Merge pull request 'Open Citation integration' (#401) from ocnew into beta

Reviewed-on: #401

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

@@ -22,12 +22,14 @@ import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.*;
 import eu.dnetlib.dhp.utils.DHPUtils;
@@ -37,16 +39,12 @@ 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 ARXIV_PREFIX = "50|arXiv_______::";
 
+	private static final String PMCID_PREFIX = "50|pmcid_______::";
 	private static final String TRUST = "0.91";
 
 	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
@@ -79,38 +77,30 @@ public class CreateActionSetSparkJob implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath {}", outputPath);
 
-		final boolean shouldDuplicateRels = Optional
-			.ofNullable(parser.get("shouldDuplicateRels"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.FALSE);
-
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
-			spark -> extractContent(spark, inputPath, outputPath, shouldDuplicateRels));
+			spark -> extractContent(spark, inputPath, outputPath));
 
 	}
 
-	private static void extractContent(SparkSession spark, String inputPath, String outputPath,
+	private static void extractContent(SparkSession spark, String inputPath, String outputPath) {
-		boolean shouldDuplicateRels) {
 
-		getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, COCI)
+		getTextTextJavaPairRDD(spark, inputPath)
-			.union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI))
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);// , GzipCodec.class);
-			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
 	}
 
-	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath,
+	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath) {
-		boolean shouldDuplicateRels, String prefix) {
 		return spark
 			.read()
-			.textFile(inputPath + "/" + prefix + "/" + prefix + "_JSON/*")
+			.textFile(inputPath)
 			.map(
 				(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
 				Encoders.bean(COCI.class))
 			.flatMap(
 				(FlatMapFunction<COCI, Relation>) value -> createRelation(
-					value, shouldDuplicateRels, prefix)
+					value)
 						.iterator(),
 				Encoders.bean(Relation.class))
 			.filter((FilterFunction<Relation>) Objects::nonNull)
@@ -121,34 +111,68 @@ public class CreateActionSetSparkJob implements Serializable {
 					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
 	}
 
-	private static List<Relation> createRelation(COCI value, boolean duplicate, String p) {
+	private static List<Relation> createRelation(COCI value) throws JsonProcessingException {
 
 		List<Relation> relationList = new ArrayList<>();
-		String prefix;
+
 		String citing;
 		String cited;
 
-		switch (p) {
+		switch (value.getCiting_pid()) {
-			case COCI:
+			case "doi":
-				prefix = DOI_PREFIX;
+				citing = DOI_PREFIX
-				citing = prefix
 					+ IdentifierFactory
 						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
-				cited = prefix
+				break;
+			case "pmid":
+				citing = PMID_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
+				break;
+			case "arxiv":
+				citing = ARXIV_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCiting()));
+				break;
+			case "pmcid":
+				citing = PMCID_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCiting()));
+				break;
+			case "isbn":
+			case "issn":
+				return relationList;
+
+			default:
+				throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
+		}
+
+		switch (value.getCited_pid()) {
+			case "doi":
+				cited = DOI_PREFIX
 					+ IdentifierFactory
 						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited()));
 				break;
-			case POCI:
+			case "pmid":
-				prefix = PMID_PREFIX;
+				cited = PMID_PREFIX
-				citing = prefix
-					+ IdentifierFactory
-						.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
-				cited = prefix
 					+ IdentifierFactory
 						.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCited()));
 				break;
+			case "arxiv":
+				cited = ARXIV_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCited()));
+				break;
+			case "pmcid":
+				cited = PMCID_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCited()));
+				break;
+			case "isbn":
+			case "issn":
+				return relationList;
 			default:
-				throw new IllegalStateException("Invalid prefix: " + p);
+				throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
 		}
 
 		if (!citing.equals(cited)) {
@@ -157,15 +181,6 @@ public class CreateActionSetSparkJob implements Serializable {
 					getRelation(
 						citing,
 						cited, ModelConstants.CITES));
-
-			if (duplicate && value.getCiting().endsWith(".refs")) {
-				citing = prefix + IdentifierFactory
-					.md5(
-						CleaningFunctions
-							.normalizePidValue(
-								"doi", value.getCiting().substring(0, value.getCiting().indexOf(".refs"))));
-				relationList.add(getRelation(citing, cited, ModelConstants.CITES));
-			}
 		}
 
 		return relationList;

