[SDG-FOS] alternative way to get input data to avoid OOM error while getting csv

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java

@@ -19,7 +19,7 @@ public class Constants {
 
 	public static final String DOI = "doi";
 
-	public static final char DEFAULT_DELIMITER = ',';
+	public static final String DEFAULT_DELIMITER = ",";
 
 	public static final String UPDATE_DATA_INFO_TYPE = "update";
 	public static final String UPDATE_SUBJECT_FOS_CLASS_ID = "subject:fos";
@@ -55,7 +55,8 @@ public class Constants {
 			.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
 	}
 
-	public static StructuredProperty getSubject(String sbj, String classid, String classname, String diqualifierclassid) {
+	public static StructuredProperty getSubject(String sbj, String classid, String classname,
+		String diqualifierclassid) {
 		if (sbj.equals(NULL))
 			return null;
 		StructuredProperty sp = new StructuredProperty();
@@ -78,7 +79,7 @@ public class Constants {
 						false,
 						OafMapperUtils
 							.qualifier(
-									diqualifierclassid,
+								diqualifierclassid,
 								UPDATE_CLASS_NAME,
 								ModelConstants.DNET_PROVENANCE_ACTIONS,
 								ModelConstants.DNET_PROVENANCE_ACTIONS),

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java

@@ -0,0 +1,91 @@
+
+package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
+
+import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
+import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.Serializable;
+import java.util.Optional;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+
+public class GetFOSSparkJob implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(GetFOSSparkJob.class);
+
+	public static void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				GetFOSSparkJob.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json"));
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		// the path where the original fos csv file is stored
+		final String sourcePath = parser.get("sourcePath");
+		log.info("sourcePath {}", sourcePath);
+
+		// the path where to put the file as json
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}", outputPath);
+
+		final String delimiter = Optional
+			.ofNullable(parser.get("delimiter"))
+			.orElse(DEFAULT_DELIMITER);
+
+		SparkConf sconf = new SparkConf();
+		runWithSparkSession(
+			sconf,
+			isSparkSessionManaged,
+			spark -> {
+				getFOS(
+					spark,
+					sourcePath,
+					outputPath,
+					delimiter);
+			});
+	}
+
+	private static void getFOS(SparkSession spark, String sourcePath, String outputPath, String delimiter) {
+		Dataset<Row> fosData = spark
+			.read()
+			.format("csv")
+			.option("sep", delimiter)
+			.option("inferSchema", "true")
+			.option("header", "true")
+			.option("quotes", "\"")
+			.load(sourcePath);
+
+		fosData.map((MapFunction<Row, FOSDataModel>) r -> {
+			FOSDataModel fosDataModel = new FOSDataModel();
+			fosDataModel.setDoi(r.getString(0).toLowerCase());
+			fosDataModel.setLevel1(r.getString(1));
+			fosDataModel.setLevel2(r.getString(2));
+			fosDataModel.setLevel3(r.getString(3));
+			return fosDataModel;
+		}, Encoders.bean(FOSDataModel.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.json(outputPath);
+
+	}
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetInputData.java

@@ -1,80 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
-
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.Serializable;
-import java.util.Objects;
-import java.util.Optional;
-import java.util.zip.GZIPInputStream;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-
-import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
-
-public class GetInputData implements Serializable {
-
-	private static final Logger log = LoggerFactory.getLogger(GetInputData.class);
-
-
-
-	public static void main(final String[] args) throws Exception {
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
-			IOUtils
-				.toString(
-					Objects
-						.requireNonNull(
-							GetInputData.class
-								.getResourceAsStream(
-									"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json"))));
-
-		parser.parseArgument(args);
-
-		// the path where the original fos csv file is stored
-		final String sourcePath = parser.get("sourcePath");
-		log.info("sourcePath {}", sourcePath);
-
-		// the path where to put the file as json
-		final String outputPath = parser.get("outputPath");
-		log.info("outputPath {}", outputPath);
-
-		final String hdfsNameNode = parser.get("hdfsNameNode");
-		log.info("hdfsNameNode {}", hdfsNameNode);
-
-		final String classForName = parser.get("classForName");
-		log.info("classForName {}", classForName);
-
-		final char delimiter = Optional
-			.ofNullable(parser.get("delimiter"))
-			.map(s -> s.charAt(0))
-			.orElse(DEFAULT_DELIMITER);
-		log.info("delimiter {}", delimiter);
-
-		Configuration conf = new Configuration();
-		conf.set("fs.defaultFS", hdfsNameNode);
-
-		FileSystem fileSystem = FileSystem.get(conf);
-
-		new GetInputData().doRewrite(sourcePath, outputPath, classForName, delimiter, fileSystem);
-
-	}
-
-	public void doRewrite(String inputPath, String outputFile, String classForName, char delimiter, FileSystem fs)
-		throws IOException, ClassNotFoundException {
-
-
-		// reads the csv and writes it as its json equivalent
-		try (InputStreamReader reader = new InputStreamReader(new GZIPInputStream(fs.open(new Path(inputPath))))) {
-			eu.dnetlib.dhp.common.collection.GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter);
-		}
-
-	}
-
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetSDGSparkJob.java

