updated unpaywall mapping

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholix.java

@@ -3,16 +3,20 @@ package eu.dnetlib.dhp.provision;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.provision.scholix.Scholix;
-import eu.dnetlib.dhp.utils.DHPUtils;
+import eu.dnetlib.dhp.provision.scholix.ScholixResource;
+import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.compress.GzipCodec;
 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.api.java.function.PairFlatMapFunction;
 import org.apache.spark.sql.SparkSession;
 import scala.Tuple2;
 
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Random;
+
 public class SparkGenerateScholix {
 
     private static final String jsonIDPath = "$.id";
@@ -21,6 +25,8 @@ public class SparkGenerateScholix {
 
 
 
+
+
     public static void main(String[] args) throws Exception {
         final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkGenerateScholix.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json")));
         parser.parseArgument(args);
@@ -37,29 +43,48 @@ public class SparkGenerateScholix {
         final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
 
 
-        final JavaRDD<String> relationToExport = sc.textFile(graphPath + "/relation").filter(ProvisionUtil::isNotDeleted).repartition(4000);
-        final JavaPairRDD<String,String> scholixSummary = sc.textFile(workingDirPath + "/summary").mapToPair((PairFunction<String, String, String>) i -> new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i));
-        scholixSummary.join(
-                relationToExport
-                        .mapToPair((PairFunction<String, String, String>) i -> new Tuple2<>(DHPUtils.getJPathString(sourceIDPath, i), i)))
-                .map(Tuple2::_2)
-                .mapToPair(summaryRelation ->
-                        new Tuple2<>(
-                                DHPUtils.getJPathString(targetIDPath, summaryRelation._2()),
-                                Scholix.generateScholixWithSource(summaryRelation._1(), summaryRelation._2())))
-//                .join(scholixSummary)
+//        final JavaRDD<String> relationToExport = sc.textFile(graphPath + "/relation").filter(ProvisionUtil::isNotDeleted).repartition(4000);
+        final JavaPairRDD<String,ScholixResource> scholixSummary =
+                sc.textFile(workingDirPath + "/summary")
+                        .flatMapToPair((PairFlatMapFunction<String, String, ScholixResource>) i -> {
+                            final ObjectMapper mapper = new ObjectMapper();
+                            final ScholixSummary summary = mapper.readValue(i, ScholixSummary.class);
+                            ScholixResource tmp = ScholixResource.fromSummary(summary);
+                            final List<Tuple2<String, ScholixResource>> result = new ArrayList<>();
+                            for (int k = 0; k<10; k++)
+                                result.add(new Tuple2<>(String.format("%s::%d", tmp.getDnetIdentifier(), k), tmp));
+                            return result.iterator();
+                        });
+//        scholixSummary.join(
+//                relationToExport
+//                        .mapToPair((PairFunction<String, String, String>) i -> new Tuple2<>(DHPUtils.getJPathString(sourceIDPath, i), i)))
 //                .map(Tuple2::_2)
-//                .map(i -> i._1().addTarget(i._2()))
-                .map(s-> {
+//                .mapToPair(summaryRelation ->
+//                        new Tuple2<>(
+//                                DHPUtils.getJPathString(targetIDPath, summaryRelation._2()),
+//                                Scholix.generateScholixWithSource(summaryRelation._1(), summaryRelation._2())))
+//
+//                .map(t-> t._2().setTarget(new ScholixResource().setDnetIdentifier(t._1())))
+//                .map(s-> {
+//                    ObjectMapper mapper = new ObjectMapper();
+//                    return mapper.writeValueAsString(s);
+//                })
+//        .saveAsTextFile(workingDirPath + "/scholix", GzipCodec.class);
+
+        sc.textFile(workingDirPath + "/scholix")
+                .mapToPair(t -> {
                     ObjectMapper mapper = new ObjectMapper();
-                    return mapper.writeValueAsString(s);
+                    Scholix scholix = mapper.readValue(t, Scholix.class);
+                    Random rand = new Random();
+                    return new Tuple2<>(String.format("%s::%d",scholix.getTarget().getDnetIdentifier(), rand.nextInt(10)), scholix);
                 })
-        .saveAsTextFile(workingDirPath + "/scholix", GzipCodec.class);
-
-
-                ;
-
-
+                .join(scholixSummary)
+                .map(t-> {
+                    Scholix item = t._2()._1().setTarget(t._2()._2());
+                    item.generateIdentifier();
+                    return item;
+                })
+                .map(s-> new ObjectMapper().writeValueAsString(s)).saveAsTextFile(workingDirPath + "/scholix_index", GzipCodec.class);
     }
 