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

@@ -12,10 +12,7 @@ import java.util.zip.ZipInputStream;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FSDataInputStream;
+import org.apache.hadoop.fs.*;
-import org.apache.hadoop.fs.FSDataOutputStream;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -37,17 +34,17 @@ public class GetOpenCitationsRefs implements Serializable {
 
 		parser.parseArgument(args);
 
-		final String[] inputFile = parser.get("inputFile").split(";");
+//		final String[] inputFile = parser.get("inputFile").split(";");
-		log.info("inputFile {}", Arrays.asList(inputFile));
+//		log.info("inputFile {}", Arrays.asList(inputFile));
 
-		final String workingPath = parser.get("workingPath");
+		final String inputPath = parser.get("inputPath");
-		log.info("workingPath {}", workingPath);
+		log.info("inputPath {}", inputPath);
 
 		final String hdfsNameNode = parser.get("hdfsNameNode");
 		log.info("hdfsNameNode {}", hdfsNameNode);
 
-		final String prefix = parser.get("prefix");
+		final String outputPath = parser.get("outputPath");
-		log.info("prefix {}", prefix);
+		log.info("outputPath {}", outputPath);
 
 		Configuration conf = new Configuration();
 		conf.set("fs.defaultFS", hdfsNameNode);
@@ -56,20 +53,20 @@ public class GetOpenCitationsRefs implements Serializable {
 
 		GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
 
-		for (String file : inputFile) {
+		ocr.doExtract(inputPath, outputPath, fileSystem);
-			ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem, prefix);
-		}
 
 	}
 
-	private void doExtract(String inputFile, String workingPath, FileSystem fileSystem, String prefix)
+	private void doExtract(String inputPath, String outputPath, FileSystem fileSystem)
 		throws IOException {
 
-		final Path path = new Path(inputFile);
+		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
-
+			.listFiles(
-		FSDataInputStream oc_zip = fileSystem.open(path);
+				new Path(inputPath), true);
-
+		while (fileStatusListIterator.hasNext()) {
-		// int count = 1;
+			LocatedFileStatus fileStatus = fileStatusListIterator.next();
+			// do stuff with the file like ...
+			FSDataInputStream oc_zip = fileSystem.open(fileStatus.getPath());
 			try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
 				ZipEntry entry = null;
 				while ((entry = zis.getNextEntry()) != null) {
@@ -81,7 +78,7 @@ public class GetOpenCitationsRefs implements Serializable {
 						// count++;
 						try (
 							FSDataOutputStream out = fileSystem
-							.create(new Path(workingPath + "/" + prefix + "/" + fileName + ".gz"));
+								.create(new Path(outputPath + "/" + fileName + ".gz"));
 							GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
 
 							IOUtils.copy(zis, gzipOs);
@@ -92,6 +89,7 @@ public class GetOpenCitationsRefs implements Serializable {
 				}
 