@@ -0,0 +1,91 @@
+
+package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
+
+import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
+import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.Serializable;
+import java.util.Optional;
+
+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.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+
+public class GetSDGSparkJob implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(GetSDGSparkJob.class);
+
+	public static void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				GetSDGSparkJob.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json"));
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		// the path where the original fos csv file is stored
+		final String sourcePath = parser.get("sourcePath");
+		log.info("sourcePath {}", sourcePath);
+
+		// the path where to put the file as json
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}", outputPath);
+
+		final String delimiter = Optional
+			.ofNullable(parser.get("delimiter"))
+			.orElse(DEFAULT_DELIMITER);
+
+		SparkConf sconf = new SparkConf();
+		runWithSparkSession(
+			sconf,
+			isSparkSessionManaged,
+			spark -> {
+				getSDG(
+					spark,
+					sourcePath,
+					outputPath,
+					delimiter);
+			});
+	}
+
+	private static void getSDG(SparkSession spark, String sourcePath, String outputPath, String delimiter) {
+		Dataset<Row> sdgData = spark
+			.read()
+			.format("csv")
+			.option("sep", delimiter)
+			.option("inferSchema", "true")
+			.option("header", "true")
+			.option("quotes", "\"")
+			.load(sourcePath);
+
+		sdgData.map((MapFunction<Row, SDGDataModel>) r -> {
+			SDGDataModel sdgDataModel = new SDGDataModel();
+			sdgDataModel.setDoi(r.getString(0).toLowerCase());
+			sdgDataModel.setSbj(r.getString(1));
+
+			return sdgDataModel;
+		}, Encoders.bean(SDGDataModel.class))
+			.filter((FilterFunction<SDGDataModel>) sdg -> sdg.getSbj() != null)
+			.write()
+			.mode(SaveMode.Overwrite)
+			.json(outputPath);
+
+	}
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java

@@ -1,11 +1,13 @@
 
 package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
 
-import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
+import static eu.dnetlib.dhp.actionmanager.Constants.*;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import eu.dnetlib.dhp.schema.oaf.Result;
+
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import java.io.Serializable;
-import eu.dnetlib.dhp.utils.DHPUtils;
+import java.util.ArrayList;
+import java.util.List;
+
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
@@ -16,71 +18,72 @@ import org.apache.spark.sql.SaveMode;
 import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import java.io.Serializable;
+
-import java.util.ArrayList;
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
-import java.util.List;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import static eu.dnetlib.dhp.actionmanager.Constants.*;
+import eu.dnetlib.dhp.schema.oaf.Result;
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import eu.dnetlib.dhp.utils.DHPUtils;
 
 public class PrepareSDGSparkJob implements Serializable {
-    private static final Logger log = LoggerFactory.getLogger(PrepareSDGSparkJob.class);
+	private static final Logger log = LoggerFactory.getLogger(PrepareSDGSparkJob.class);
 
-    public static void main(String[] args) throws Exception {
+	public static void main(String[] args) throws Exception {
 
-        String jsonConfiguration = IOUtils
+		String jsonConfiguration = IOUtils
-                .toString(
+			.toString(
-                        PrepareSDGSparkJob.class
+				PrepareSDGSparkJob.class
-                                .getResourceAsStream(
+					.getResourceAsStream(
-                                        "/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json"));
+						"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json"));
 
-        final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
 
-        parser.parseArgument(args);
+		parser.parseArgument(args);
 
