Merge branch 'master' into propagationCommunityToResult

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/PropagationConstant.java

@@ -23,6 +23,9 @@ public class PropagationConstant {
     public final static String PROPAGATION_COUNTRY_INSTREPO_CLASS_NAME = "Propagation of country to result collected from datasources of type institutional repositories";
     public final static String PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID = "result:organization:instrepo";
     public final static String PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME = "Propagation of affiliation to result collected from datasources of type institutional repository";
+    public final static String PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID = "result:project:semrel";
+    public final static String PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME = "Propagation of result to project through semantic relation";
+
 
     public final static String RELATION_DATASOURCEORGANIZATION_REL_TYPE = "datasourceOrganization";
     public final static String RELATION_DATASOURCEORGANIZATION_SUBREL_TYPE = "provision";
@@ -34,6 +37,14 @@ public class PropagationConstant {
     public final static String RELATION_ORGANIZATION_RESULT_REL_CLASS = "isAuthorInstitutionOf";
     public final static String RELATION_RESULT_ORGANIZATION_REL_CLASS = "hasAuthorInstitution";
 
+    public static final String RELATION_RESULTRESULT_REL_TYPE = "resultResult";
+    public static final String RELATION_RESULTRESULT_SUBREL_TYPE = "supplement";
+
+    public static final String RELATION_RESULTPROJECT_REL_TYPE = "resultProject";
+    public static final String RELATION_RESULTPROJECT_SUBREL_TYPE = "outcome";
+    public static final String RELATION_RESULT_PROJECT_REL_CLASS = "isProducedBy";
+    public static final String RELATION_PROJECT_RESULT_REL_CLASS = "produces";
+
 
     public static Country getCountry(String country){
         Country nc = new Country();

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java

@@ -0,0 +1,120 @@
+package eu.dnetlib.dhp.projecttoresult;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.TypedRow;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.oaf.*;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+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.sql.SparkSession;
+import scala.Tuple2;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+
+import static eu.dnetlib.dhp.PropagationConstant.*;
+import static eu.dnetlib.dhp.PropagationConstant.toPair;
+
+public class SparkResultToProjectThroughSemRelJob {
+    public static void main(String[] args) throws Exception {
+
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToProjectThroughSemRelJob.class.getResourceAsStream("/eu/dnetlib/dhp/projecttoresult/input_projecttoresult_parameters.json")));
+        parser.parseArgument(args);
+        final SparkSession spark = SparkSession
+                .builder()
+                .appName(SparkResultToProjectThroughSemRelJob.class.getSimpleName())
+                .master(parser.get("master"))
+                .enableHiveSupport()
+                .getOrCreate();
+
+        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+        final String inputPath = parser.get("sourcePath");
+        final String outputPath = "/tmp/provision/propagation/projecttoresult";
+
+        final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
+
+        File directory = new File(outputPath);
+
+        if (!directory.exists()) {
+            directory.mkdirs();
+        }
+
+        JavaRDD<Relation> relations = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
+                .map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class)).cache();
+
+        JavaPairRDD<String, TypedRow> result_result = relations
+                .filter(r -> !r.getDataInfo().getDeletedbyinference())
+                .filter(r -> allowedsemrel.contains(r.getRelClass()) && RELATION_RESULTRESULT_REL_TYPE.equals(r.getRelType()))
+                .map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
+                .mapToPair(toPair());
+
+        JavaPairRDD<String, TypedRow> result_project = relations
+                .filter(r -> !r.getDataInfo().getDeletedbyinference())
+                .filter(r -> RELATION_RESULT_PROJECT_REL_CLASS.equals(r.getRelClass()) && RELATION_RESULTPROJECT_REL_TYPE.equals(r.getRelType()))
+                .map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
+                .mapToPair(toPair());
+
+        //relationships from project to result. One pair for each relationship for results having allowed semantics relation with another result
+        JavaPairRDD<String, TypedRow> project_result = result_project.join(result_result)
+                .map(c -> {
+                    String projectId = c._2()._1().getTargetId();
+                    String resultId = c._2()._2().getTargetId();
+                    return new TypedRow().setSourceId(projectId).setTargetId(resultId);
+                })
+                .mapToPair(toPair());
+
+        //relationships from project to result. One Pair for each project => project id list of results related to the project
+        JavaPairRDD<String, TypedRow> project_results = relations
+                .filter(r -> !r.getDataInfo().getDeletedbyinference())
+                .filter(r -> RELATION_PROJECT_RESULT_REL_CLASS.equals(r.getRelClass()) && RELATION_RESULTPROJECT_REL_TYPE.equals(r.getRelType()))
+                .map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
+                .mapToPair(toPair())
+                .reduceByKey((a, b) -> {
+                    if (a == null) {
+                        return b;
+                    }
+                    if (b == null) {
+                        return a;
+                    }
+                    a.addAll(b.getAccumulator());
+                    return a;
+                });
+
+
+
+        JavaRDD<Relation> newRels = project_result.join(project_results)
+                .flatMap(c -> {
+                    String resId = c._2()._1().getTargetId();
+
+                    if (c._2()._2().getAccumulator().contains(resId)) {
+                        return null;
+                    }
+                    String progId = c._2()._1().getSourceId();
+                    List<Relation> rels = new ArrayList();
+
+                    rels.add(getRelation(progId, resId, RELATION_PROJECT_RESULT_REL_CLASS,
+                            RELATION_RESULTPROJECT_REL_TYPE, RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
+                            PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
+                    rels.add(getRelation(resId, progId, RELATION_RESULT_PROJECT_REL_CLASS,
+                            RELATION_RESULTPROJECT_REL_TYPE, RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
+                            PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
+                    return rels.iterator();
+                })
+                .cache();
+
+        newRels.map(p -> new ObjectMapper().writeValueAsString(p))
+                .saveAsTextFile(outputPath + "/relation_new");
+
+        newRels.union(relations).map(p -> new ObjectMapper().writeValueAsString(p))
+                .saveAsTextFile(outputPath + "/relation");
+
+    }
+
+
+}

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/projecttoresult/input_projecttoresult_parameters.json

@@ -0,0 +1,21 @@
+[
+  {
+    "paramName":"mt",
+    "paramLongName":"master",
+    "paramDescription": "should be local or yarn",
+    "paramRequired": true
+  },
+  {
+    "paramName":"s",
+    "paramLongName":"sourcePath",
+    "paramDescription": "the path of the sequencial file to read",
+    "paramRequired": true
+  },
+
+  {
+    "paramName":"asr",
+    "paramLongName":"allowedsemrels",
+    "paramDescription": "the types of the allowed datasources. Split by ;",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/config-default.xml

@@ -0,0 +1,18 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+</configuration>

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

@@ -0,0 +1,55 @@
+<workflow-app name="project_to_result_propagation" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>sourcePath</name>
+            <description>the source path</description>
+        </property>
+        <property>
+            <name>allowedsemrels</name>
+            <description>the allowed semantics </description>
+        </property>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+    </parameters>
+
+    <start to="ProjectPropagation"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="ProjectPropagation">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>ProjectToResultPropagation</name>
+            <class>eu.dnetlib.dhp.projecttoresult.SparkResultToProjectThroughSemRelJob</class>
+            <jar>dhp-propagation-${projectVersion}.jar</jar>
+            <spark-opts>--executor-memory ${sparkExecutorMemory}
+                --executor-cores ${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
+                --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
+            </spark-opts>
+            <arg>-mt</arg> <arg>yarn-cluster</arg>
+            <arg>--sourcePath</arg><arg>${sourcePath}</arg>
+            <arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>