 			}
+		}
 
 	}
 

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

@@ -0,0 +1,171 @@
+
+package eu.dnetlib.dhp.actionmanager.opencitations;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.Arrays;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.stream.Collectors;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FSDataInputStream;
+import org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.ForeachFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import scala.Tuple2;
+
+/**
+ * @author miriam.baglioni
+ * @Date 29/02/24
+ */
+public class MapOCIdsInPids implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
+	private static final String DELIMITER = ",";
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static void main(final String[] args) throws IOException, ParseException {
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					Objects
+						.requireNonNull(
+							MapOCIdsInPids.class
+								.getResourceAsStream(
+									"/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json"))));
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String inputPath = parser.get("inputPath");
+		log.info("inputPath {}", inputPath);
+
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}", outputPath);
+
+		final String nameNode = parser.get("nameNode");
+		log.info("nameNode {}", nameNode);
+
+		unzipCorrespondenceFile(inputPath, nameNode);
+		SparkConf conf = new SparkConf();
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> mapIdentifiers(spark, inputPath, outputPath));
+
+	}
+
+	private static void unzipCorrespondenceFile(String inputPath, String hdfsNameNode) throws IOException {
+		Configuration conf = new Configuration();
+		conf.set("fs.defaultFS", hdfsNameNode);
+
+		final Path path = new Path(inputPath + "/correspondence/omid.zip");
+		FileSystem fileSystem = FileSystem.get(conf);
+
+		FSDataInputStream project_zip = fileSystem.open(path);
+
+		try (ZipInputStream zis = new ZipInputStream(project_zip)) {
+			ZipEntry entry = null;
+			while ((entry = zis.getNextEntry()) != null) {
+
+				if (!entry.isDirectory()) {
+					String fileName = entry.getName();
+					byte buffer[] = new byte[1024];
+					int count;
+
+					try (
+						FSDataOutputStream out = fileSystem
+							.create(new Path(inputPath + "/correspondence/omid.csv"))) {
+
+						while ((count = zis.read(buffer, 0, buffer.length)) != -1)
+							out.write(buffer, 0, count);
+
+					}
+
+				}
+
+			}
+
+		}
+
+	}
+
+	private static void mapIdentifiers(SparkSession spark, String inputPath, String outputPath) {
+		Dataset<COCI> coci = spark
+			.read()
+			.textFile(inputPath + "/JSON")
+			.map(
+				(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
+				Encoders.bean(COCI.class));
+
+		Dataset<Tuple2<String, String>> correspondenceData = spark
+			.read()
+			.format("csv")
+			.option("sep", DELIMITER)
+			.option("inferSchema", "true")
+			.option("header", "true")
+			.option("quotes", "\"")
+			.load(inputPath + "/correspondence/omid.csv")
+			.repartition(5000)
+			.flatMap((FlatMapFunction<Row, Tuple2<String, String>>) r -> {
+				String ocIdentifier = r.getAs("omid");
+				String[] correspondentIdentifiers = ((String) r.getAs("id")).split(" ");
+				return Arrays
+					.stream(correspondentIdentifiers)
+					.map(ci -> new Tuple2<String, String>(ocIdentifier, ci))
+					.collect(Collectors.toList())
+					.iterator();
+			}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
+
+		Dataset<COCI> mappedCitingDataset = coci
+			.joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1")))
+			.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
+				String correspondent = t2._2()._2();
+				t2._1().setCiting_pid(correspondent.substring(0, correspondent.indexOf(":")));
+				t2._1().setCiting(correspondent.substring(correspondent.indexOf(":") + 1));
+				return t2._1();
+			}, Encoders.bean(COCI.class));
+
+		mappedCitingDataset
+			.joinWith(correspondenceData, mappedCitingDataset.col("cited").equalTo(correspondenceData.col("_1")))
+			.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
+				String correspondent = t2._2()._2();
+				t2._1().setCited_pid(correspondent.substring(0, correspondent.indexOf(":")));
+				t2._1().setCited(correspondent.substring(correspondent.indexOf(":") + 1));
+				return t2._1();
+			}, Encoders.bean(COCI.class))
+			.write()
+			.mode(SaveMode.Append)
+			.option("compression", "gzip")
+			.json(outputPath);
+
+			}
+
+}

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

@@ -12,11 +12,9 @@ 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.hadoop.fs.*;
-import org.apache.hadoop.fs.LocatedFileStatus;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.fs.RemoteIterator;
 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;
@@ -42,19 +40,21 @@ public class ReadCOCI implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
-		final String[] inputFile = parser.get("inputFile").split(";");
+		final String hdfsNameNode = parser.get("hdfsNameNode");
-		log.info("inputFile {}", Arrays.asList(inputFile));
+		log.info("hdfsNameNode {}", hdfsNameNode);
+
 		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-		final String workingPath = parser.get("workingPath");
+		final String workingPath = parser.get("inputPath");
 		log.info("workingPath {}", workingPath);
 