-        Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
+		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
-        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-        String sourcePath = parser.get("sourcePath");
+		String sourcePath = parser.get("sourcePath");
-        log.info("sourcePath: {}", sourcePath);
+		log.info("sourcePath: {}", sourcePath);
 
-        final String outputPath = parser.get("outputPath");
+		final String outputPath = parser.get("outputPath");
-        log.info("outputPath: {}", outputPath);
+		log.info("outputPath: {}", outputPath);
 
-        SparkConf conf = new SparkConf();
+		SparkConf conf = new SparkConf();
-        runWithSparkSession(
+		runWithSparkSession(
-                conf,
+			conf,
-                isSparkSessionManaged,
+			isSparkSessionManaged,
-                spark -> {
+			spark -> {
-                    doPrepare(
+				doPrepare(
-                            spark,
+					spark,
-                            sourcePath,
+					sourcePath,
-
-                            outputPath);
-                });
-    }
-
-    private static void doPrepare(SparkSession spark, String sourcePath, String outputPath) {
-        Dataset<SDGDataModel> sdgDataset = readPath(spark, sourcePath, SDGDataModel.class);
-
-
-        sdgDataset.groupByKey((MapFunction<SDGDataModel,String>)r -> r.getDoi().toLowerCase(),Encoders.STRING())
-                .mapGroups((MapGroupsFunction<String, SDGDataModel, Result>)(k,it) -> {
-                    Result r = new Result();
-                    r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
-                    SDGDataModel first = it.next();
-                    List<StructuredProperty>sbjs = new ArrayList<>();
-                    sbjs.add(getSubject(first.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID));
-                    it.forEachRemaining(s -> sbjs.add(getSubject(s.getSbj(),SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
-                    r.setSubject(sbjs);
-                    return r;
-                },Encoders.bean(Result.class))
-                .write()
-                .mode(SaveMode.Overwrite)
-                .option("compression", "gzip")
-                .json(outputPath + "/sdg");
-    }
 
+					outputPath);
+			});
+	}
 
+	private static void doPrepare(SparkSession spark, String sourcePath, String outputPath) {
+		Dataset<SDGDataModel> sdgDataset = readPath(spark, sourcePath, SDGDataModel.class);
 
+		sdgDataset
+			.groupByKey((MapFunction<SDGDataModel, String>) r -> r.getDoi().toLowerCase(), Encoders.STRING())
+			.mapGroups((MapGroupsFunction<String, SDGDataModel, Result>) (k, it) -> {
+				Result r = new Result();
+				r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
+				SDGDataModel first = it.next();
+				List<StructuredProperty> sbjs = new ArrayList<>();
+				sbjs.add(getSubject(first.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID));
+				it
+					.forEachRemaining(
+						s -> sbjs
+							.add(getSubject(s.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
+				r.setSubject(sbjs);
+				return r;
+			}, Encoders.bean(Result.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.json(outputPath + "/sdg");
+	}
 
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/SDGDataModel.java

@@ -1,48 +1,47 @@
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
 
-import com.opencsv.bean.CsvBindByPosition;
+package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
 
 import java.io.Serializable;
 
-public class SDGDataModel implements Serializable{
+import com.opencsv.bean.CsvBindByPosition;
 
-    @CsvBindByPosition(position = 0)
+public class SDGDataModel implements Serializable {
+
+	@CsvBindByPosition(position = 0)
 //    @CsvBindByName(column = "doi")
-    private String doi;
+	private String doi;
 
-    @CsvBindByPosition(position = 1)
+	@CsvBindByPosition(position = 1)
 //    @CsvBindByName(column = "sdg")
-    private String sbj;
+	private String sbj;
 
+	public SDGDataModel() {
 
-    public SDGDataModel() {
+	}
 
-    }
+	public SDGDataModel(String doi, String sbj) {
+		this.doi = doi;
+		this.sbj = sbj;
 
-    public SDGDataModel(String doi, String sbj) {
+	}
-        this.doi = doi;
-        this.sbj = sbj;
 
-    }
+	public static SDGDataModel newInstance(String d, String sbj) {
+		return new SDGDataModel(d, sbj);
+	}
 
-    public static SDGDataModel newInstance(String d, String sbj) {
+	public String getDoi() {
-        return new SDGDataModel(d, sbj);
+		return doi;
-    }
+	}
 
