Merge branch 'beta' into peer_reviewed

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

@@ -12,6 +12,7 @@ import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaPairRDD;
 import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.MapFunction;
@@ -30,12 +31,16 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
 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.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";
-	private static final String ID_PREFIX = "50|doi_________::";
+	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);
@@ -84,34 +89,56 @@ public class CreateActionSetSparkJob implements Serializable {
 
 	private static void extractContent(SparkSession spark, String inputPath, String outputPath,
 		boolean shouldDuplicateRels) {
-		spark
+
+		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,
+		boolean shouldDuplicateRels, String prefix) {
+		return spark
 			.read()
-			.textFile(inputPath + "/*")
+			.textFile(inputPath + "/" + prefix + "/" + prefix + "_JSON/*")
 			.map(
 				(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
 				Encoders.bean(COCI.class))
 			.flatMap(
-				(FlatMapFunction<COCI, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
+				(FlatMapFunction<COCI, Relation>) value -> createRelation(
+					value, shouldDuplicateRels, prefix)
+						.iterator(),
 				Encoders.bean(Relation.class))
 			.filter((FilterFunction<Relation>) value -> value != null)
 			.toJavaRDD()
 			.map(p -> new AtomicAction(p.getClass(), p))
 			.mapToPair(
 				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
-
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
 	}
 
-	private static List<Relation> createRelation(COCI value, boolean duplicate) {
+	private static List<Relation> createRelation(COCI value, boolean duplicate, String p) {
 
 		List<Relation> relationList = new ArrayList<>();
-
-		String citing = ID_PREFIX
+		String prefix;
+		String citing;
+		String cited;
+		if (p.equals("COCI")) {
+			prefix = DOI_PREFIX;
+			citing = prefix
 				+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCiting()));
-		final String cited = ID_PREFIX
+			cited = prefix
 				+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCited()));
 
+		} else {
+			prefix = PMID_PREFIX;
+			citing = prefix
+				+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("pmid", value.getCiting()));
+			cited = prefix
+				+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("pmid", value.getCited()));
+
+		}
+
 		if (!citing.equals(cited)) {
 			relationList
 				.add(
@@ -120,7 +147,7 @@ public class CreateActionSetSparkJob implements Serializable {
 						cited, ModelConstants.CITES));
 
 			if (duplicate && value.getCiting().endsWith(".refs")) {
-				citing = ID_PREFIX + IdentifierFactory
+				citing = prefix + IdentifierFactory
 					.md5(
 						CleaningFunctions
 							.normalizePidValue(
@@ -132,59 +159,30 @@ public class CreateActionSetSparkJob implements Serializable {
 		return relationList;
 	}
 
-	private static Collection<Relation> getRelations(String citing, String cited) {
-
-		return Arrays
-			.asList(
-				getRelation(citing, cited, ModelConstants.CITES),
-				getRelation(cited, citing, ModelConstants.IS_CITED_BY));
-	}
-
 	public static Relation getRelation(
 		String source,
 		String target,
 		String relclass) {
-		Relation r = new Relation();
-		r.setCollectedfrom(getCollectedFrom());
-		r.setSource(source);
-		r.setTarget(target);
-		r.setRelClass(relclass);
-		r.setRelType(ModelConstants.RESULT_RESULT);
-		r.setSubRelType(ModelConstants.CITATION);
-		r
-			.setDataInfo(
-				getDataInfo());
-		return r;
-	}
 
-	public static List<KeyValue> getCollectedFrom() {
-		KeyValue kv = new KeyValue();
-		kv.setKey(ModelConstants.OPENOCITATIONS_ID);
-		kv.setValue(ModelConstants.OPENOCITATIONS_NAME);
-
-		return Arrays.asList(kv);
-	}
-
-	public static DataInfo getDataInfo() {
-		DataInfo di = new DataInfo();
-		di.setInferred(false);
-		di.setDeletedbyinference(false);
-		di.setTrust(TRUST);
-
-		di
-			.setProvenanceaction(
-				getQualifier(OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS));
-		return di;
-	}
-
-	public static Qualifier getQualifier(String class_id, String class_name,
-		String qualifierSchema) {
-		Qualifier pa = new Qualifier();
-		pa.setClassid(class_id);
-		pa.setClassname(class_name);
-		pa.setSchemeid(qualifierSchema);
-		pa.setSchemename(qualifierSchema);
-		return pa;
-	}
+		return OafMapperUtils
+			.getRelation(
+				source,
+				target,
+				ModelConstants.RESULT_RESULT,
+				ModelConstants.CITATION,
+				relclass,
+				Arrays
+					.asList(
+						OafMapperUtils.keyValue(ModelConstants.OPENOCITATIONS_ID, ModelConstants.OPENOCITATIONS_NAME)),
+				OafMapperUtils
+					.dataInfo(
+						false, null, false, false,
+						OafMapperUtils
+							.qualifier(
+								OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME,
+								ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
+						TRUST),
+				null);
 
 	}
+}

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

@@ -45,6 +45,9 @@ public class GetOpenCitationsRefs implements Serializable {
 		final String hdfsNameNode = parser.get("hdfsNameNode");
 		log.info("hdfsNameNode {}", hdfsNameNode);
 