 

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java

@@ -24,6 +24,7 @@ public class SparkIndexCollectionOnES {
 
         final String sourcePath = parser.get("sourcePath");
         final String index = parser.get("index");
+        final String idPath = parser.get("idPath");
 
         final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
 
@@ -34,7 +35,7 @@ public class SparkIndexCollectionOnES {
 
         Map<String, String> esCfg = new HashMap<>();
         esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54");
-        esCfg.put("es.mapping.id", "id");
+        esCfg.put("es.mapping.id", idPath);
         esCfg.put("es.batch.write.retry.count", "8");
         esCfg.put("es.batch.write.retry.wait", "60s");
         esCfg.put("es.batch.size.entries", "200");

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/provision/scholix/Scholix.java

@@ -47,7 +47,7 @@ public class Scholix implements Serializable {
     }
 
 
-    private void generateIdentifier( ) {
+    public void generateIdentifier( ) {
         setIdentifier(DHPUtils.md5(String.format("%s::%s::%s",source.getDnetIdentifier(),relationship.getName(), target.getDnetIdentifier())));
 
     }

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/Application/provision/oozie_app/workflow.xml

@@ -25,9 +25,19 @@
             <description>number of cores used by single executor</description>
         </property>
 
+        <property>
+            <name>idScholix</name>
+            <description>the </description>
+        </property>
+        <property>
+            <name>idSummary</name>
+            <description>number of cores used by single executor</description>
+        </property>
+
+
     </parameters>
 
-    <start to="generateScholix"/>
+    <start to="indexScholix"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
@@ -103,7 +113,7 @@
             <name-node>${nameNode}</name-node>
             <master>yarn-cluster</master>
             <mode>cluster</mode>
-            <name>generate Summary</name>
+            <name>generate Scholix</name>
             <class>eu.dnetlib.dhp.provision.SparkGenerateScholix</class>
             <jar>dhp-graph-provision-${projectVersion}.jar</jar>
             <spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT}</spark-opts>
@@ -111,9 +121,29 @@
             <arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
             <arg>--graphPath</arg><arg>${graphPath}</arg>
         </spark>
+        <ok to="indexScholix"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <action name="indexScholix">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>index scholix</name>
+            <class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
+            <spark-opts>--executor-memory ${sparkExecutorMemory} --num-executors 20 --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="32" </spark-opts>
+            <arg>-mt</arg> <arg>yarn-cluster</arg>
+            <arg>--sourcePath</arg><arg>${workingDirPath}/scholix_index</arg>
+            <arg>--index</arg><arg>${index}_scholix</arg>
+        </spark>
         <ok to="End"/>
         <error to="Kill"/>
     </action>
 
+
     <end name="End"/>
 </workflow-app>

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/provision/index_on_es.json

@@ -16,5 +16,11 @@
     "paramLongName": "index",
     "paramDescription": "the index name",
     "paramRequired": true
+  },
+  {
+    "paramName": "id",
+    "paramLongName": "idPath",
+    "paramDescription": "the identifier field name",
+    "paramRequired": true
   }
 ]

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

@@ -1,5 +1,6 @@
 package eu.dnetlib.dhp.provision;
 
+import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dnetlib.dhp.provision.scholix.Scholix;
 import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary;
@@ -7,14 +8,13 @@ import org.apache.commons.io.IOUtils;
 import org.junit.Ignore;
 import org.junit.Test;
 
+import scala.Tuple2;
+
 public class ExtractInfoTest {
 
     @Test
     public void test() throws Exception {
-
         final String json = IOUtils.toString(getClass().getResourceAsStream("record.json"));
-
-
         ProvisionUtil.getItemType(json,ProvisionUtil.TARGETJSONPATH);
 
     }
@@ -43,6 +43,7 @@ public class ExtractInfoTest {
     }
 
 
+
     @Test
     @Ignore
     public void testIndex() throws Exception {