-    public String getDoi() {
+	public void setDoi(String doi) {
-        return doi;
+		this.doi = doi;
-    }
+	}
 
-    public void setDoi(String doi) {
+	public String getSbj() {
-        this.doi = doi;
+		return sbj;
-    }
+	}
 
-
+	public void setSbj(String sbj) {
-    public String getSbj() {
+		this.sbj = sbj;
-        return sbj;
+	}
-    }
-
-    public void setSbj(String sbj) {
-        this.sbj = sbj;
-    }
 }

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json

@@ -19,15 +19,9 @@
     "paramRequired": false
   },
   {
-    "paramName": "hnn",
+    "paramName": "d",
-    "paramLongName": "hdfsNameNode",
+    "paramLongName": "delimiter",
-    "paramDescription": "the path used to store the HostedByMap",
+    "paramDescription": "the delimiter if different from the default one (,)",
-    "paramRequired": true
+    "paramRequired": false
-  },
-  {
-    "paramName": "cfn",
-    "paramLongName": "classForName",
-    "paramDescription": "the path used to store the HostedByMap",
-    "paramRequired": true
   }
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml

@@ -107,17 +107,30 @@
     </action>
 
     <action name="getFOS">
-        <java>
+        <spark xmlns="uri:oozie:spark-action:0.2">
-            <main-class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetInputData</main-class>
+            <master>yarn</master>
-            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
+            <mode>cluster</mode>
+            <name>Gets Data from FOS csv file</name>
+            <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSSparkJob</class>
+            <jar>dhp-aggregation-${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=${sparkSqlWarehouseDir}
+            </spark-opts>
             <arg>--sourcePath</arg><arg>${fosPath}</arg>
             <arg>--outputPath</arg><arg>${workingDir}/input/fos</arg>
-            <arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel</arg>
+        </spark>
-        </java>
         <ok to="prepareFos"/>
         <error to="Kill"/>
     </action>
 
+
     <action name="prepareFos">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -144,17 +157,30 @@
     </action>
 
     <action name="getSDG">
-        <java>
+        <spark xmlns="uri:oozie:spark-action:0.2">
-            <main-class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetInputData</main-class>
+            <master>yarn</master>
-            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
+            <mode>cluster</mode>
+            <name>Gets Data from SDG csv file</name>
+            <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetSDGSparkJob</class>
+            <jar>dhp-aggregation-${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=${sparkSqlWarehouseDir}
+            </spark-opts>
             <arg>--sourcePath</arg><arg>${sdgPath}</arg>
             <arg>--outputPath</arg><arg>${workingDir}/input/sdg</arg>
-            <arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel</arg>
+        </spark>
-        </java>
         <ok to="prepareSDG"/>
         <error to="Kill"/>
     </action>
 
+
     <action name="prepareSDG">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java

@@ -10,7 +10,6 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
 import org.apache.commons.io.FileUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
@@ -26,6 +25,7 @@ import org.slf4j.LoggerFactory;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
 import eu.dnetlib.dhp.schema.oaf.Result;
 
 public class PrepareTest {
@@ -148,37 +148,6 @@ public class PrepareTest {
 
 	}
 
-	@Test
-	void getFOSFileTest() throws IOException, ClassNotFoundException {
-
-		final String sourcePath = getClass()
-			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs.csv")
-			.getPath();
-		final String outputPath = workingDir.toString() + "/fos.json";
-
-		new GetInputData()
-			.doRewrite(
-				sourcePath, outputPath, "eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel",
-				',', fs);
-
-		BufferedReader in = new BufferedReader(
-			new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
-
-		String line;
-		int count = 0;
-		while ((line = in.readLine()) != null) {
-			FOSDataModel fos = new ObjectMapper().readValue(line, FOSDataModel.class);
-
-			System.out.println(new ObjectMapper().writeValueAsString(fos));
-			count += 1;
-		}
-
-		assertEquals(39, count);
-
-	}
-
-
-
 	@Test
 	void fosPrepareTest() throws Exception {
 		final String sourcePath = getClass()
@@ -206,7 +175,6 @@ public class PrepareTest {
 		assertEquals(20, tmp.count());
 		assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
 
-
 		assertTrue(
 			tmp
 				.filter(r -> r.getId().equals(doi1))
@@ -249,105 +217,101 @@ public class PrepareTest {
 