+		final String prefix = parser.get("prefix");
+		log.info("prefix {}", prefix);
+
 		Configuration conf = new Configuration();
 		conf.set("fs.defaultFS", hdfsNameNode);
 
@@ -53,30 +56,31 @@ public class GetOpenCitationsRefs implements Serializable {
 		GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
 
 		for (String file : inputFile) {
-			ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem);
+			ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem, prefix);
 		}
 
 	}
 
-	private void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
+	private void doExtract(String inputFile, String workingPath, FileSystem fileSystem, String prefix)
 		throws IOException {
 
 		final Path path = new Path(inputFile);
 
 		FSDataInputStream oc_zip = fileSystem.open(path);
 
-		int count = 1;
+		// int count = 1;
 		try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
 			ZipEntry entry = null;
 			while ((entry = zis.getNextEntry()) != null) {
 
 				if (!entry.isDirectory()) {
 					String fileName = entry.getName();
-					fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
-					count++;
+					// fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
+					fileName = fileName.substring(0, fileName.lastIndexOf("."));
+					// count++;
 					try (
 						FSDataOutputStream out = fileSystem
-							.create(new Path(workingPath + "/COCI/" + fileName + ".gz"));
+							.create(new Path(workingPath + "/" + prefix + "/" + fileName + ".gz"));
 						GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
 
 						IOUtils.copy(zis, gzipOs);

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

@@ -49,6 +49,9 @@ public class ReadCOCI implements Serializable {
 		final String workingPath = parser.get("workingPath");
 		log.info("workingPath {}", workingPath);
 
+		final String format = parser.get("format");
+		log.info("format {}", format);
+
 		SparkConf sconf = new SparkConf();
 
 		final String delimiter = Optional
@@ -64,13 +67,14 @@ public class ReadCOCI implements Serializable {
 					workingPath,
 					inputFile,
 					outputPath,
-					delimiter);
+					delimiter,
+					format);
 			});
 	}
 
 	private static void doRead(SparkSession spark, String workingPath, String[] inputFiles,
 		String outputPath,
-		String delimiter) throws IOException {
+		String delimiter, String format) throws IOException {
 
 		for (String inputFile : inputFiles) {
 			String p_string = workingPath + "/" + inputFile + ".gz";
@@ -87,9 +91,15 @@ public class ReadCOCI implements Serializable {
 
 			cociData.map((MapFunction<Row, COCI>) row -> {
 				COCI coci = new COCI();
-				coci.setOci(row.getString(0));
+				if (format.equals("COCI")) {
 					coci.setCiting(row.getString(1));
 					coci.setCited(row.getString(2));
+				} else {
+					coci.setCiting(String.valueOf(row.getInt(1)));
+					coci.setCited(String.valueOf(row.getInt(2)));
+				}
+				coci.setOci(row.getString(0));
+
 				return coci;
 			}, Encoders.bean(COCI.class))
 				.write()

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

@@ -21,5 +21,10 @@
   "paramLongName": "shouldDuplicateRels",
   "paramDescription": "the hdfs name node",
   "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/input_parameters.json

@@ -16,5 +16,11 @@
     "paramLongName": "hdfsNameNode",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
+  },
+  {
+    "paramName": "p",
+    "paramLongName": "prefix",
+    "paramDescription": "COCI or POCI",
+    "paramRequired": true
   }
 ]

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

@@ -30,6 +30,11 @@
     "paramLongName": "inputFile",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
+  }, {
+  "paramName": "f",
+  "paramLongName": "format",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": true
 }
 ]
 

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

@@ -46,7 +46,7 @@
             </configuration>
             <exec>download.sh</exec>
             <argument>${filelist}</argument>
-            <argument>${workingPath}/Original</argument>
+            <argument>${workingPath}/${prefix}/Original</argument>
             <env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
             <file>download.sh</file>
             <capture-output/>
@@ -59,7 +59,8 @@
             <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
             <arg>--inputFile</arg><arg>${inputFile}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}/${prefix}</arg>
+            <arg>--prefix</arg><arg>${prefix}</arg>
         </java>
         <ok to="read"/>
         <error to="Kill"/>
@@ -82,10 +83,11 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}/COCI</arg>
-            <arg>--outputPath</arg><arg>${workingPath}/COCI_JSON/</arg>
+            <arg>--workingPath</arg><arg>${workingPath}/${prefix}/${prefix}</arg>
+            <arg>--outputPath</arg><arg>${workingPath}/${prefix}/${prefix}_JSON/</arg>
             <arg>--delimiter</arg><arg>${delimiter}</arg>
             <arg>--inputFile</arg><arg>${inputFileCoci}</arg>
+            <arg>--format</arg><arg>${prefix}</arg>
         </spark>
         <ok to="create_actionset"/>
         <error to="Kill"/>
@@ -108,8 +110,9 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--inputPath</arg><arg>${workingPath}/COCI_JSON</arg>
+            <arg>--inputPath</arg><arg>${workingPath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
+            <arg>--prefix</arg><arg>${prefix}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>