Merge branch 'beta' into SWH_integration

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

@@ -32,18 +32,28 @@ import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import eu.dnetlib.dhp.schema.oaf.utils.PidType;
 import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
 
 public class CreateActionSetSparkJob implements Serializable {
 	public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
 	public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
+
+	// DOI-to-DOI citations
+	public static final String COCI = "COCI";
+
+	// PMID-to-PMID citations
+	public static final String POCI = "POCI";
+
 	private static final String DOI_PREFIX = "50|doi_________::";
 
 	private static final String PMID_PREFIX = "50|pmid________::";
+
 	private static final String TRUST = "0.91";
 
 	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
+
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
 	public static void main(final String[] args) throws IOException, ParseException {
@@ -67,7 +77,7 @@ public class CreateActionSetSparkJob implements Serializable {
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
 		final String inputPath = parser.get("inputPath");
-		log.info("inputPath {}", inputPath.toString());
+		log.info("inputPath {}", inputPath);
 
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath {}", outputPath);
@@ -81,19 +91,16 @@ public class CreateActionSetSparkJob implements Serializable {
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
-			spark -> {
-				extractContent(spark, inputPath, outputPath, shouldDuplicateRels);
-			});
+			spark -> extractContent(spark, inputPath, outputPath, shouldDuplicateRels));
 
 	}
 
 	private static void extractContent(SparkSession spark, String inputPath, String outputPath,
 		boolean shouldDuplicateRels) {
 
-		getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, "COCI")
-			.union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, "POCI"))
+		getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, COCI)
+			.union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI))
 			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
-
 	}
 
 	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath,
@@ -109,7 +116,7 @@ public class CreateActionSetSparkJob implements Serializable {
 					value, shouldDuplicateRels, prefix)
 						.iterator(),
 				Encoders.bean(Relation.class))
-			.filter((FilterFunction<Relation>) value -> value != null)
+			.filter((FilterFunction<Relation>) Objects::nonNull)
 			.toJavaRDD()
 			.map(p -> new AtomicAction(p.getClass(), p))
 			.mapToPair(
@@ -123,20 +130,28 @@ public class CreateActionSetSparkJob implements Serializable {
 		String prefix;
 		String citing;
 		String cited;
-		if (p.equals("COCI")) {
+
+		switch (p) {
+			case COCI:
 				prefix = DOI_PREFIX;
 				citing = prefix
-				+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCiting()));
+					+ IdentifierFactory
+						.md5(CleaningFunctions.normalizePidValue(PidType.doi.toString(), value.getCiting()));
 				cited = prefix
-				+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCited()));
-
-		} else {
+					+ IdentifierFactory
+						.md5(CleaningFunctions.normalizePidValue(PidType.doi.toString(), value.getCited()));
+				break;
+			case POCI:
 				prefix = PMID_PREFIX;
 				citing = prefix
-				+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("pmid", value.getCiting()));
+					+ IdentifierFactory
+						.md5(CleaningFunctions.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
 				cited = prefix
-				+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("pmid", value.getCited()));
-
+					+ IdentifierFactory
+						.md5(CleaningFunctions.normalizePidValue(PidType.pmid.toString(), value.getCited()));
+				break;
+			default:
+				throw new IllegalStateException("Invalid prefix: " + p);
 		}
 
 		if (!citing.equals(cited)) {
@@ -162,7 +177,7 @@ public class CreateActionSetSparkJob implements Serializable {
 	public static Relation getRelation(
 		String source,
 		String target,
-		String relclass) {
+		String relClass) {
 
 		return OafMapperUtils
 			.getRelation(
@@ -170,7 +185,7 @@ public class CreateActionSetSparkJob implements Serializable {
 				target,
 				ModelConstants.RESULT_RESULT,
 				ModelConstants.CITATION,
-				relclass,
+				relClass,
 				Arrays
 					.asList(
 						OafMapperUtils.keyValue(ModelConstants.OPENOCITATIONS_ID, ModelConstants.OPENOCITATIONS_NAME)),
@@ -183,6 +198,6 @@ public class CreateActionSetSparkJob implements Serializable {
 								ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
 						TRUST),
 				null);
-
 	}
+
 }

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

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.actionmanager.opencitations;
 
 import java.io.*;
 import java.io.Serializable;
+import java.util.Arrays;
 import java.util.Objects;
 import java.util.zip.GZIPOutputStream;
 import java.util.zip.ZipEntry;
@@ -37,7 +38,7 @@ public class GetOpenCitationsRefs implements Serializable {
 		parser.parseArgument(args);
 
 		final String[] inputFile = parser.get("inputFile").split(";");
-		log.info("inputFile {}", inputFile.toString());
+		log.info("inputFile {}", Arrays.asList(inputFile));
 
 		final String workingPath = parser.get("workingPath");
 		log.info("workingPath {}", workingPath);

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

@@ -7,6 +7,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.IOException;
 import java.io.Serializable;
+import java.util.Arrays;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
@@ -42,7 +43,7 @@ public class ReadCOCI implements Serializable {
 		log.info("outputPath: {}", outputPath);
 
 		final String[] inputFile = parser.get("inputFile").split(";");
-		log.info("inputFile {}", inputFile.toString());
+		log.info("inputFile {}", Arrays.asList(inputFile));
 		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
@@ -74,10 +75,10 @@ public class ReadCOCI implements Serializable {
 
 	private static void doRead(SparkSession spark, String workingPath, String[] inputFiles,
 		String outputPath,
-		String delimiter, String format) throws IOException {
+		String delimiter, String format) {
 
 		for (String inputFile : inputFiles) {
-			String p_string = workingPath + "/" + inputFile + ".gz";
+			String pString = workingPath + "/" + inputFile + ".gz";
 
 			Dataset<Row> cociData = spark
 				.read()
@@ -86,7 +87,7 @@ public class ReadCOCI implements Serializable {
 				.option("inferSchema", "true")
 				.option("header", "true")
 				.option("quotes", "\"")
-				.load(p_string)
+				.load(pString)
 				.repartition(100);
 
 			cociData.map((MapFunction<Row, COCI>) row -> {

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json

@@ -16,15 +16,11 @@
     "paramLongName": "isSparkSessionManaged",
     "paramDescription": "the hdfs name node",
     "paramRequired": false
-  },  {
+  },
+  {
     "paramName": "sdr",
     "paramLongName": "shouldDuplicateRels",
-  "paramDescription": "the hdfs name node",
+    "paramDescription": "activates/deactivates the construction of bidirectional relations Cites/IsCitedBy",
     "paramRequired": false
-},{
-  "paramName": "p",
-  "paramLongName": "prefix",
-  "paramDescription": "the hdfs name node",
-  "paramRequired": true
-}
+  }
 ]

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

@@ -34,6 +34,7 @@
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
+
     <action name="download">
         <shell xmlns="uri:oozie:shell-action:0.2">
             <job-tracker>${jobTracker}</job-tracker>
@@ -54,6 +55,7 @@
         <ok to="extract"/>
         <error to="Kill"/>
     </action>
+
     <action name="extract">
         <java>
             <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
@@ -112,7 +114,6 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${workingPath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
-            <arg>--prefix</arg><arg>${prefix}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>