 	}
 
-	@Test
-	void getSDGFileTest() throws IOException, ClassNotFoundException {
-
-		final String sourcePath = getClass()
-				.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/sdg/sdg_sbs.csv")
-				.getPath();
-		final String outputPath = workingDir.toString() + "/sdg.json";
-
-		new GetInputData()
-				.doRewrite(
-						sourcePath, outputPath, "eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel",
-						',', fs);
-
-		BufferedReader in = new BufferedReader(
-				new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
-
-		String line;
-		int count = 0;
-		while ((line = in.readLine()) != null) {
-			SDGDataModel sdg = new ObjectMapper().readValue(line, SDGDataModel.class);
-
-			System.out.println(new ObjectMapper().writeValueAsString(sdg));
-			count += 1;
-		}
-
-		assertEquals(37, count);
-
-	}
-
 	@Test
 	void sdgPrepareTest() throws Exception {
 		final String sourcePath = getClass()
-				.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/sdg/sdg.json")
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/sdg/sdg.json")
-				.getPath();
+			.getPath();
 
 		PrepareSDGSparkJob
-				.main(
+			.main(
-						new String[] {
+				new String[] {
-								"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
-								"--sourcePath", sourcePath,
+					"--sourcePath", sourcePath,
 
-								"-outputPath", workingDir.toString() + "/work"
+					"-outputPath", workingDir.toString() + "/work"
 
-						});
+				});
 
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Result> tmp = sc
-				.textFile(workingDir.toString() + "/work/sdg")
+			.textFile(workingDir.toString() + "/work/sdg")
-				.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
+			.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
 
 		String doi1 = "unresolved::10.1001/amaguidesnewsletters.2019.sepoct02::doi";
 
 		assertEquals(32, tmp.count());
 		assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
 
-
 		assertTrue(
-				tmp
+			tmp
-						.filter(r -> r.getId().equals(doi1))
+				.filter(r -> r.getId().equals(doi1))
-						.flatMap(r -> r.getSubject().iterator())
+				.flatMap(r -> r.getSubject().iterator())
-						.map(sbj -> sbj.getValue())
+				.map(sbj -> sbj.getValue())
-						.collect()
+				.collect()
-						.contains("3. Good health"));
+				.contains("3. Good health"));
 		assertTrue(
-				tmp
+			tmp
-						.filter(r -> r.getId().equals(doi1))
+				.filter(r -> r.getId().equals(doi1))
-						.flatMap(r -> r.getSubject().iterator())
+				.flatMap(r -> r.getSubject().iterator())
-						.map(sbj -> sbj.getValue())
+				.map(sbj -> sbj.getValue())
-						.collect()
+				.collect()
-						.contains("8. Economic growth"));
+				.contains("8. Economic growth"));
-
 
 	}
-	@Disabled
+
 	@Test
-	void test2() throws Exception {
+	void test3() throws Exception {
+		final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_fos_results_20_12_2021.csv.gz";
+
+		final String outputPath = workingDir.toString() + "/fos.json";
+		GetFOSSparkJob
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", sourcePath,
+
+					"-outputPath", outputPath
+
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<FOSDataModel> tmp = sc
+			.textFile(outputPath)
+			.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
+
+		tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
+
+	}
+
+	@Test
+	void test4() throws Exception {
 		final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_sdg_results_20_12_21.csv.gz";
 
-
 		final String outputPath = workingDir.toString() + "/sdg.json";
+		GetSDGSparkJob
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", sourcePath,
 
-		new GetInputData()
+					"-outputPath", outputPath
-				.doRewrite(
-						sourcePath, outputPath, "eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel",
-						',', fs);
 
-		BufferedReader in = new BufferedReader(
+				});
-				new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
 
-		String line;
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-		int count = 0;
-		while ((line = in.readLine()) != null) {
-			SDGDataModel sdg = new ObjectMapper().readValue(line, SDGDataModel.class);
 
-			System.out.println(new ObjectMapper().writeValueAsString(sdg));
+		JavaRDD<SDGDataModel> tmp = sc
-			count += 1;
+			.textFile(outputPath)
-		}
+			.map(item -> OBJECT_MAPPER.readValue(item, SDGDataModel.class));
 
+		tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getSbj() != null));
 
