[raw_all] added extra workflow step for patching the identifiers in the relations, given an id mapping dataset

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java

@@ -0,0 +1,115 @@
+package eu.dnetlib.dhp.oa.graph.raw;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.oa.graph.dump.Utils;
+import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import scala.Tuple2;
+
+import java.io.FileNotFoundException;
+import java.util.Objects;
+import java.util.Optional;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+public class PatchRelationsApplication {
+
+    private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    public static void main(final String[] args) throws Exception {
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+                IOUtils
+                        .toString(
+                                Optional.ofNullable(
+                                PatchRelationsApplication.class
+                                        .getResourceAsStream(
+                                                "/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json"))
+                                .orElseThrow(FileNotFoundException::new)
+                        ));
+        parser.parseArgument(args);
+
+        final Boolean isSparkSessionManaged = Optional
+                .ofNullable(parser.get("isSparkSessionManaged"))
+                .map(Boolean::valueOf)
+                .orElse(Boolean.TRUE);
+        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+        final String graphBasePath = parser.get("graphBasePath");
+        log.info("graphBasePath: {}", graphBasePath);
+
+        final String workingDir = parser.get("workingDir");
+        log.info("workingDir: {}", workingDir);
+
+        final String idMappingPath = parser.get("idMappingPath");
+        log.info("idMappingPath: {}", idMappingPath);
+
+        final SparkConf conf = new SparkConf();
+        runWithSparkSession(
+                conf,
+                isSparkSessionManaged,
+                spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath));
+    }
+
+    /**
+     * Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the
+     * mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location.
+     *
+     * @param spark the SparkSession
+     * @param graphBasePath base graph path providing the set of relations to patch
+     * @param workingDir intermediate storage location
+     * @param idMappingPath dataset providing the old -> new identifier mapping
+     */
+    private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir, final String idMappingPath) {
+
+        final String relationPath = graphBasePath + "/relation";
+
+        final Dataset<Relation> rels = Utils.readPath(spark, relationPath, Relation.class);
+        final Dataset<RelationIdMapping> idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class);
+
+        rels
+                .joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left")
+                .map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
+                    final Relation r = t._1();
+                    Optional.ofNullable(t._2())
+                            .map(RelationIdMapping::getNewId)
+                            .ifPresent(r::setSource);
+                    return r;
+                }, Encoders.bean(Relation.class))
+                .joinWith(idMapping, rels.col("target").equalTo(idMapping.col("oldId")), "left")
+                .map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
+                    final Relation r = t._1();
+                    Optional.ofNullable(t._2())
+                            .map(RelationIdMapping::getNewId)
+                            .ifPresent(r::setTarget);
+                    return r;
+                }, Encoders.bean(Relation.class))
+                .map(
+                        (MapFunction<Relation, String>) OBJECT_MAPPER::writeValueAsString,
+                        Encoders.STRING())
+                .write()
+                .mode(SaveMode.Overwrite)
+                .option("compression", "gzip")
+                .text(workingDir);
+
+        spark.read().textFile(workingDir)
+                .write()
+                .mode(SaveMode.Overwrite)
+                .option("compression", "gzip")
+                .text(relationPath);
+    }
+
+
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java

@@ -0,0 +1,24 @@
+package eu.dnetlib.dhp.oa.graph.raw.common;
+
+public class RelationIdMapping {
+
+    private String oldId;
+
+    private String newId;
+
+    public String getOldId() {
+        return oldId;
+    }
+
+    public void setOldId(final String oldId) {
+        this.oldId = oldId;
+    }
+
+    public String getNewId() {
+        return newId;
+    }
+
+    public void setNewId(final String newId) {
+        this.newId = newId;
+    }
+}

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

@@ -0,0 +1,26 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "g",
+    "paramLongName": "graphBasePath",
+    "paramDescription": "base graph path providing the set of relations to patch",
+    "paramRequired": true
+  },
+  {
+    "paramName": "w",
+    "paramLongName": "workingDir",
+    "paramDescription": "intermediate storage location",
+    "paramRequired": true
+  },
+  {
+    "paramName": "i",
+    "paramLongName": "idMappingPath",
+    "paramDescription": "dataset providing the old -> new identifier mapping",
+    "paramRequired": true
+  }
+]

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

@@ -100,6 +100,16 @@
             <value></value>
             <description>a blacklist of nsprefixes (comma separeted)</description>
         </property>
+        <property>
+            <name>shouldPatchRelations</name>
+            <value>false</value>
+            <description>activates the relation patching phase, driven by the content in ${idMappingPath}</description>
+        </property>
+        <property>
+            <name>idMappingPath</name>
+            <value></value>
+            <description>path pointing to the relations identifiers mapping dataset</description>
+        </property>
         <property>
             <name>sparkDriverMemory</name>
             <description>memory for driver process</description>
@@ -538,7 +548,42 @@
         <error to="Kill"/>
     </action>
 
-    <join name="wait_graphs" to="fork_merge_claims"/>
+    <join name="wait_graphs" to="patchRelations"/>
+
+    <decision name="decisionPatchRelations">
+        <switch>
+            <case to="patchRelations">
+                ${(shouldPatchRelations eq "true") and
+                (fs:exists(concat(concat(wf:conf('nameNode'),'/'),wf:conf('idMappingPath'))) eq "true")}
+            </case>
+            <default to="fork_merge_claims"/>
+        </switch>
+    </decision>
+
+    <action name="patchRelations">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>PatchRelations</name>
+            <class>eu.dnetlib.dhp.oa.graph.raw.PatchRelationsApplication</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory ${sparkExecutorMemory}
+                --executor-cores ${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+            </spark-opts>
+            <arg>--graphBasePath</arg><arg>${workingDir}/graph_raw</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/patch_relations</arg>
+            <arg>--idMappingPath</arg><arg>${idMappingPath}</arg>
+        </spark>
+        <ok to="fork_merge_claims"/>
+        <error to="Kill"/>
+    </action>
 
     <fork name="fork_merge_claims">
         <path start="merge_claims_publication"/>