDir, SparkSession spark) throws IOException {
+        final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+        final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
+
+        for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) {
+
+            LinkedList<String> pathQ =
+                    Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath));
+
+            final String rawset = pathQ.pollLast();
+            final String actionSetDirectory = pathQ.pollLast();
+
+            final Path targetDirectory =
+                    new Path(targetBaseDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawset);
+
+            if (fs.exists(targetDirectory)) {
+                log.info("found target directory '{}", targetDirectory);
+                fs.delete(targetDirectory, true);
+                log.info("deleted target directory '{}", targetDirectory);
+            }
+
+            log.info("transforming actions from '{}' to '{}'", sourcePath, targetDirectory);
+
+            sc.sequenceFile(sourcePath, Text.class, Text.class)
+                    .map(
+                            a ->
+                                    eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(
+                                            a._2().toString()))
+                    .map(TransformActions::doTransform)
+                    .filter(Objects::nonNull)
+                    .mapToPair(
+                            a ->
+                                    new Tuple2<>(
+                                            a.getClazz().toString(),
+                                            OBJECT_MAPPER.writeValueAsString(a)))
+                    .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
+                    .saveAsNewAPIHadoopFile(
+                            targetDirectory.toString(),
+                            Text.class,
+                            Text.class,
+                            SequenceFileOutputFormat.class,
+                            sc.hadoopConfiguration());
+        }
+    }
+
+    private static AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa)
+            throws InvalidProtocolBufferException {
+
+        // dedup similarity relations had empty target value, don't migrate them
+        if (aa.getTargetValue().length == 0) {
+            return null;
+        }
+        final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue());
+        final Oaf oaf = ProtoConverter.convert(proto_oaf);
+        switch (proto_oaf.getKind()) {
+            case entity:
+                switch (proto_oaf.getEntity().getType()) {
+                    case datasource:
+                        return new AtomicAction<>(Datasource.class, (Datasource) oaf);
+                    case organization:
+                        return new AtomicAction<>(Organization.class, (Organization) oaf);
+                    case project:
+                        return new AtomicAction<>(Project.class, (Project) oaf);
+                    case result:
+                        final String resulttypeid =
+                                proto_oaf
+                                        .getEntity()
+                                        .getResult()
+                                        .getMetadata()
+                                        .getResulttype()
+                                        .getClassid();
+                        switch (resulttypeid) {
+                            case "publication":
+                                return new AtomicAction<>(Publication.class, (Publication) oaf);
+                            case "software":
+                                return new AtomicAction<>(Software.class, (Software) oaf);
+                            case "other":
+                                return new AtomicAction<>(
+                                        OtherResearchProduct.class, (OtherResearchProduct) oaf);
+                            case "dataset":
+                                return new AtomicAction<>(Dataset.class, (Dataset) oaf);
+                            default:
+                                // can be an update, where the resulttype is not specified
+                                return new AtomicAction<>(Result.class, (Result) oaf);
+                        }
+                    default:
+                        throw new IllegalArgumentException(
+                                "invalid entity type: " + proto_oaf.getEntity().getType());
+                }
+            case relation:
+                return new AtomicAction<>(Relation.class, (Relation) oaf);
+            default:
+                throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind());
+        }
+    }
+
+    private static String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
+        ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
+        String XQUERY =
+                "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()";
+        return isLookUp.getResourceProfileByQuery(XQUERY);
+    }
+}

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json

@@ -0,0 +1,56 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "is",
+    "paramLongName": "isLookupUrl",
+    "paramDescription": "URL of the isLookUp Service",
+    "paramRequired": true
+  },
+  {
+    "paramName": "sn",
+    "paramLongName": "sourceNameNode",
+    "paramDescription": "nameNode of the source cluster",
+    "paramRequired": true
+  },
+  {
+    "paramName": "tn",
+    "paramLongName": "targetNameNode",
+    "paramDescription": "namoNode of the target cluster",
+    "paramRequired": true
+  },
+  {
+    "paramName": "w",
+    "paramLongName": "workingDirectory",
+    "paramDescription": "working directory",
+    "paramRequired": true
+  },
+  {
+    "paramName": "nm",
+    "paramLongName": "distcp_num_maps",
+    "paramDescription": "maximum number of map tasks used in the distcp process",
+    "paramRequired": true
+  },
+  {
+    "paramName": "mm",
+    "paramLongName": "distcp_memory_mb",
+    "paramDescription": "memory for distcp action copying actionsets from remote cluster",
+    "paramRequired": true
+  },
+  {
+    "paramName": "tt",
+    "paramLongName": "distcp_task_timeout",
+    "paramDescription": "timeout for distcp copying actions from remote cluster",
+    "paramRequired": true
+  },
+  {
+    "paramName": "tr",
+    "paramLongName": "transform_only",
+    "paramDescription": "activate tranform-only mode. Only apply transformation step",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "is",
+    "paramLongName": "isLookupUrl",
+    "paramDescription": "URL of the isLookUp Service",
+    "paramRequired": true
+  },
+  {
+    "paramName": "i",
+    "paramLongName": "inputPaths",
+    "paramDescription": "URL of the isLookUp Service",
+    "paramRequired": true
+  }
+]

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

@@ -10,7 +10,6 @@
         </property>
         <property>
             <name>workingDirectory</name>
-            <value>/tmp/actionsets</value>
             <description>working directory</description>
         </property>
         <property>
@@ -44,6 +43,20 @@
             <name>sparkExecutorCores</name>
             <description>number of cores used by single executor</description>
         </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
         <property>
             <name>spark2YarnHistoryServerAddress</name>
             <description>spark 2.* yarn history server address</description>
@@ -66,23 +79,27 @@
                 <name>oozie.launcher.mapred.job.queue.name</name>
                 <value>${oozieLauncherQueueName}</value>
             </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
         </configuration>
     </global>
 