 	}
 }

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java

@@ -7,7 +7,6 @@ import java.nio.file.Path;
 import java.util.List;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.actionmanager.Constants;
 import org.apache.commons.io.FileUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
@@ -25,6 +24,7 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
+import eu.dnetlib.dhp.actionmanager.Constants;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.*;
 
@@ -349,60 +349,58 @@ public class ProduceTest {
 
 	}
 
-
 	private JavaRDD<Result> getResultJavaRDDPlusSDG() throws Exception {
 		final String bipPath = getClass()
-				.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
-				.getPath();
+			.getPath();
 
 		PrepareBipFinder
-				.main(
+			.main(
-						new String[] {
+				new String[] {
-								"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
-								"--sourcePath", bipPath,
+					"--sourcePath", bipPath,
-								"--outputPath", workingDir.toString() + "/work"
+					"--outputPath", workingDir.toString() + "/work"
 
-						});
+				});
 		final String fosPath = getClass()
-				.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
-				.getPath();
+			.getPath();
 
 		PrepareFOSSparkJob
-				.main(
+			.main(
-						new String[] {
+				new String[] {
-								"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
-								"--sourcePath", fosPath,
+					"--sourcePath", fosPath,
-								"-outputPath", workingDir.toString() + "/work"
+					"-outputPath", workingDir.toString() + "/work"
-						});
+				});
 
 		final String sdgPath = getClass()
-				.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/sdg/sdg.json")
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/sdg/sdg.json")
-				.getPath();
+			.getPath();
 
 		PrepareSDGSparkJob
-				.main(
+			.main(
-						new String[] {
+				new String[] {
-								"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
-								"--sourcePath", sdgPath,
+					"--sourcePath", sdgPath,
-								"-outputPath", workingDir.toString() + "/work"
+					"-outputPath", workingDir.toString() + "/work"
-						});
+				});
 
 		SparkSaveUnresolved.main(new String[] {
-				"--isSparkSessionManaged", Boolean.FALSE.toString(),
+			"--isSparkSessionManaged", Boolean.FALSE.toString(),
-				"--sourcePath", workingDir.toString() + "/work",
+			"--sourcePath", workingDir.toString() + "/work",
 
-				"-outputPath", workingDir.toString() + "/unresolved"
+			"-outputPath", workingDir.toString() + "/unresolved"
 
 		});
 
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		return sc
-				.textFile(workingDir.toString() + "/unresolved")
+			.textFile(workingDir.toString() + "/unresolved")
-				.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
+			.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
 	}
 
-
 	@Test
 	void produceTestSomeNumbersWithSDG() throws Exception {
 
@@ -414,19 +412,19 @@ public class ProduceTest {
 		Assertions.assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count());
 
 		Assertions
-				.assertEquals(
+			.assertEquals(
-						50, tmp
+				50, tmp
-								.filter(row -> !row.getId().equals(doi))
+					.filter(row -> !row.getId().equals(doi))
-								.filter(row -> row.getSubject() != null)
+					.filter(row -> row.getSubject() != null)
-								.count());
+					.count());
 
 		Assertions
-				.assertEquals(
+			.assertEquals(
-						85,
+				85,
-						tmp
+				tmp
-								.filter(row -> !row.getId().equals(doi))
+					.filter(row -> !row.getId().equals(doi))
-								.filter(r -> r.getInstance() != null && r.getInstance().size() > 0)
+					.filter(r -> r.getInstance() != null && r.getInstance().size() > 0)
-								.count());
+					.count());
 
 	}
 
@@ -437,35 +435,35 @@ public class ProduceTest {
 		JavaRDD<Result> tmp = getResultJavaRDDPlusSDG();
 
 		Assertions
-				.assertEquals(
+			.assertEquals(
-						7, tmp
+				7, tmp
-								.filter(row -> row.getId().equals(doi))
+					.filter(row -> row.getId().equals(doi))
-								.collect()
+					.collect()
-								.get(0)
+					.get(0)
-								.getSubject()
+					.getSubject()
-								.size());
+					.size());
 
 		List<StructuredProperty> sbjs = tmp
-				.filter(row -> row.getId().equals(doi))
+			.filter(row -> row.getId().equals(doi))
-				.flatMap(row -> row.getSubject().iterator())
+			.flatMap(row -> row.getSubject().iterator())
-				.collect();
+			.collect();
 