-		final String format = parser.get("format");
-		log.info("format {}", format);
-
 		SparkConf sconf = new SparkConf();
 
+		Configuration conf = new Configuration();
+		conf.set("fs.defaultFS", hdfsNameNode);
+
+		FileSystem fileSystem = FileSystem.get(conf);
 		final String delimiter = Optional
 			.ofNullable(parser.get("delimiter"))
 			.orElse(DEFAULT_DELIMITER);
@@ -66,20 +66,21 @@ public class ReadCOCI implements Serializable {
 				doRead(
 					spark,
 					workingPath,
-					inputFile,
+					fileSystem,
 					outputPath,
-					delimiter,
+					delimiter);
-					format);
 			});
 	}
 
-	private static void doRead(SparkSession spark, String workingPath, String[] inputFiles,
+	private static void doRead(SparkSession spark, String workingPath, FileSystem fileSystem,
 		String outputPath,
-		String delimiter, String format) {
+		String delimiter) throws IOException {
-
+		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
-		for (String inputFile : inputFiles) {
+			.listFiles(
-			String pString = workingPath + "/" + inputFile + ".gz";
+				new Path(workingPath), true);
-
+		while (fileStatusListIterator.hasNext()) {
+			LocatedFileStatus fileStatus = fileStatusListIterator.next();
+			log.info("extracting file {}", fileStatus.getPath().toString());
 			Dataset<Row> cociData = spark
 				.read()
 				.format("csv")
@@ -87,26 +88,26 @@ public class ReadCOCI implements Serializable {
 				.option("inferSchema", "true")
 				.option("header", "true")
 				.option("quotes", "\"")
-				.load(pString)
+				.load(fileStatus.getPath().toString())
 				.repartition(100);
 
 			cociData.map((MapFunction<Row, COCI>) row -> {
+
 				COCI coci = new COCI();
-				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))
+				.filter((FilterFunction<COCI>) c -> c != null)
 				.write()
-				.mode(SaveMode.Overwrite)
+				.mode(SaveMode.Append)
 				.option("compression", "gzip")
-				.json(outputPath + inputFile);
+				.json(outputPath);
+			fileSystem.rename(fileStatus.getPath(), new Path("/tmp/miriam/OC/DONE"));
 		}
 
 	}

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

@@ -9,8 +9,10 @@ public class COCI implements Serializable {
 	private String oci;
 
 	private String citing;
+	private String citing_pid;
 
 	private String cited;
+	private String cited_pid;
 
 	public String getOci() {
 		return oci;
@@ -25,6 +27,8 @@ public class COCI implements Serializable {
 	}
 
 	public void setCiting(String citing) {
+		if (citing != null && citing.startsWith("omid:"))
+			citing = citing.substring(5);
 		this.citing = citing;
 	}
 
@@ -33,7 +37,24 @@ public class COCI implements Serializable {
 	}
 
 	public void setCited(String cited) {
+		if (cited != null && cited.startsWith("omid:"))
+			cited = cited.substring(5);
 		this.cited = cited;
 	}
 
+	public String getCiting_pid() {
+		return citing_pid;
+	}
+
+	public void setCiting_pid(String citing_pid) {
+		this.citing_pid = citing_pid;
+	}
+
+	public String getCited_pid() {
+		return cited_pid;
+	}
+
+	public void setCited_pid(String cited_pid) {
+		this.cited_pid = cited_pid;
+	}
 }

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

@@ -1,13 +1,13 @@
 [
   {
-    "paramName": "if",
+    "paramName": "ip",
-    "paramLongName": "inputFile",
+    "paramLongName": "inputPath",
     "paramDescription": "the zipped opencitations file",
     "paramRequired": true
   },
   {
-    "paramName": "wp",
+    "paramName": "op",
-    "paramLongName": "workingPath",
+    "paramLongName": "outputPath",
     "paramDescription": "the working path",
     "paramRequired": true
   },
@@ -16,11 +16,5 @@
     "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