-    <start to='migrate_actionsets' />
+    <start to="migrate_actionsets"/>
 
-    <action name='migrate_actionsets'>
+    <action name="migrate_actionsets">
         <java>
-            <main-class>eu.dnetlib.dhp.migration.actions.MigrateActionSet</main-class>
+            <main-class>eu.dnetlib.dhp.actionmanager.migration.MigrateActionSet</main-class>
             <java-opt>-Dmapred.task.timeout=${distcp_task_timeout}</java-opt>
-            <arg>-is</arg><arg>${isLookupUrl}</arg>
-            <arg>-sn</arg><arg>${sourceNN}</arg>
-            <arg>-tn</arg><arg>${nameNode}</arg>
-            <arg>-w</arg><arg>${workingDirectory}</arg>
-            <arg>-nm</arg><arg>${distcp_num_maps}</arg>
-            <arg>-mm</arg><arg>${distcp_memory_mb}</arg>
-            <arg>-tt</arg><arg>${distcp_task_timeout}</arg>
-            <arg>-tr</arg><arg>${transform_only}</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--sourceNameNode</arg><arg>${sourceNN}</arg>
+            <arg>--targetNameNode</arg><arg>${nameNode}</arg>
+            <arg>--workingDirectory</arg><arg>${workingDirectory}</arg>
+            <arg>--distcp_num_maps</arg><arg>${distcp_num_maps}</arg>
+            <arg>--distcp_memory_mb</arg><arg>${distcp_memory_mb}</arg>
+            <arg>--distcp_task_timeout</arg><arg>${distcp_task_timeout}</arg>
+            <arg>--transform_only</arg><arg>${transform_only}</arg>
             <capture-output/>
         </java>
         <ok to="transform_actions" />
@@ -94,19 +111,18 @@
             <master>yarn</master>
             <mode>cluster</mode>
             <name>transform_actions</name>
-            <class>eu.dnetlib.dhp.migration.actions.TransformActions</class>
-            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <class>eu.dnetlib.dhp.actionmanager.migration.TransformActions</class>
+            <jar>dhp-actionmanager-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-cores ${sparkExecutorCores}
-                --executor-memory ${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
-                --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
-            <arg>-mt</arg><arg>yarn</arg>
-            <arg>-is</arg><arg>${isLookupUrl}</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
             <arg>--inputPaths</arg><arg>${wf:actionData('migrate_actionsets')['target_paths']}</arg>
         </spark>
         <ok to="end"/>

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

@@ -1,213 +0,0 @@
-package eu.dnetlib.dhp.migration.actions;
-
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.google.common.base.Splitter;
-import com.google.common.collect.Lists;
-import com.google.protobuf.InvalidProtocolBufferException;
-import eu.dnetlib.data.proto.OafProtos;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.utils.ISLookupClientFactory;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
-import java.io.IOException;
-import java.io.Serializable;
-import java.util.LinkedList;
-import java.util.Objects;
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.compress.GzipCodec;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.sql.SparkSession;
-
-public class TransformActions implements Serializable {
-
-    private static final Log log = LogFactory.getLog(TransformActions.class);
-    private static final String SEPARATOR = "/";
-
-    public static void main(String[] args) throws Exception {
-        final ArgumentApplicationParser parser =
-                new ArgumentApplicationParser(
-                        IOUtils.toString(
-                                MigrateActionSet.class.getResourceAsStream(
-                                        "/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json")));
-        parser.parseArgument(args);
-
-        new TransformActions().run(parser);
-    }
-
-    private void run(ArgumentApplicationParser parser) throws ISLookUpException, IOException {
-
-        final String isLookupUrl = parser.get("isLookupUrl");
-        log.info("isLookupUrl: " + isLookupUrl);
-
-        final String inputPaths = parser.get("inputPaths");
-
-        if (StringUtils.isBlank(inputPaths)) {
-            throw new RuntimeException("empty inputPaths");
-        }
-        log.info("inputPaths: " + inputPaths);
-
-        final String targetBaseDir = getTargetBaseDir(isLookupUrl);
-
-        try (SparkSession spark = getSparkSession(parser)) {
-            final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-            final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
-
-            for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) {
-
-                LinkedList<String> pathQ =
-                        Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath));
-
-                final String rawset = pathQ.pollLast();
-                final String actionSetDirectory = pathQ.pollLast();
-
-                final Path targetDirectory =
-                        new Path(
-                                targetBaseDir
-                                        + SEPARATOR
-                                        + actionSetDirectory
-                                        + SEPARATOR
-                                        + rawset);
-
-                if (fs.exists(targetDirectory)) {
-                    log.info(String.format("found target directory '%s", targetDirectory));
-                    fs.delete(targetDirectory, true);
-                    log.info(String.format("deleted target directory '%s", targetDirectory));
-                }
-
-                log.info(
-                        String.format(
-                                "transforming actions from '%s' to '%s'",
-                                sourcePath, targetDirectory));
-
-                sc.sequenceFile(sourcePath, Text.class, Text.class)
-                        .map(
-                                a ->
-                                        eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(
-                                                a._2().toString()))
-                        .map(a -> doTransform(a))
-                        .filter(Objects::isNull)
-                        .filter(a -> a.getPayload() == null)
-                        .map(a -> new ObjectMapper().writeValueAsString(a))
-                        .saveAsTextFile(targetDirectory.toString(), GzipCodec.class);
-            }
-        }
-    }
-
-    private Text transformAction(eu.dnetlib.actionmanager.actions.AtomicAction aa)
-            throws InvalidProtocolBufferException, JsonProcessingException {
-        final Text out = new Text();
-        final ObjectMapper mapper = new ObjectMapper();
-        if (aa.getTargetValue() != null && aa.getTargetValue().length > 0) {
-            out.set(mapper.writeValueAsString(doTransform(aa)));
-        }
-        return out;
-    }
-
-    private AtomicAction<Relation> getRelationAtomicAction(String atomicaActionId) {
-        final String[] splitId = atomicaActionId.split("@");
-
-        String source = splitId[0];
-        String target = splitId[2];
-
-        String[] relSemantic = splitId[1].split("_");
-
-        Relation rel = new Relation();
-        rel.setSource(source);
-        rel.setTarget(target);
-        rel.setRelType(relSemantic[0]);
-        rel.setSubRelType(relSemantic[1]);
-        rel.setRelClass(relSemantic[2]);
-
-        DataInfo d = new DataInfo();
-        d.setDeletedbyinference(false);
-        d.setInferenceprovenance("deduplication");
-        d.setInferred(true);
-        d.setInvisible(false);
-        Qualifier provenanceaction = new Qualifier();
-
-        provenanceaction.setClassid("deduplication");
-        provenanceaction.setClassname("deduplication");
-        provenanceaction.setSchemeid("dnet:provenanceActions");
-        provenanceaction.setSchemename("dnet:provenanceActions");
-
-        d.setProvenanceaction(provenanceaction);
-
-        rel.setDataInfo(d);
-
-        return new AtomicAction<>(Relation.class, rel);
-    }
-
-    private AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa)
-            throws InvalidProtocolBufferException {
-        final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue());
-        final Oaf oaf = ProtoConverter.convert(proto_oaf);
-        switch (proto_oaf.getKind()) {
-            case entity:
-                switch (proto_oaf.getEntity().getType()) {
-                    case datasource:
-                        return new AtomicAction<>(Datasource.class, (Datasource) oaf);
-                    case organization:
-                        return new AtomicAction<>(Organization.class, (Organization) oaf);
-                    case project:
-                        return new AtomicAction<>(Project.class, (Project) oaf);
-                    case result:
-                        final String resulttypeid =
-                                proto_oaf
-                                        .getEntity()
-                                        .getResult()
-                                        .getMetadata()
-                                        .getResulttype()
-                                        .getClassid();
-                        switch (resulttypeid) {
-                            case "publication":
-                                return new AtomicAction<>(Publication.class, (Publication) oaf);
-                            case "software":
-                                return new AtomicAction<>(Software.class, (Software) oaf);
-                            case "other":
-                                return new AtomicAction<>(
-                                        OtherResearchProduct.class, (OtherResearchProduct) oaf);
-                            case "dataset":
-                                return new AtomicAction<>(Dataset.class, (Dataset) oaf);
-                            default:
-                                // can be an update, where the resulttype is not specified
-                                return new AtomicAction<>(Result.class, (Result) oaf);
-                        }
-                    default:
-                        throw new IllegalArgumentException(
-                                "invalid entity type: " + proto_oaf.getEntity().getType());
-                }
-            case relation:
-                return new AtomicAction<>(Relation.class, (Relation) oaf);
-            default:
-                throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind());
-        }
-    }
-
-    private String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
-        ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
-        String XQUERY =
-                "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()";
-        return isLookUp.getResourceProfileByQuery(XQUERY);
-    }
-
-    private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
-        SparkConf conf = new SparkConf();
-
-        return SparkSession.builder()
-                .appName(TransformActions.class.getSimpleName())
-                .master(parser.get("master"))
-                .config(conf)
-                .enableHiveSupport()
-                .getOrCreate();
-    }
-}

