new workflow and parameter for country propagation

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java

@@ -1,4 +1,134 @@
+
 package eu.dnetlib.dhp.countrypropagation;
 
+import static eu.dnetlib.dhp.PropagationConstant.*;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+
+import java.util.Arrays;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.*;
+import org.apache.spark.sql.Dataset;
+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.*;
+
 public class PrepareResultCountrySet {
+	private static final Logger log = LoggerFactory.getLogger(PrepareResultCountrySet.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static void main(String[] args) throws Exception {
+		String jsonConfiguration = IOUtils
+			.toString(
+				SparkCountryPropagationJob2.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/countrypropagation/input_prepareresultcountry_parameters.json"));
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		String inputPath = parser.get("sourcePath");
+		log.info("inputPath: {}", inputPath);
+
+		final String datasourcecountrypath = parser.get("preparedInfoPath");
+		log.info("preparedInfoPath: {}", datasourcecountrypath);
+
+		final String resultClassName = parser.get("resultTableName");
+		log.info("resultTableName: {}", resultClassName);
+
+		Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
+
+		SparkConf conf = new SparkConf();
+		conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
+
+		runWithSparkHiveSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				getPotentialResultToUpdate(
+					spark,
+					inputPath,
+					datasourcecountrypath,
+					resultClazz);
+			});
+
+	}
+
+	private static <R extends Result> void getPotentialResultToUpdate(
+		SparkSession spark,
+		String inputPath,
+		String datasourcecountrypath,
+		Class<R> resultClazz) {
+
+		Dataset<R> result = readPathEntity(spark, inputPath, resultClazz);
+		result.createOrReplaceTempView("result");
+		// log.info("number of results: {}", result.count());
+		createCfHbforresult(spark);
+		Dataset<DatasourceCountry> datasourcecountryassoc = readAssocDatasourceCountry(spark, datasourcecountrypath);
+		countryPropagationAssoc(spark, datasourcecountryassoc)
+			.map((MapFunction<ResultCountrySet, R>) value -> {
+				R ret = resultClazz.newInstance();
+				ret.setId(value.getResultId());
+				ret
+					.setCountry(
+						value
+							.getCountrySet()
+							.stream()
+							.map(c -> getCountry(c.getClassid(), c.getClassname()))
+							.collect(Collectors.toList()));
+				return ret;
+			}, Encoders.bean(resultClazz))
+			.write()
+			.option("compression", "gzip")
+			.mode(SaveMode.Append)
+			.json(inputPath);
+	}
+
+	private static Dataset<ResultCountrySet> countryPropagationAssoc(
+		SparkSession spark,
+		Dataset<DatasourceCountry> datasource_country) {
+
+		// Dataset<DatasourceCountry> datasource_country = broadcast_datasourcecountryassoc.value();
+		datasource_country.createOrReplaceTempView("datasource_country");
+		log.info("datasource_country number : {}", datasource_country.count());
+
+		String query = "SELECT id resultId, collect_set(country) countrySet "
+			+ "FROM ( SELECT id, country "
+			+ "FROM datasource_country "
+			+ "JOIN cfhb "
+			+ " ON cf = dataSourceId     "
+			+ "UNION ALL "
+			+ "SELECT id , country     "
+			+ "FROM datasource_country "
+			+ "JOIN cfhb "
+			+ " ON hb = dataSourceId   ) tmp "
+			+ "GROUP BY id";
+		Dataset<ResultCountrySet> potentialUpdates = spark
+			.sql(query)
+			.as(Encoders.bean(ResultCountrySet.class));
+		// log.info("potential update number : {}", potentialUpdates.count());
+		return potentialUpdates;
+	}
+
+	private static Dataset<DatasourceCountry> readAssocDatasourceCountry(
+		SparkSession spark, String relationPath) {
+		return spark
+			.read()
+			.textFile(relationPath)
+			.map(
+				value -> OBJECT_MAPPER.readValue(value, DatasourceCountry.class),
+				Encoders.bean(DatasourceCountry.class));
+	}
 }

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json

@@ -9,7 +9,7 @@
     "paramName":"h",
     "paramLongName":"hive_metastore_uris",
     "paramDescription": "the hive metastore uris",
-    "paramRequired": true
+    "paramRequired": false
   },
   {
     "paramName":"sg",
@@ -33,7 +33,7 @@
     "paramName": "p",
     "paramLongName": "preparedInfoPath",
     "paramDescription": "the path where prepared info have been stored",
-    "paramRequired": true
+    "paramRequired": false
   },
   {
     "paramName": "ssm",