@@ -1,7 +1,7 @@
 [
   {
-    "paramName": "wp",
+    "paramName": "ip",
-    "paramLongName": "workingPath",
+    "paramLongName": "inputPath",
     "paramDescription": "the zipped opencitations file",
     "paramRequired": true
   },
@@ -24,15 +24,9 @@
     "paramLongName": "outputPath",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
-  },
-  {
-    "paramName": "if",
-    "paramLongName": "inputFile",
-    "paramDescription": "the hdfs name node",
-    "paramRequired": true
   },  {
-  "paramName": "f",
+  "paramName": "nn",
-  "paramLongName": "format",
+  "paramLongName": "hdfsNameNode",
   "paramDescription": "the hdfs name node",
   "paramRequired": true
 }

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

@@ -27,7 +27,9 @@
             <case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
             <case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case>
             <case to="read">${wf:conf('resumeFrom') eq 'ReadContent'}</case>
-            <default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed -->
+            <case to="remap">${wf:conf('resumeFrom') eq 'MapContent'}</case>
+            <case to="create_actionset">${wf:conf('resumeFrom') eq 'CreateAS'}</case>
+            <default to="deleteoutputpath"/> <!-- first action to be done when downloadDump is to be performed -->
         </switch>
     </decision>
 
@@ -35,6 +37,15 @@
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
+    <action name="deleteoutputpath">
+        <fs>
+            <delete path='${inputPath}'/>
+            <mkdir path='${inputPath}'/>
+        </fs>
+        <ok to="download"/>
+        <error to="Kill"/>
+    </action>
+
     <action name="download">
         <shell xmlns="uri:oozie:shell-action:0.2">
             <job-tracker>${jobTracker}</job-tracker>
@@ -47,7 +58,28 @@
             </configuration>
             <exec>download.sh</exec>
             <argument>${filelist}</argument>
-            <argument>${workingPath}/${prefix}/Original</argument>
+            <argument>${inputPath}/Original</argument>
+            <env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
+            <file>download.sh</file>
+            <capture-output/>
+        </shell>
+        <ok to="download_correspondence"/>
+        <error to="Kill"/>
+    </action>
+<!--    downloads the correspondence from the omid and the pid (doi, pmid etc)-->
+    <action name="download_correspondence">
+        <shell xmlns="uri:oozie:shell-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <configuration>
+                <property>
+                    <name>mapred.job.queue.name</name>
+                    <value>${queueName}</value>
+                </property>
+            </configuration>
+            <exec>download_corr.sh</exec>
+            <argument>${filecorrespondence}</argument>
+            <argument>${inputPath}/correspondence</argument>
             <env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
             <file>download.sh</file>
             <capture-output/>
@@ -60,9 +92,19 @@
         <java>
             <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
-            <arg>--inputFile</arg><arg>${inputFile}</arg>
+            <arg>--inputPath</arg><arg>${inputPath}/Original</arg>
-            <arg>--workingPath</arg><arg>${workingPath}/${prefix}</arg>
+            <arg>--outputPath</arg><arg>${inputPath}/Extracted</arg>
-            <arg>--prefix</arg><arg>${prefix}</arg>
+        </java>
+        <ok to="read"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="extract_correspondence">
+        <java>
+            <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
+            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
+            <arg>--inputPath</arg><arg>${inputPath}/correspondence</arg>
+            <arg>--outputPath</arg><arg>${inputPath}/correspondence_extracted</arg>
         </java>
         <ok to="read"/>
         <error to="Kill"/>
@@ -85,11 +127,35 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}/${prefix}/${prefix}</arg>
+            <arg>--inputPath</arg><arg>${inputPath}/Extracted</arg>
-            <arg>--outputPath</arg><arg>${workingPath}/${prefix}/${prefix}_JSON/</arg>
+            <arg>--outputPath</arg><arg>${inputPath}/JSON</arg>
             <arg>--delimiter</arg><arg>${delimiter}</arg>
-            <arg>--inputFile</arg><arg>${inputFileCoci}</arg>
+            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
-            <arg>--format</arg><arg>${prefix}</arg>
+        </spark>
+        <ok to="remap"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="remap">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the AS for OC</name>
+            <class>eu.dnetlib.dhp.actionmanager.opencitations.MapOCIdsInPids</class>
+            <jar>dhp-aggregation-${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=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}</arg>
+            <arg>--outputPath</arg><arg>${outputPathExtraction}</arg>
+            <arg>--nameNode</arg><arg>${nameNode}</arg>
         </spark>
         <ok to="create_actionset"/>
         <error to="Kill"/>
@@ -112,7 +178,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--inputPath</arg><arg>${workingPath}</arg>
+            <arg>--inputPath</arg><arg>${outputPathExtraction}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
         </spark>
         <ok to="End"/>