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

@@ -1,10 +0,0 @@
-[
-  {"paramName":"is", "paramLongName":"isLookupUrl",      "paramDescription": "URL of the isLookUp Service",       "paramRequired": true},
-  {"paramName":"sn", "paramLongName":"sourceNameNode",   "paramDescription": "nameNode of the source cluster",    "paramRequired": true},
-  {"paramName":"tn", "paramLongName":"targetNameNode",   "paramDescription": "namoNode of the target cluster",    "paramRequired": true},
-  {"paramName":"w",  "paramLongName":"workingDirectory", "paramDescription": "working directory",    "paramRequired": true},
-  {"paramName":"nm", "paramLongName":"distcp_num_maps",  "paramDescription": "maximum number of map tasks used in the distcp process",    "paramRequired": true},
-  {"paramName":"mm", "paramLongName":"distcp_memory_mb", "paramDescription": "memory for distcp action copying actionsets from remote cluster",    "paramRequired": true},
-  {"paramName":"tt", "paramLongName":"distcp_task_timeout", "paramDescription": "timeout for distcp copying actions from remote cluster",   "paramRequired": true},
-  {"paramName":"tr", "paramLongName":"transform_only",   "paramDescription": "activate tranform-only mode. Only apply transformation step", "paramRequired": true}
-]

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

@@ -1,5 +0,0 @@
-[
-  {"paramName":"mt", "paramLongName":"master",        "paramDescription": "should be local or yarn",        "paramRequired": true},
-  {"paramName":"is", "paramLongName":"isLookupUrl",   "paramDescription": "URL of the isLookUp Service",    "paramRequired": true},
-  {"paramName":"i",  "paramLongName":"inputPaths",    "paramDescription": "URL of the isLookUp Service",    "paramRequired": true}
-]

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java

@@ -14,9 +14,7 @@ import java.io.StringReader;
 import java.util.ArrayList;
 import java.util.List;
 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.dom4j.Document;
@@ -26,9 +24,6 @@ import org.dom4j.io.SAXReader;
 
 abstract class AbstractSparkAction implements Serializable {
 
-    protected static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
-    protected static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
-
     protected static final ObjectMapper OBJECT_MAPPER =
             new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
@@ -89,29 +84,8 @@ abstract class AbstractSparkAction implements Serializable {
         return SparkSession.builder().config(conf).getOrCreate();
     }
 
-    protected static <T extends Oaf> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
-        dataset.map(
-                        (MapFunction<T, String>) value -> OBJECT_MAPPER.writeValueAsString(value),
-                        Encoders.STRING())
-                .write()
-                .option("compression", "gzip")
-                .mode(mode)
-                .text(outPath);
-    }
-
-    protected static DataInfo getDataInfo() {
-        DataInfo info = new DataInfo();
-        info.setDeletedbyinference(false);
-        info.setInferred(true);
-        info.setInvisible(false);
-
-        Qualifier provenanceAction = new Qualifier();
-        provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
-        provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
-        provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
-        provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
-        info.setProvenanceaction(provenanceAction);
-        return info;
+    protected static <T> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
+        dataset.write().option("compression", "gzip").mode(mode).json(outPath);
     }
 
     protected static void removeOutputDir(SparkSession spark, String path) {

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java

@@ -5,29 +5,29 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.collect.Lists;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.pace.config.DedupConfig;
 import java.util.Collection;
 import java.util.Iterator;
-import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.MapGroupsFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import scala.Tuple2;
 
 public class DedupRecordFactory {
 
+    private static final Logger log = LoggerFactory.getLogger(DedupRecordFactory.class);
+
     protected static final ObjectMapper OBJECT_MAPPER =
-            new com.fasterxml.jackson.databind.ObjectMapper()
-                    .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+            new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
     public static <T extends OafEntity> Dataset<T> createDedupRecord(
             final SparkSession spark,
             final String mergeRelsInputPath,
             final String entitiesInputPath,
-            final Class<T> clazz,
-            final DedupConfig dedupConf) {
+            final Class<T> clazz) {
 
         long ts = System.currentTimeMillis();
 
@@ -54,40 +54,39 @@ public class DedupRecordFactory {
                                         r -> new Tuple2<>(r.getSource(), r.getTarget()),
                                 Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
 
