parallel implementation for graph Hive importer

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java

@@ -0,0 +1,79 @@
+
+package eu.dnetlib.dhp.oa.graph.hive;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+import static eu.dnetlib.dhp.schema.common.ModelSupport.tableIdentifier;
+
+import java.util.Optional;
+
+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.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+
+public class GraphHiveTableImporterJob {
+
+	private static final Logger log = LoggerFactory.getLogger(GraphHiveTableImporterJob.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static void main(String[] args) throws Exception {
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					GraphHiveTableImporterJob.class
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/graph/hive_table_importer_parameters.json")));
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		String inputPath = parser.get("inputPath");
+		log.info("inputPath: {}", inputPath);
+
+		String hiveDbName = parser.get("hiveDbName");
+		log.info("hiveDbName: {}", hiveDbName);
+
+		final String className = parser.get("className");
+		log.info("className: {}", className);
+
+		Class<? extends Oaf> clazz = (Class<? extends Oaf>) Class.forName(className);
+
+		String hiveMetastoreUris = parser.get("hiveMetastoreUris");
+		log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
+
+		SparkConf conf = new SparkConf();
+		conf.set("hive.metastore.uris", hiveMetastoreUris);
+
+		runWithSparkHiveSession(
+			conf, isSparkSessionManaged, spark -> loadGraphTable(spark, inputPath, hiveDbName, clazz));
+	}
+
+	// protected for testing
+	private static <T extends Oaf> void loadGraphTable(SparkSession spark, String inputPath, String hiveDbName,
+		Class<T> clazz) {
+
+		spark
+			.read()
+			.textFile(inputPath)
+			.map((MapFunction<String, T>) s -> OBJECT_MAPPER.readValue(s, clazz), Encoders.bean(clazz))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.saveAsTable(tableIdentifier(hiveDbName, clazz));
+	}
+
+}

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/reset_db.sql

@@ -0,0 +1,2 @@
+DROP DATABASE IF EXISTS ${hiveDbName} CASCADE;
+CREATE DATABASE ${hiveDbName};

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

@@ -72,18 +72,44 @@
         </configuration>
     </global>
 
-    <start to="MapGraphAsHiveDB"/>
+    <start to="reset_DB"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
-    <action name="MapGraphAsHiveDB">
+    <action name="reset_DB">
+        <hive2 xmlns="uri:oozie:hive2-action:0.1">
+            <configuration>
+                <property>
+                    <name>hive.metastore.uris</name>
+                    <value>${hiveMetastoreUris}</value>
+                </property>
+            </configuration>
+            <jdbc-url>${hiveJdbcUrl}/${hiveDbName}</jdbc-url>
+            <script>lib/scripts/reset_db.sql</script>
+            <param>hiveDbName=${hiveDbName}</param>
+        </hive2>
+        <ok to="fork_import"/>
+        <error to="Kill"/>
+    </action>
+
+    <fork name="fork_import">
+        <path start="import_publication"/>
+        <path start="import_dataset"/>
+        <path start="import_orp"/>
+        <path start="import_software"/>
+        <path start="import_datasource"/>
+        <path start="import_organization"/>
+        <path start="import_project"/>
+    </fork>
+
+    <action name="import_publication">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
-            <name>MapGraphAsHiveDB</name>
+            <name>Import table publication</name>
-            <class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveImporterJob</class>
+            <class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
             <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-memory=${sparkExecutorMemory}
@@ -95,18 +121,175 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--inputPath</arg><arg>${inputPath}</arg>
+            <arg>--inputPath</arg><arg>${inputPath}/publication</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
+            <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
         </spark>
-        <ok to="PostProcessing"/>
+        <ok to="join_import"/>
         <error to="Kill"/>
     </action>
 
+    <action name="import_dataset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Import table dataset</name>
+            <class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</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}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}/dataset</arg>
+            <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
+            <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
+        </spark>
+        <ok to="join_import"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="import_orp">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Import table otherresearchproduct</name>
+            <class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
+            <jar>dhp-graph-mapper-${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.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
+            <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
+            <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
+        </spark>
+        <ok to="join_import"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="import_software">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Import table software</name>
+            <class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</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}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}/software</arg>
+            <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
+            <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
+        </spark>
+        <ok to="join_import"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="import_datasource">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Import table datasource</name>
+            <class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
+            <jar>dhp-graph-mapper-${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.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}/datasource</arg>
+            <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
+            <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
+        </spark>
+        <ok to="join_import"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="import_organization">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Import table organization</name>
+            <class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</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}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}/organization</arg>
+            <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
+            <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
+        </spark>
+        <ok to="join_import"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="import_project">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Import table project</name>
+            <class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
+            <jar>dhp-graph-mapper-${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.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}/project</arg>
+            <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
+            <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
+        </spark>
+        <ok to="join_import"/>
+        <error to="Kill"/>
+    </action>
+
+    <join name="join_import" to="PostProcessing"/>
+
     <action name="PostProcessing">
         <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
             <configuration>
                 <property>
                     <name>hive.metastore.uris</name>
@@ -122,4 +305,5 @@
     </action>
 
     <end name="End"/>
+
 </workflow-app>

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

@@ -0,0 +1,26 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "in",
+    "paramLongName": "inputPath",
+    "paramDescription": "the path to the graph data dump to read",
+    "paramRequired": true
+  },
+  {
+    "paramName": "hmu",
+    "paramLongName": "hiveMetastoreUris",
+    "paramDescription": "the hive metastore uris",
+    "paramRequired": true
+  },
+  {
+    "paramName": "db",
+    "paramLongName": "hiveDbName",
+    "paramDescription": "the target hive database name",
+    "paramRequired": true
+  }
+]

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

@@ -0,0 +1,32 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "in",
+    "paramLongName": "inputPath",
+    "paramDescription": "the path to the graph data dump to read",
+    "paramRequired": true
+  },
+  {
+    "paramName": "hmu",
+    "paramLongName": "hiveMetastoreUris",
+    "paramDescription": "the hive metastore uris",
+    "paramRequired": true
+  },
+  {
+    "paramName": "db",
+    "paramLongName": "hiveDbName",
+    "paramDescription": "the target hive database name",
+    "paramRequired": true
+  },
+  {
+    "paramName": "tn",
+    "paramLongName": "className",
+    "paramDescription": "the class modelling the target table",
+    "paramRequired": true
+  }
+]