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

@@ -0,0 +1,25 @@
+[
+  {
+    "paramName": "ip",
+    "paramLongName": "inputPath",
+    "paramDescription": "the zipped opencitations file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "the working path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManged",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },{
+  "paramName": "nn",
+  "paramLongName": "nameNode",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": true
+}
+]

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java

@@ -76,7 +76,7 @@ public class CreateOpenCitationsASTest {
 
 		String inputPath = getClass()
 			.getResource(
-				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/jsonforas")
 			.getPath();
 
 		CreateActionSetSparkJob
@@ -84,8 +84,6 @@ public class CreateOpenCitationsASTest {
 				new String[] {
 					"-isSparkSessionManaged",
 					Boolean.FALSE.toString(),
-					"-shouldDuplicateRels",
-					Boolean.TRUE.toString(),
 					"-inputPath",
 					inputPath,
 					"-outputPath",
@@ -99,9 +97,10 @@ public class CreateOpenCitationsASTest {
 			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
 			.map(aa -> ((Relation) aa.getPayload()));
 
-		assertEquals(31, tmp.count());
+		Assertions.assertEquals(27, tmp.count());
+		tmp.foreach(r -> Assertions.assertEquals(1, r.getCollectedfrom().size()));
 
-		// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
+		tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
 
 	}
 

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/RemapTest.java

@@ -0,0 +1,90 @@
+
+package eu.dnetlib.dhp.actionmanager.opencitations;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.LocalFileSystem;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
+
+/**
+ * @author miriam.baglioni
+ * @Date 07/03/24
+ */
+public class RemapTest {
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+	private static final Logger log = LoggerFactory
+		.getLogger(RemapTest.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+			.createTempDirectory(RemapTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(RemapTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(RemapTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void testRemap() throws Exception {
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap")
+			.getPath();
+
+		MapOCIdsInPids
+			.main(
+				new String[] {
+					"-isSparkSessionManged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/out/",
+					"-nameNode", "input1;input2;input3;input4;input5"
+				});
+
+	}
+}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/JSON/part-00000