-        // <dedup_id, json_entity_merged>
         return mergeRels
-                .joinWith(entities, mergeRels.col("_1").equalTo(entities.col("_1")), "left_outer")
-                .filter(
-                        (FilterFunction<Tuple2<Tuple2<String, String>, Tuple2<String, T>>>)
-                                value -> value._2() != null)
+                .joinWith(entities, mergeRels.col("_2").equalTo(entities.col("_1")), "inner")
                 .map(
-                        (MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, T>>, T>)
-                                value -> value._2()._2(),
-                        Encoders.kryo(clazz))
-                .groupByKey((MapFunction<T, String>) value -> value.getId(), Encoders.STRING())
+                        (MapFunction<
+                                        Tuple2<Tuple2<String, String>, Tuple2<String, T>>,
+                                        Tuple2<String, T>>)
+                                value -> new Tuple2<>(value._1()._1(), value._2()._2()),
+                        Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)))
+                .groupByKey(
+                        (MapFunction<Tuple2<String, T>, String>) entity -> entity._1(),
+                        Encoders.STRING())
                 .mapGroups(
-                        (MapGroupsFunction<String, T, T>)
+                        (MapGroupsFunction<String, Tuple2<String, T>, T>)
                                 (key, values) -> entityMerger(key, values, ts, clazz),
                         Encoders.bean(clazz));
     }
 
     private static <T extends OafEntity> T entityMerger(
-            String id, Iterator<T> entities, final long ts, Class<T> clazz) {
+            String id, Iterator<Tuple2<String, T>> entities, long ts, Class<T> clazz) {
         try {
             T entity = clazz.newInstance();
             entity.setId(id);
-            if (entity.getDataInfo() == null) {
             entity.setDataInfo(new DataInfo());
-            }
             entity.getDataInfo().setTrust("0.9");
             entity.setLastupdatetimestamp(ts);
 
             final Collection<String> dates = Lists.newArrayList();
             entities.forEachRemaining(
-                    e -> {
-                        entity.mergeFrom(e);
-                        if (ModelSupport.isSubClass(e, Result.class)) {
-                            Result r1 = (Result) e;
+                    t -> {
+                        T duplicate = t._2();
+                        entity.mergeFrom(duplicate);
+                        if (ModelSupport.isSubClass(duplicate, Result.class)) {
+                            Result r1 = (Result) duplicate;
                             Result er = (Result) entity;
                             er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor()));
 

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java

@@ -11,6 +11,8 @@ import eu.dnetlib.pace.config.DedupConfig;
 import java.io.IOException;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
 import org.apache.spark.sql.SparkSession;
 import org.dom4j.DocumentException;
@@ -69,11 +71,14 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
 
             Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
 
-            save(
-                    DedupRecordFactory.createDedupRecord(
-                            spark, mergeRelPath, entityPath, clazz, dedupConf),
-                    outputPath,
-                    SaveMode.Overwrite);
+            DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz)
+                    .map(
+                            (MapFunction<OafEntity, String>)
+                                    value -> OBJECT_MAPPER.writeValueAsString(value),
+                            Encoders.STRING())
+                    .write()
+                    .mode(SaveMode.Overwrite)
+                    .json(outputPath);
         }
     }
 }

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java

@@ -6,6 +6,7 @@ import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent;
 import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@@ -34,7 +35,9 @@ import scala.Tuple2;
 
 public class SparkCreateMergeRels extends AbstractSparkAction {
 
+    public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
     private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class);
+    public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
 
     public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) {
         super(parser, spark);
@@ -145,13 +148,22 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
         r.setRelClass(relClass);
         r.setSubRelType("dedup");
 
-        DataInfo info = getDataInfo();
+        DataInfo info = new DataInfo();
+        info.setDeletedbyinference(false);
+        info.setInferred(true);
+        info.setInvisible(false);
         info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
+        Qualifier provenanceAction = new Qualifier();
+        provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
+        provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
+        provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
+        provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
+        info.setProvenanceaction(provenanceAction);
 
         // TODO calculate the trust value based on the similarity score of the elements in the CC
         // info.setTrust();
 
-        r.setDataInfo(getDataInfo());
+        r.setDataInfo(info);
         return r;
     }
 

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java

@@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.dedup;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.oa.dedup.model.Block;
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@@ -114,7 +115,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
         r.setTarget(target);
         r.setSubRelType("dedupSimilarity");
         r.setRelClass("isSimilarTo");
-        r.setDataInfo(getDataInfo());
+        r.setDataInfo(new DataInfo());
 
         switch (entity) {
             case "result":

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java

@@ -4,6 +4,7 @@ import static org.apache.spark.sql.functions.col;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -124,7 +125,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
         return value -> {
             final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
             if (rel.getDataInfo() == null) {
-                rel.setDataInfo(getDataInfo());
+                rel.setDataInfo(new DataInfo());
             }
             return rel;
         };
@@ -148,7 +149,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
                 Relation r = value._1()._2();
                 String id = value._2()._2();
                 if (r.getDataInfo() == null) {
-                    r.setDataInfo(getDataInfo());
+                    r.setDataInfo(new DataInfo());
                 }
                 r.getDataInfo().setDeletedbyinference(false);
                 switch (type) {
@@ -172,7 +173,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
             if (value._2() != null) {
                 Relation r = value._1()._2();
                 if (r.getDataInfo() == null) {
-                    r.setDataInfo(getDataInfo());
+                    r.setDataInfo(new DataInfo());
                 }
                 r.getDataInfo().setDeletedbyinference(true);
                 return r;

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java

@@ -8,6 +8,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import eu.dnetlib.pace.util.MapDocumentUtil;
 import java.io.File;
 import java.io.IOException;
 import java.io.Serializable;
@@ -16,14 +17,20 @@ import java.nio.file.Paths;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaPairRDD;
+import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.PairFunction;
+import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
 import org.junit.jupiter.api.*;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.mockito.junit.jupiter.MockitoExtension;
+import scala.Tuple2;
 
 @ExtendWith(MockitoExtension.class)
 @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
@@ -41,7 +48,7 @@ public class SparkDedupTest implements Serializable {
     private static final String testActionSetId = "test-orchestrator";
 
     @BeforeAll
-    private static void cleanUp() throws IOException, URISyntaxException {
+    public static void cleanUp() throws IOException, URISyntaxException {
 
         testGraphBasePath =
                 Paths.get(
@@ -74,7 +81,7 @@ public class SparkDedupTest implements Serializable {
     }
 
     @BeforeEach
-    private void setUp() throws IOException, ISLookUpException {
+    public void setUp() throws IOException, ISLookUpException {
 
         lenient()
                 .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
@@ -96,6 +103,13 @@ public class SparkDedupTest implements Serializable {
                         IOUtils.toString(
                                 SparkDedupTest.class.getResourceAsStream(
                                         "/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
+
+        lenient()
+                .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
+                .thenReturn(
+                        IOUtils.toString(
+                                SparkDedupTest.class.getResourceAsStream(
+                                        "/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
     }
 
