implemented workflow of creation action set for scholexplorer

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala

@@ -64,9 +64,9 @@ abstract class AbstractRestClient extends Iterator[String]{
       .setSocketTimeout(timeout * 1000).build()
     val client =HttpClientBuilder.create().setDefaultRequestConfig(config).build()
     var tries = 4
-    try {
        while (tries > 0) {
         println(s"requesting ${r.getURI}")
+        try {
           val response = client.execute(r)
           println(s"get response with status${response.getStatusLine.getStatusCode}")
           if (response.getStatusLine.getStatusCode > 400) {
@@ -74,16 +74,14 @@ abstract class AbstractRestClient extends Iterator[String]{
           }
           else
             return IOUtils.toString(response.getEntity.getContent)
-      }
-      ""
         } catch {
           case e: Throwable =>
-        throw new RuntimeException("Error on executing request ", e)
+            println(s"Error on requesting ${r.getURI}")
-    } finally try client.close()
+            e.printStackTrace()
-    catch {
+            tries-=1
-      case e: IOException =>
-        throw new RuntimeException("Unable to close client ", e)
         }
       }
+      ""
+   }
   getBufferData()
 }

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

@@ -9,6 +9,41 @@
 
     <artifactId>dhp-graph-provision</artifactId>
 
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>net.alchim31.maven</groupId>
+                <artifactId>scala-maven-plugin</artifactId>
+                <version>4.0.1</version>
+                <executions>
+                    <execution>
+                        <id>scala-compile-first</id>
+                        <phase>initialize</phase>
+                        <goals>
+                            <goal>add-source</goal>
+                            <goal>compile</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>scala-test-compile</id>
+                        <phase>process-test-resources</phase>
+                        <goals>
+                            <goal>testCompile</goal>
+                        </goals>
+                    </execution>
+                </executions>
+                <configuration>
+                    <args>
+                        <arg>-Xmax-classfile-name</arg>
+                        <arg>200</arg>
+                    </args>
+                    <scalaVersion>${scala.version}</scalaVersion>
+                </configuration>
+            </plugin>
+        </plugins>
+
+    </build>
+
     <dependencies>
 
         <dependency>

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/sx/provision/SparkCreateActionset.scala

@@ -43,7 +43,7 @@ object SparkCreateActionset {
     val relation = spark.read.load(s"$sourcePath/relation").as[Relation]
 
     relation.filter(r => (r.getDataInfo== null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
-      .flatMap(r => List(r.getSource,r.getTarget)).distinct().write.save(s"$workingDirFolder/id_relation")
+      .flatMap(r => List(r.getSource,r.getTarget)).distinct().write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/id_relation")
 
 
     val idRelation = spark.read.load(s"$workingDirFolder/id_relation").as[String]
@@ -56,35 +56,18 @@ object SparkCreateActionset {
     relation.filter(r => (r.getDataInfo== null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
       .write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/actionSetOaf")
 
-    log.info("saving publication")
+    log.info("saving entities")
 
-    val publication:Dataset[(String, Result)] = spark.read.load(s"$sourcePath/publication").as[Result].map(p => (p.getId, p))
+    val entities:Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders))
 
-    publication
+
-      .joinWith(idRelation, publication("_1").equalTo(idRelation("value")))
+    entities.filter(r => r.isInstanceOf[Result]).map(r => r.asInstanceOf[Result])
+    entities
+      .joinWith(idRelation, entities("_1").equalTo(idRelation("value")))
       .map(p => p._1._2)
       .write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
 
-    log.info("saving dataset")
-    val dataset:Dataset[(String, Result)] = spark.read.load(s"$sourcePath/dataset").as[Result].map(p => (p.getId, p))
-    dataset
-      .joinWith(idRelation, publication("_1").equalTo(idRelation("value")))
-      .map(p => p._1._2)
-      .write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
 
-    log.info("saving software")
-    val software:Dataset[(String, Result)] = spark.read.load(s"$sourcePath/software").as[Result].map(p => (p.getId, p))
-    software
-      .joinWith(idRelation, publication("_1").equalTo(idRelation("value")))
-      .map(p => p._1._2)
-      .write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
-
-    log.info("saving Other Research product")
-    val orp:Dataset[(String, Result)] = spark.read.load(s"$sourcePath/otherresearchproduct").as[Result].map(p => (p.getId, p))
-    orp
-      .joinWith(idRelation, publication("_1").equalTo(idRelation("value")))
-      .map(p => p._1._2)
-      .write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
   }
 
 }

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

@@ -14,7 +14,7 @@
         </property>
     </parameters>
 
-    <start to="ExportDataset"/>
+    <start to="createActionSet"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
@@ -26,7 +26,7 @@
             <mode>cluster</mode>
             <name>Create Action Set</name>
             <class>eu.dnetlib.dhp.sx.provision.SparkCreateActionset</class>
-            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
@@ -42,7 +42,7 @@
             <arg>--workingDirFolder</arg><arg>${workingDirFolder}</arg>
             <arg>--master</arg><arg>yarn-cluster</arg>
         </spark>
-        <ok to="End"/>
+        <ok to="SaveActionSet"/>
         <error to="Kill"/>
     </action>
 
@@ -53,7 +53,7 @@
             <mode>cluster</mode>
             <name>Save Action Set</name>
             <class>eu.dnetlib.dhp.sx.provision.SparkSaveActionSet</class>
-            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}