@@ -0,0 +1,31 @@
+{"cited":"br/061201599020", "citing":"br/06203041400","oci":"oci:06701327944-06504326071"}
+{"cited":"br/061201599020","citing":"br/06502272390","oci":"oci:06502272390-061301355525"}
+{"cited":"br/061201599020",   "citing":"br/06120941789","oci":"oci:0670804699-067055659"}
+{"cited":"br/06210273177","citing":"br/06203041400","oci":"oci:061502003994-062201281456"}
+{"cited":"br/06210273177",  "citing":"br/06502272390","oci":"oci:06502272390-0660806688"}
+{"cited":"br/06210273177",  "citing":"br/06120941789","oci":"oci:06502307119-0620223645"}
+{"cited":"br/0660613430","citing":"br/06203041400","oci":"oci:061502004011-061902692285"}
+{"cited":"br/0660613430",  "citing":"br/06502272390","oci":"oci:0660549063-0610398792"}
+{"cited":"br/0660613430", "citing":"br/06120941789","oci":"oci:06420189324-06301543046"}
+{"cited":"br/062602732073","citing":"br/06203041400","oci":"oci:06380130275-061502004367"}
+{"cited":"br/062602732073","citing":"br/06502272390","oci":"oci:062403449086-062501448395"}
+{"cited":"br/062602732073","citing":"br/06120941789","oci":"oci:06420189328-061202007182"}
+{"cited":"br/061103703697","citing":"br/06203041400","oci":"oci:062603906965-061701362658"}
+{"cited":"br/061103703697", "citing":"br/06502272390","oci":"oci:0670294309-06104327031"}
+{"cited":"br/061103703697","citing":"br/06120941789","oci":"oci:061702060228-061301712529"}
+{"cited":"br/06230199640", "citing":"br/0670517081","oci":"oci:06901104174-06503692526"}
+{"cited":"br/061703513967","citing":"br/061702310822","oci":"oci:061702310822-061703513967"}
+{"cited":"br/062104002953","citing":"br/061702311472","oci":"oci:061702311472-062104002953"}
+{"cited":"br/061101204417","citing":"br/062102701590","oci":"oci:062102701590-061101204417"}
+{"cited":"br/062403787088","citing":"br/061401499173","oci":"oci:061401499173-062403787088"}
+{"cited":"br/061203576338","citing":"br/06110279619","oci":"oci:06110279619-061203576338"}
+{"cited":"br/061601962207","citing":"br/061502004018","oci":"oci:061502004018-061601962207"}
+{"cited":"br/06101014588", "citing":"br/061502004027","oci":"oci:061502004027-06101014588"}
+{"cited":"br/06704040804", "citing":"br/06220799044","oci":"oci:06220799044-06704040804"}
+{"cited":"br/061401105151","citing":"br/061502004037","oci":"oci:061502004037-061401105151"}
+{"cited":"br/0640821079",  "citing":"br/061702311537","oci":"oci:061702311537-0640821079"}
+{"cited":"br/06604165310", "citing":"br/062501970289","oci":"oci:062501970289-06604165310"}
+{"cited":"br/061501351689","citing":"br/061203895786","oci":"oci:061203895786-061501351689"}
+{"cited":"br/06202223692", "citing":"br/06110298832","oci":"oci:06110298832-06202223692"}
+{"cited":"br/06104310727", "citing":"br/0660439086","oci":"oci:0660439086-06104310727"}
+{"cited":"br/06150216214", "citing":"br/06340150329","oci":"oci:06340150329-06150216214"}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/correspondence/omid.csv

@@ -0,0 +1,48 @@
+omid,id
+br/061201599020,doi:10.1142/s0219887817501687
+br/06203041400,doi:10.1111/j.1523-5378.2005.00327.x pmid:16104945
+br/06210273177,doi:10.1090/qam/20394
+br/06502272390,pmid:32235596 doi:10.3390/nano10040644
+br/0660613430,doi:10.1007/bf00470411
+br/06120941789,doi:10.1098/rspa.2006.1747
+br/062602732073,doi:10.1007/978-3-642-38844-6_25
+br/06230199640,pmid:25088780 doi:10.1016/j.ymeth.2014.07.008
+br/061103703697,pmid:2682767
+br/0670517081,doi:10.1016/j.foodpol.2021.102189
+br/06502310477,doi:10.1142/s0218127416500450
+br/06520113284,doi:10.1109/cfasta57821.2023.10243367
+br/062303652439,pmid:5962654 doi:10.1016/0020-708x(66)90001-9
+br/06250691436,doi:10.1042/bst20150052 pmid:26009172
+br/061201665577,doi:10.1097/00115550-200205000-00018
+br/06503490336,pmid:34689254 doi:10.1007/s10072-021-05687-0
+br/06220615942,pmid:25626134 doi:10.1016/j.jcis.2015.01.008
+br/061103389243,doi:10.4324/9780203702819-10
+br/062303011271,doi:10.1109/icassp.2011.5946250
+br/061302926083,doi:10.4018/978-1-6684-3937-1.ch002
+br/061402485360,doi:10.1109/iciict.2015.7396079
+br/06410101083,doi:10.1016/j.autcon.2023.104828
+br/062202243386,doi:10.1016/0001-8791(81)90022-1
+br/06170421486,doi:10.1130/0016-7606(2003)115<0166:dsagmf>2.0.co;2
+br/061201983865,doi:10.4324/9781315109008 isbn:9781315109008
+br/061701697230,doi:10.1016/j.trd.2012.07.006
+br/061201137111,doi:10.1109/access.2020.2971656
+br/06120436283,pmid:2254430 doi:10.1128/jcm.28.11.2551-2554.1990
+br/061903968916,doi:10.1111/j.1742-1241.1988.tb08627.x
+br/06201583482,doi:10.1016/0016-5085(78)93139-6
+br/06130338317,doi:10.2134/agronj1952.00021962004400080013x
+br/062601538320,doi:10.1371/journal.pone.0270593 pmid:35789338
+br/062401098626,pmid:22385804 doi:10.1016/j.talanta.2011.12.034
+br/06190436492,doi:10.1039/c7dt01499f pmid:28644489
+br/06202819247,doi:10.1007/978-3-319-45823-6_57
+br/0648013560,doi:10.1080/14772000.2012.705356
+br/0690214059,doi:10.2752/175630608x329217
+br/06601640415,doi:10.1080/18128600508685647
+br/061503394761,doi:10.1002/0471443395.img018
+br/061702861849,pmid:31203682 doi:10.1080/10428194.2019.1627538
+br/06450133713,doi:10.1093/acprof:oso/9780199670888.003.0008
+br/0628074892,doi:10.1097/hnp.0000000000000597
+br/061601032219,doi:10.1002/bdm.2102
+br/06602079930,doi:10.1101/2020.08.25.267500
+br/0604192147,doi:10.11501/3307395
+br/061101933800,doi:10.1142/s0217732398002242
+br/06504184118,pmid:10091417