     @Test
@@ -109,7 +123,6 @@ public class SparkDedupTest implements Serializable {
                                         "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
         parser.parseArgument(
                 new String[] {
-                    "-mt", "local[*]",
                     "-i", testGraphBasePath,
                     "-asi", testActionSetId,
                     "-la", "lookupurl",
@@ -126,9 +139,14 @@ public class SparkDedupTest implements Serializable {
                 spark.read()
                         .load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
                         .count();
+        long sw_simrel =
+                spark.read()
+                        .load(testOutputBasePath + "/" + testActionSetId + "/software_simrel")
+                        .count();
 
-        assertEquals(3288, orgs_simrel);
+        assertEquals(3432, orgs_simrel);
         assertEquals(7260, pubs_simrel);
+        assertEquals(344, sw_simrel);
     }
 
     @Test
@@ -142,7 +160,6 @@ public class SparkDedupTest implements Serializable {
                                         "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
         parser.parseArgument(
                 new String[] {
-                    "-mt", "local[*]",
                     "-i", testGraphBasePath,
                     "-asi", testActionSetId,
                     "-la", "lookupurl",
@@ -159,9 +176,14 @@ public class SparkDedupTest implements Serializable {
                 spark.read()
                         .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
                         .count();
+        long sw_mergerel =
+                spark.read()
+                        .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
+                        .count();
 
-        assertEquals(1244, orgs_mergerel);
+        assertEquals(1276, orgs_mergerel);
         assertEquals(1460, pubs_mergerel);
+        assertEquals(288, sw_mergerel);
     }
 
     @Test
@@ -175,7 +197,6 @@ public class SparkDedupTest implements Serializable {
                                         "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
         parser.parseArgument(
                 new String[] {
-                    "-mt", "local[*]",
                     "-i", testGraphBasePath,
                     "-asi", testActionSetId,
                     "-la", "lookupurl",
@@ -198,9 +219,13 @@ public class SparkDedupTest implements Serializable {
                                         + testActionSetId
                                         + "/publication_deduprecord")
                         .count();
+        long sw_deduprecord =
+                jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord")
+                        .count();
 
         assertEquals(82, orgs_deduprecord);
         assertEquals(66, pubs_deduprecord);
+        assertEquals(51, sw_deduprecord);
     }
 
     @Test
@@ -214,7 +239,6 @@ public class SparkDedupTest implements Serializable {
                                         "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
         parser.parseArgument(
                 new String[] {
-                    "-mt", "local[*]",
                     "-i", testGraphBasePath,
                     "-w", testOutputBasePath,
                     "-o", testDedupGraphBasePath
@@ -224,6 +248,9 @@ public class SparkDedupTest implements Serializable {
 
         long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
         long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
+        long projects = jsc.textFile(testDedupGraphBasePath + "/project").count();
+        long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count();
+        long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count();
 
         long mergedOrgs =
                 spark.read()
@@ -245,13 +272,17 @@ public class SparkDedupTest implements Serializable {
                         .distinct()
                         .count();
 
-        assertEquals(897, publications);
+        assertEquals(831, publications);
         assertEquals(835, organizations);
+        assertEquals(100, projects);
+        assertEquals(100, datasource);
+        assertEquals(200, softwares);
 
         long deletedOrgs =
                 jsc.textFile(testDedupGraphBasePath + "/organization")
                         .filter(this::isDeletedByInference)
                         .count();
+
         long deletedPubs =
                 jsc.textFile(testDedupGraphBasePath + "/publication")
                         .filter(this::isDeletedByInference)
@@ -272,7 +303,6 @@ public class SparkDedupTest implements Serializable {
                                         "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
         parser.parseArgument(
                 new String[] {
-                    "-mt", "local[*]",
                     "-i", testGraphBasePath,
                     "-w", testOutputBasePath,
                     "-o", testDedupGraphBasePath
@@ -283,6 +313,43 @@ public class SparkDedupTest implements Serializable {
         long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
 
         assertEquals(826, relations);
+
+        // check deletedbyinference
+        final Dataset<Relation> mergeRels =
+                spark.read()
+                        .load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*"))
+                        .as(Encoders.bean(Relation.class));
+        final JavaPairRDD<String, String> mergedIds =
+                mergeRels
+                        .where("relClass == 'merges'")
+                        .select(mergeRels.col("target"))
+                        .distinct()
+                        .toJavaRDD()
+                        .mapToPair(
+                                (PairFunction<Row, String, String>)
+                                        r -> new Tuple2<String, String>(r.getString(0), "d"));
+
+        JavaRDD<String> toCheck =
+                jsc.textFile(testDedupGraphBasePath + "/relation")
+                        .mapToPair(
+                                json ->
+                                        new Tuple2<>(
+                                                MapDocumentUtil.getJPathString("$.source", json),
+                                                json))
+                        .join(mergedIds)
+                        .map(t -> t._2()._1())
+                        .mapToPair(
+                                json ->
+                                        new Tuple2<>(
+                                                MapDocumentUtil.getJPathString("$.target", json),
+                                                json))
+                        .join(mergedIds)
+                        .map(t -> t._2()._1());
+
+        long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
+        long updated = toCheck.count();
+
+        assertEquals(updated, deletedbyinference);
     }
 