 		Assertions
-				.assertEquals(
+			.assertEquals(
-						true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("04 agricultural and veterinary sciences")));
+				true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("04 agricultural and veterinary sciences")));
 
 		Assertions
-				.assertEquals(
+			.assertEquals(
-						true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0404 agricultural biotechnology")));
+				true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0404 agricultural biotechnology")));
 		Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("040502 food science")));
 
 		Assertions
-				.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("03 medical and health sciences")));
+			.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("03 medical and health sciences")));
 		Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0303 health sciences")));
 		Assertions
-				.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("030309 nutrition & dietetics")));
+			.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("030309 nutrition & dietetics")));
 		Assertions
-				.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("1. No poverty")));
+			.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("1. No poverty")));
 
 	}
 
@@ -475,25 +473,25 @@ public class ProduceTest {
 		JavaRDD<Result> tmp = getResultJavaRDDPlusSDG();
 
 		List<StructuredProperty> sbjs_sdg = tmp
-				.filter(row -> row.getSubject() != null && row.getSubject().size() > 0)
+			.filter(row -> row.getSubject() != null && row.getSubject().size() > 0)
-				.flatMap(row -> row.getSubject().iterator())
+			.flatMap(row -> row.getSubject().iterator())
-				.filter(sbj -> sbj.getQualifier().getClassid().equals(Constants.SDG_CLASS_ID))
+			.filter(sbj -> sbj.getQualifier().getClassid().equals(Constants.SDG_CLASS_ID))
-				.collect();
+			.collect();
 
 		sbjs_sdg.forEach(sbj -> Assertions.assertEquals("SDG", sbj.getQualifier().getClassid()));
 		sbjs_sdg
-				.forEach(
+			.forEach(
-						sbj -> Assertions
+				sbj -> Assertions
-								.assertEquals(
+					.assertEquals(
-										"Sustainable Development Goals", sbj.getQualifier().getClassname()));
+						"Sustainable Development Goals", sbj.getQualifier().getClassname()));
 		sbjs_sdg
-				.forEach(
+			.forEach(
-						sbj -> Assertions
+				sbj -> Assertions
-								.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemeid()));
+					.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemeid()));
 		sbjs_sdg
-				.forEach(
+			.forEach(
-						sbj -> Assertions
+				sbj -> Assertions
-								.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemename()));
+					.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemename()));
 
 		sbjs_sdg.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getDeletedbyinference()));
 		sbjs_sdg.forEach(sbj -> Assertions.assertEquals(true, sbj.getDataInfo().getInferred()));
@@ -501,23 +499,23 @@ public class ProduceTest {
 		sbjs_sdg.forEach(sbj -> Assertions.assertEquals("", sbj.getDataInfo().getTrust()));
 		sbjs_sdg.forEach(sbj -> Assertions.assertEquals("update", sbj.getDataInfo().getInferenceprovenance()));
 		sbjs_sdg
-				.forEach(
+			.forEach(
-						sbj -> Assertions.assertEquals("subject:sdg", sbj.getDataInfo().getProvenanceaction().getClassid()));
+				sbj -> Assertions.assertEquals("subject:sdg", sbj.getDataInfo().getProvenanceaction().getClassid()));
 		sbjs_sdg
-				.forEach(
+			.forEach(
-						sbj -> Assertions
+				sbj -> Assertions
-								.assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname()));
+					.assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname()));
 		sbjs_sdg
-				.forEach(
+			.forEach(
-						sbj -> Assertions
+				sbj -> Assertions
-								.assertEquals(
+					.assertEquals(
-										ModelConstants.DNET_PROVENANCE_ACTIONS, sbj.getDataInfo().getProvenanceaction().getSchemeid()));
+						ModelConstants.DNET_PROVENANCE_ACTIONS, sbj.getDataInfo().getProvenanceaction().getSchemeid()));
 		sbjs_sdg
-				.forEach(
+			.forEach(
-						sbj -> Assertions
+				sbj -> Assertions
-								.assertEquals(
+					.assertEquals(
-										ModelConstants.DNET_PROVENANCE_ACTIONS,
+						ModelConstants.DNET_PROVENANCE_ACTIONS,
-										sbj.getDataInfo().getProvenanceaction().getSchemename()));
+						sbj.getDataInfo().getProvenanceaction().getSchemename()));
 	}
 
 }