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

@@ -27,6 +27,10 @@
     <action name="reset-outputpath">
         <fs>
             <delete path='${workingDir}/preparedInfo'/>
+            <delete path='${workingDir}/publication'/>
+            <delete path='${workingDir}/dataset'/>
+            <delete path='${workingDir}/otherresearchproduct'/>
+            <delete path='${workingDir}/software'/>
             <delete path='${outputPath}/relation'/>
             <delete path='${outputPath}/dataset'/>
             <delete path='${outputPath}/software'/>
@@ -45,6 +49,10 @@
         <path start="copy_organization"/>
         <path start="copy_projects"/>
         <path start="copy_datasources"/>
+        <path start="copy_publication"/>
+        <path start="copy_dataset"/>
+        <path start="copy_orp"/>
+        <path start="copy_software"/>
     </fork>
     <action name="copy_relation">
         <distcp xmlns="uri:oozie:distcp-action:0.2">
@@ -89,6 +97,50 @@
         <error to="Kill"/>
     </action>
 
+    <action name="copy_publication">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <arg>${nameNode}/${sourcePath}/publication</arg>
+            <arg>${nameNode}/${workingDir}/publication</arg>
+        </distcp>
+        <ok to="copy_wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="copy_dataset">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <arg>${nameNode}/${sourcePath}/dataset</arg>
+            <arg>${nameNode}/${workingDir}/dataset</arg>
+        </distcp>
+        <ok to="copy_wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="copy_orp">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <arg>${nameNode}/${sourcePath}/otherresearchproduct</arg>
+            <arg>${nameNode}/${workingDir}/otherresearchproduct</arg>
+        </distcp>
+        <ok to="copy_wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="copy_software">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <arg>${nameNode}/${sourcePath}/software</arg>
+            <arg>${nameNode}/${workingDir}/software</arg>
+        </distcp>
+        <ok to="copy_wait"/>
+        <error to="Kill"/>
+    </action>
+
     <join name="copy_wait" to="prepare_datasource_country_association"/>
 