     @AfterAll

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json

@@ -0,0 +1,118 @@
+{
+  "wf" : {
+    "threshold" : "0.99",
+    "dedupRun" : "001",
+    "entityType" : "result",
+    "subEntityType" : "resulttype",
+    "subEntityValue" : "dataset",
+    "orderField" : "title",
+    "queueMaxSize" : "2000",
+    "groupMaxSize" : "100",
+    "maxChildren" : "100",
+    "slidingWindowSize" : "200",
+    "rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
+    "includeChildren" : "true"
+  },
+  "pace" : {
+    "clustering" : [
+      { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
+      { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
+      { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
+    ],
+    "decisionTree" : {
+      "start" : {
+        "fields": [
+          {
+            "field": "pid",
+            "comparator": "jsonListMatch",
+            "weight": 1.0,
+            "countIfUndefined": "false",
+            "params": {
+              "jpath_value": "$.value",
+              "jpath_classid": "$.qualifier.classid"
+            }
+          }
+        ],
+        "threshold": 0.5,
+        "aggregation": "AVG",
+        "positive": "MATCH",
+        "negative": "layer2",
+        "undefined": "layer2",
+        "ignoreUndefined": "true"
+      },
+      "layer2" : {
+        "fields": [
+          {
+            "field": "title",
+            "comparator": "titleVersionMatch",
+            "weight": 1.0,
+            "countIfUndefined": "false",
+            "params": {}
+          },
+          {
+            "field": "authors",
+            "comparator": "sizeMatch",
+            "weight": 1.0,
+            "countIfUndefined": "false",
+            "params": {}
+          }
+        ],
+        "threshold": 1.0,
+        "aggregation": "AND",
+        "positive": "layer3",
+        "negative": "NO_MATCH",
+        "undefined": "layer3",
+        "ignoreUndefined": "false"
+      },
+      "layer3" : {
+        "fields": [
+          {
+            "field": "title",
+            "comparator": "levensteinTitle",
+            "weight": 1.0,
+            "countIfUndefined": "true"
+          }
+        ],
+        "threshold": 0.99,
+        "aggregation": "AVG",
+        "positive": "MATCH",
+        "negative": "NO_MATCH",
+        "undefined": "NO_MATCH",
+        "ignoreUndefined": "true"
+      }
+    },
+    "model" : [
+      {
+        "name" : "doi",
+        "type" : "String",
+        "path" : "$.pid[@.qualifier.classid = 'doi'].value"
+      },
+      {
+        "name" : "pid",
+        "type" : "JSON",
+        "path" : "$.pid",
+        "overrideMatch" : "true"
+      },
+      {
+        "name" : "title",
+        "type" : "String",
+        "path" : "$.title[@.qualifier.classid = 'main title'].value",
+        "length" : 250,
+        "size" : 5
+      },
+      {
+        "name" : "authors",
+        "type" : "String",
+        "path" : "$.author[*].fullname",
+        "size" : 200
+      },
+      {
+        "name" : "resulttype",
+        "type" : "String",
+        "path" : "$.resulttype.classid"
+      }
+    ],
+    "blacklists" : {},
+    "synonyms" : {}
+  }
+}

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json

@@ -0,0 +1,118 @@
+{
+  "wf" : {
+    "threshold" : "0.99",
+    "dedupRun" : "001",
+    "entityType" : "result",
+    "subEntityType" : "resulttype",
+    "subEntityValue" : "otherresearchproduct",
+    "orderField" : "title",
+    "queueMaxSize" : "2000",
+    "groupMaxSize" : "100",
+    "maxChildren" : "100",
+    "slidingWindowSize" : "200",
+    "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
+    "includeChildren" : "true"
+  },
+  "pace" : {
+    "clustering" : [
+      { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
+      { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
+      { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
+    ],
+    "decisionTree" : {
+      "start" : {
+        "fields": [
+          {
+            "field": "pid",
+            "comparator": "jsonListMatch",
+            "weight": 1.0,
+            "countIfUndefined": "false",
+            "params": {
+              "jpath_value": "$.value",
+              "jpath_classid": "$.qualifier.classid"
+            }
+          }
+        ],
+        "threshold": 0.5,
+        "aggregation": "AVG",
+        "positive": "MATCH",
+        "negative": "layer2",
+        "undefined": "layer2",
+        "ignoreUndefined": "true"
+      },
+      "layer2" : {
+        "fields": [
+          {
+            "field": "title",
+            "comparator": "titleVersionMatch",
+            "weight": 1.0,
+            "countIfUndefined": "false",
+            "params": {}
+          },
+          {
+            "field": "authors",
+            "comparator": "sizeMatch",
+            "weight": 1.0,
+            "countIfUndefined": "false",
+            "params": {}
+          }
+        ],
+        "threshold": 1.0,
+        "aggregation": "AND",
+        "positive": "layer3",
+        "negative": "NO_MATCH",
+        "undefined": "layer3",
+        "ignoreUndefined": "false"
+      },
+      "layer3" : {
+        "fields": [
+          {
+            "field": "title",
+            "comparator": "levensteinTitle",
+            "weight": 1.0,
+            "countIfUndefined": "true"
+          }
+        ],
+        "threshold": 0.99,
+        "aggregation": "AVG",
+        "positive": "MATCH",
+        "negative": "NO_MATCH",
+        "undefined": "NO_MATCH",
+        "ignoreUndefined": "true"
+      }
+    },
+    "model" : [
+      {
+        "name" : "doi",
+        "type" : "String",
+        "path" : "$.pid[@.qualifier.classid = 'doi'}].value"
+      },
+      {
+        "name" : "pid",
+        "type" : "JSON",
+        "path" : "$.pid",
+        "overrideMatch" : "true"
+      },
+      {
+        "name" : "title",
+        "type" : "String",
+        "path" : "$.title[@.qualifier.classid = 'main title'].value",
+        "length" : 250,
+        "size" : 5
+      },
+      {
+        "name" : "authors",
+        "type" : "String",
+        "path" : "$.author[*].fullname",
+        "size" : 200
+      },
+      {
+        "name" : "resulttype",
+        "type" : "String",
+        "path" : "$.resulttype.classid"
+      }
+    ],
+    "blacklists" : {},
+    "synonyms" : {}
+  }
+}

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json

@@ -0,0 +1,92 @@
+  {
+    "wf" : {
+      "threshold" : "0.99",
+      "dedupRun" : "001",
+      "entityType" : "result",
+      "subEntityType" : "resulttype",
+      "subEntityValue" : "software",
+      "orderField" : "title",
+      "queueMaxSize" : "2000",
+      "groupMaxSize" : "100",
+      "maxChildren" : "100",
+      "slidingWindowSize" : "200",
+      "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
+      "includeChildren" : "true"
+    },
+    "pace" : {
+      "clustering" : [
+        { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
+        { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
+        { "name" : "lowercase", "fields" : [ "doi", "url" ], "params" : { } }
+      ],
+      "decisionTree": {
+        "start": {
+          "fields": [
+            {
+              "field": "doi",
+              "comparator": "exactMatch",
+              "weight": 1,
+              "countIfUndefined": "false",
+              "params": {}
+            },
+            {
+              "field": "url",
+              "comparator": "exactMatch",
+              "weight": 1,
+              "countIfUndefined": "false",
+              "params": {}
+            }
+          ],
+          "threshold": 1,
+          "aggregation": "OR",
+          "positive": "MATCH",
+          "negative": "layer2",
+          "undefined": "layer2",
+          "ignoreUndefined": "false"
+        },
+    "layer2": {
+      "fields": [
+        {
+          "field": "title",
+          "comparator": "levensteinTitleIgnoreVersion",
+          "weight": 1,
+          "countIfUndefined": "false",
+          "params": {}
+        }
+      ],
+      "threshold": 0.99,
+      "aggregation": "AVG",
+      "positive": "MATCH",
+      "negative": "NO_MATCH",
+      "undefined": "NO_MATCH",
+      "ignoreUndefined": "false"
+    }
+  },
+      "model" : [
+          {
+            "name" : "doi",
+            "type" : "String",
+            "path" : "$.pid[?(@.qualifier.classid == 'doi')].value"
+          },
+          {
+            "name" : "title",
+            "type" : "String",
+            "path" : "$.title[?(@.qualifier.classid == 'main title')].value",
+            "length" : 250,
+            "size" : 5
+          },
+          {
+            "name" : "url",
+            "type" : "String",
+            "path" : "$.instance.url"
+          },
+          {
+            "name" : "resulttype",
+            "type" : "String",
+            "path" : "$.resulttype.classid"
+          }
+      ],
+      "blacklists" : {},
+      "synonyms": {}
+    }
+  }

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/relation

@@ -98,305 +98,305 @@
 {"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::21abe5a91c2949aba6ef77033a5f98f3", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eac934a34bf16c5f0de8ce743bd0b4"}
 {"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|dedup_wf_001::5614cb4fbc9f3be07aedd6d627470e58", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eb4e57e351343377f693ee714500b4"}
 {"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::c3534dbd02b4a4aa35f235671f7631aa", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00eb4e57e351343377f693ee714500b4"}
-{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|dedup_wf_001::032546390e513e50571bf2aae948548f", "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
-{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|dedup_wf_001::04516dab6afef5fc35f02066c192ac1c", "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
-{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::51fa34d45c0025e25f996420d70de235", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|dedup_wf_001::04516dab6afef5fc35f02066c192ac1c", "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
-{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::0b2e661ec89ddc6cb9b30b28307ff6aa", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|dedup_wf_001::05c768e457a1da1c5aceb5647aa4dcf9", "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
-{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|dedup_wf_001::05c768e457a1da1c5aceb5647aa4dcf9", "collectedfrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
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+{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::0b2e661ec89ddc6cb9b30b28307ff6aa", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::ea3b8ff16c4488ce5fd2cedd3e0bc4b0", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
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+{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::f42cac35d9e8dd17b1a175afa512c13a", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
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+{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::f7f3b7f8caf2520e2fcaa7f3a704ec03", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
+{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::fcc8d792603a72774ecbd9fe4504b3da", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
 {"subRelType": "outcome", "relClass": "produces", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|erc_________::8511e17e153877fecd5a9a4ea8eb0969", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::07c370987d51b8273071fedf5931acf6"}
 {"subRelType": "outcome", "relClass": "produces", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|erc_________::67b1c4d6876a12e265e965c1451a7f36", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::ae9a0c1b9384e04476ad3571d04be237"}
 {"subRelType": "outcome", "relClass": "produces", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|od______1106::aabdb9c07beef7bdf7a93b6455f75e06", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::ae9a0c1b9384e04476ad3571d04be237"}

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml

@@ -14,6 +14,7 @@
                 <SCAN_SEQUENCE>
                     <SCAN id="organization"/>
                     <SCAN id="publication"/>
+                    <SCAN id="software"/>
                 </SCAN_SEQUENCE>
             </DEDUPLICATION>
         </CONFIGURATION>

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

@@ -2,8 +2,10 @@ package eu.dnetlib.doiboost.crossref
 
 import eu.dnetlib.dhp.schema.oaf._
 import eu.dnetlib.dhp.utils.DHPUtils
+import org.apache.commons.lang.StringUtils
 import org.json4s
 import org.json4s.DefaultFormats
+import org.json4s.JsonAST._
 import org.json4s.jackson.JsonMethods._
 import org.slf4j.Logger
 
@@ -108,12 +110,58 @@ class Crossref2Oaf {
     result.setLastupdatetimestamp((json \ "indexed" \ "timestamp").extract[Long])
     result.setDateofcollection((json \ "indexed" \ "date-time").extract[String])
 
-    //result.setCollectedfrom()
+    result.setCollectedfrom(List(createCollectedFrom()).asJava)
 
+    // Publisher ( Name of work's publisher mapped into  Result/Publisher)
+    val publisher = (json \ "publisher").extract[String]
+    result.setPublisher(asField(publisher))
+
+    // TITLE
+    val mainTitles = for {JString(title) <- json \ "title"} yield createSP(title, "main title", "dnet:dataCite_title")
+    val originalTitles = for {JString(title) <- json \ "original-title"} yield createSP(title, "alternative title", "dnet:dataCite_title")
+    val shortTitles = for {JString(title) <- json \ "short-title"} yield createSP(title, "alternative title", "dnet:dataCite_title")
+    result.setTitle((mainTitles ::: originalTitles ::: shortTitles).asJava)
+
+    // DESCRIPTION
+    val descriptionList = for {JString(description) <- json \ "abstract"} yield asField(description)
+    result.setDescription(descriptionList.asJava)
+    // Source
+    val sourceList = for {JString(source) <- json \ "source"} yield asField(source)
+
+    result.setSource(sourceList.asJava)
+
+
+    //RELEVANT DATE Mapping
+    val createdDate =generateDate((json \ "created" \"date-time").extract[String],(json \ "created"\"date-parts").extract[List[List[Int]]],"created", "dnet:dataCite_date" )
+    val postedDate =generateDate((json \ "posted" \"date-time").extractOrElse[String](null),(json \ "posted"\"date-parts").extract[List[List[Int]]],"available", "dnet:dataCite_date" )
+    val acceptedDate =generateDate((json \ "accepted" \"date-time").extractOrElse[String](null),(json \ "accepted"\"date-parts").extract[List[List[Int]]],"accepted", "dnet:dataCite_date" )
+    val publishedPrintDate =generateDate((json \ "published-print" \"date-time").extractOrElse[String](null),(json \ "published-print"\"date-parts").extract[List[List[Int]]],"published-print", "dnet:dataCite_date" )
+    val publishedOnlineDate =generateDate((json \ "published-online" \"date-time").extractOrElse[String](null),(json \ "published-online"\"date-parts").extract[List[List[Int]]],"published-online", "dnet:dataCite_date" )
+
+    result.setRelevantdate(List(createdDate ,postedDate, acceptedDate,publishedOnlineDate, publishedPrintDate).asJava)
     result
   }
 