     <action name="prepare_datasource_country_association">
@@ -113,9 +165,139 @@
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg>
         </spark>
-        <ok to="fork_join_apply_country_propagation"/>
+        <ok to="fork_join_prepare_result_country"/>
         <error to="Kill"/>
     </action>
+
+    <fork name="fork_join_prepare_result_country">
+        <path start="join_prepareresult_publication"/>
+        <path start="join_prepareresult_dataset"/>
+        <path start="join_prepareresult_otherresearchproduct"/>
+        <path start="join_prepareresult_software"/>
+    </fork>
+
+    <action name="join_prepareresult_publication">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>prepareResultCountry-Publication</name>
+            <class>eu.dnetlib.dhp.countrypropagation.PrepareResultCountrySet</class>
+            <jar>dhp-propagation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
+                --conf spark.speculation=false
+                --conf spark.hadoop.mapreduce.map.speculative=false
+                --conf spark.hadoop.mapreduce.reduce.speculative=false
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${workingDir}/publication</arg>
+            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
+            <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
+        </spark>
+        <ok to="wait_prepare"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="join_prepareresult_dataset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>prepareResultCountry-Dataset</name>
+            <class>eu.dnetlib.dhp.countrypropagation.PrepareResultCountrySet</class>
+            <jar>dhp-propagation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --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.dynamicAllocation.enabled=true
+                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
+                --conf spark.speculation=false
+                --conf spark.hadoop.mapreduce.map.speculative=false
+                --conf spark.hadoop.mapreduce.reduce.speculative=false
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${workingDir}/dataset</arg>
+            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
+            <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
+        </spark>
+        <ok to="wait_prepare"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="join_prepareresult_otherresearchproduct">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>prepareResultCountry-ORP</name>
+            <class>eu.dnetlib.dhp.countrypropagation.PrepareResultCountrySet</class>
+            <jar>dhp-propagation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
+                --conf spark.speculation=false
+                --conf spark.hadoop.mapreduce.map.speculative=false
+                --conf spark.hadoop.mapreduce.reduce.speculative=false
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${workingDir}/otherresearchproduct</arg>
+            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
+            <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
+        </spark>
+        <ok to="wait_prepare"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="join_prepareresult_software">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>prepareResultCountry-Software</name>
+            <class>eu.dnetlib.dhp.countrypropagation.PrepareResultCountrySet</class>
+            <jar>dhp-propagation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --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.dynamicAllocation.enabled=true
+                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
+                --conf spark.speculation=false
+                --conf spark.hadoop.mapreduce.map.speculative=false
+                --conf spark.hadoop.mapreduce.reduce.speculative=false
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${workingDir}/software</arg>
+            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
+            <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
+        </spark>
+        <ok to="wait_prepare"/>
+        <error to="Kill"/>
+    </action>
+
+    <join name="wait_prepare" to="fork_join_apply_country_propagation"/>
+
     <fork name="fork_join_apply_country_propagation">
         <path start="join_propagation_publication"/>
         <path start="join_propagation_dataset"/>
@@ -128,26 +310,27 @@
             <master>yarn</master>
             <mode>cluster</mode>
             <name>countryPropagationForPublications</name>
-            <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
+            <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob3</class>
             <jar>dhp-propagation-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-cores=${sparkExecutorCores}
+<!--                &#45;&#45;executor-cores=${sparkExecutorCores}-->
-                --executor-memory=${sparkExecutorMemory}
+<!--                &#45;&#45;executor-memory=${sparkExecutorMemory}-->
                 --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
+<!--                &#45;&#45;conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}-->
                 --conf spark.speculation=false
+                --conf spark.hadoop.mapreduce.map.speculative=false
+                --conf spark.hadoop.mapreduce.reduce.speculative=false
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
+            <arg>--sourcePath</arg><arg>${workingDir}/publication</arg>
-            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--saveGraph</arg><arg>${saveGraph}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
             <arg>--outputPath</arg><arg>${outputPath}/publication</arg>
-            <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
         </spark>
         <ok to="wait"/>
         <error to="Kill"/>
@@ -158,7 +341,7 @@
             <master>yarn</master>
             <mode>cluster</mode>
             <name>countryPropagationForDataset</name>
-            <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
+            <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob3</class>
             <jar>dhp-propagation-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-cores=${sparkExecutorCores}
@@ -171,13 +354,13 @@
                 --conf spark.dynamicAllocation.enabled=true
                 --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
                 --conf spark.speculation=false
+                --conf spark.hadoop.mapreduce.map.speculative=false
+                --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
-            <arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
+            <arg>--sourcePath</arg><arg>${workingDir}/dataset</arg>
-            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--saveGraph</arg><arg>${saveGraph}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
             <arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
-            <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
         </spark>
         <ok to="wait"/>
         <error to="Kill"/>
@@ -188,7 +371,7 @@
             <master>yarn</master>
             <mode>cluster</mode>
             <name>countryPropagationForORP</name>
-            <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
+            <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob3</class>
             <jar>dhp-propagation-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-cores=${sparkExecutorCores}
@@ -201,13 +384,13 @@
                 --conf spark.dynamicAllocation.enabled=true
                 --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
                 --conf spark.speculation=false
+                --conf spark.hadoop.mapreduce.map.speculative=false
+                --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
-            <arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
+            <arg>--sourcePath</arg><arg>${workingDir}/otherresearchproduct</arg>
-            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--saveGraph</arg><arg>${saveGraph}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
             <arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
-            <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
         </spark>
         <ok to="wait"/>
         <error to="Kill"/>
@@ -218,7 +401,7 @@
             <master>yarn</master>
             <mode>cluster</mode>
             <name>countryPropagationForSoftware</name>
-            <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
+            <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob3</class>
             <jar>dhp-propagation-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-cores=${sparkExecutorCores}
@@ -231,13 +414,13 @@
                 --conf spark.dynamicAllocation.enabled=true
                 --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
                 --conf spark.speculation=false
+                --conf spark.hadoop.mapreduce.map.speculative=false
+                --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
-            <arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
+            <arg>--sourcePath</arg><arg>${workingDir}/software</arg>
-            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--saveGraph</arg><arg>${saveGraph}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
             <arg>--outputPath</arg><arg>${outputPath}/software</arg>
-            <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
         </spark>
         <ok to="wait"/>
         <error to="Kill"/>