 
+  def generateDate(dt: String, datePart: List[List[Int]], classId: String, schemeId: String): StructuredProperty = {
+    if (StringUtils.isNotBlank(dt))
+      return createSP(dt, classId, schemeId)
+
+
+    if (datePart != null && datePart.size == 1) {
+      val res = datePart.head
+      if (res.size == 3) {
+        val dp = f"${res.head}-${res(1)}%02d-${res(2)}%02d"
+        println(dp)
+        if (dp.length == 10) {
+          return createSP(dp, classId, schemeId)
+        }
+      }
+    }
+    null
+  }
+
+
     def generateIdentifier(oaf: Result, doi: String): String = {
       val id = DHPUtils.md5(doi.toLowerCase)
       if (oaf.isInstanceOf[Dataset])
@@ -121,6 +169,15 @@ class Crossref2Oaf {
       s"50|${doiBoostNSPREFIX}${SEPARATOR}${id}"
     }
 
+    def asField[T](value: T): Field[T] = {
+      val tmp = new Field[T]
+      tmp.setValue(value)
+      tmp
+
+
+    }
+
+
     def generateDataInfo(): DataInfo = {
       val di = new DataInfo
       di.setDeletedbyinference(false)
@@ -140,6 +197,15 @@ class Crossref2Oaf {
 
     }
 
+    def createCollectedFrom(): KeyValue = {
+
+      val cf = new KeyValue
+      cf.setValue(CROSSREF)
+      cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5("crossref"))
+      cf
+
+    }
+
     def createQualifier(cls: String, sch: String): Qualifier = {
       val q = new Qualifier
       q.setClassid(cls)

dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/DoiBoostTest.java

@@ -1,68 +1,107 @@
 package eu.dnetlib.doiboost;
 
+import static org.junit.jupiter.api.Assertions.*;
+
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.SerializationFeature;
 import com.jayway.jsonpath.JsonPath;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.doiboost.crossref.Crossref2Oaf;
 import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF;
+import java.io.IOException;
+import java.util.List;
 import org.apache.commons.io.IOUtils;
-import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.junit.platform.commons.util.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-
-import java.io.IOException;
-import java.util.List;
-
 public class DoiBoostTest {
 
     Logger logger = LoggerFactory.getLogger(DoiBoostTest.class);
 
-
     public void test() throws Exception {
 
         // SparkDownloadContentFromCrossref.main(null);
-        //CrossrefImporter.main("-n file:///tmp -t file:///tmp/p.seq -ts 1586110000749".split(" "));
-        SparkMapDumpIntoOAF.main("-m local[*] -s file:///data/doiboost/crossref_dump.seq".split(" "));
+        // CrossrefImporter.main("-n file:///tmp -t file:///tmp/p.seq -ts 1586110000749".split("
+        // "));
+        SparkMapDumpIntoOAF.main(
+                "-m local[*] -s file:///data/doiboost/crossref_dump.seq".split(" "));
     }
 
-
-
     @Test
     public void testConvertCrossRef2Oaf() throws IOException {
 
         final String json = IOUtils.toString(getClass().getResourceAsStream("pc.json"));
         ObjectMapper mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT);
-        Assertions.assertNotNull(json);
-        Assertions.assertFalse(StringUtils.isBlank(json));
-
-
-
+        assertNotNull(json);
+        assertFalse(StringUtils.isBlank(json));
         Crossref2Oaf cf = new Crossref2Oaf();
         final Result result = cf.convert(json, logger);
-        Assertions.assertNotNull(result);
+        assertNotNull(result);
+
+        assertNotNull(result.getDataInfo(), "Datainfo test not null Failed");
+        assertNotNull(
+                result.getDataInfo().getProvenanceaction(),
+                "DataInfo/Provenance test not null Failed");
+        assertFalse(
+                StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getClassid()),
+                "DataInfo/Provenance/classId test not null Failed");
+        assertFalse(
+                StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getClassname()),
+                "DataInfo/Provenance/className test not null Failed");
+        assertFalse(
+                StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getSchemeid()),
+                "DataInfo/Provenance/SchemeId test not null Failed");
+        assertFalse(
+                StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getSchemename()),
+                "DataInfo/Provenance/SchemeName test not null Failed");
+
+        assertNotNull(result.getCollectedfrom(), "CollectedFrom test not null Failed");
+        assertTrue(result.getCollectedfrom().size() > 0);
+        assertTrue(
+                result.getCollectedfrom().stream()
+                        .anyMatch(
+                                c ->
+                                        c.getKey()
+                                                .equalsIgnoreCase(
+                                                        "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")));
+        assertTrue(
+                result.getCollectedfrom().stream()
+                        .anyMatch(c -> c.getValue().equalsIgnoreCase("crossref")));
+
+        assertTrue(
+                result.getRelevantdate().stream()
+                        .anyMatch(d -> d.getQualifier().getClassid().equalsIgnoreCase("created")));
+        assertTrue(
+                result.getRelevantdate().stream()
+                        .anyMatch(
+                                d -> d.getQualifier().getClassid().equalsIgnoreCase("available")));
+        assertTrue(
+                result.getRelevantdate().stream()
+                        .anyMatch(d -> d.getQualifier().getClassid().equalsIgnoreCase("accepted")));
+        assertTrue(
+                result.getRelevantdate().stream()
+                        .anyMatch(
+                                d ->
+                                        d.getQualifier()
+                                                .getClassid()
+                                                .equalsIgnoreCase("published-online")));
+        assertTrue(
+                result.getRelevantdate().stream()
+                        .anyMatch(
+                                d ->
+                                        d.getQualifier()
+                                                .getClassid()
+                                                .equalsIgnoreCase("published-print")));
 
         logger.info(mapper.writeValueAsString(result));
-
     }
 
-
-
-
-
     @Test
     public void testPath() throws Exception {
         final String json = IOUtils.toString(getClass().getResourceAsStream("response.json"));
         final List<String> res = JsonPath.read(json, "$.hits.hits[*]._source.blob");
         System.out.println(res.size());
-
     }
-
-
-
-
-
 }

dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/pc.json

@@ -112,9 +112,35 @@
       ]
     ]
   },
+  "published-print": {
+    "timestamp": 1446095513000,
+    "date-time": "2015-10-29T05:11:53Z",
+    "date-parts": [
+      [
+        2015,
+        2,
+        29
+      ]
+    ]
+  },
+  "published-online": {
+        "date-parts": [
+      [
+        2015,
+        2,
+        2
+      ]
+    ]
+  },
   "title": [
     "Genetic transformation of micropropagated shoots ofPinus radiataD.Don"
   ],
+  "original-title": [
+    "OR TITLE"
+  ],
+  "short-title": [
+    "SHORT TITLE"
+  ],
   "group-title": "Plant Biology",
   "subtype": "preprint"
 }