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/jsonforas

@@ -0,0 +1,27 @@
+{"oci":"oci:06701327944-06504326071","citing":"16104945","citing_pid":"pmid","cited":"10.1142/s0219887817501687","cited_pid":"doi"}
+{"oci":"oci:06701327944-06504326071","citing":"10.1111/j.1523-5378.2005.00327.x","citing_pid":"doi","cited":"10.1142/s0219887817501687","cited_pid":"doi"}
+{"oci":"oci:06502272390-061301355525","citing":"10.3390/nano10040644","citing_pid":"doi","cited":"10.1142/s0219887817501687","cited_pid":"doi"}
+{"oci":"oci:06502272390-061301355525","citing":"32235596","citing_pid":"pmid","cited":"10.1142/s0219887817501687","cited_pid":"doi"}
+{"oci":"oci:0670804699-067055659","citing":"10.1098/rspa.2006.1747","citing_pid":"doi","cited":"10.1142/s0219887817501687","cited_pid":"doi"}
+{"oci":"oci:061502003994-062201281456","citing":"16104945","citing_pid":"pmid","cited":"10.1090/qam/20394","cited_pid":"doi"}
+{"oci":"oci:061502003994-062201281456","citing":"10.1111/j.1523-5378.2005.00327.x","citing_pid":"doi","cited":"10.1090/qam/20394","cited_pid":"doi"}
+{"oci":"oci:06502272390-0660806688","citing":"10.3390/nano10040644","citing_pid":"doi","cited":"10.1090/qam/20394","cited_pid":"doi"}
+{"oci":"oci:06502272390-0660806688","citing":"32235596","citing_pid":"pmid","cited":"10.1090/qam/20394","cited_pid":"doi"}
+{"oci":"oci:06502307119-0620223645","citing":"10.1098/rspa.2006.1747","citing_pid":"doi","cited":"10.1090/qam/20394","cited_pid":"doi"}
+{"oci":"oci:061502004011-061902692285","citing":"16104945","citing_pid":"pmid","cited":"10.1007/bf00470411","cited_pid":"doi"}
+{"oci":"oci:061502004011-061902692285","citing":"10.1111/j.1523-5378.2005.00327.x","citing_pid":"doi","cited":"10.1007/bf00470411","cited_pid":"doi"}
+{"oci":"oci:0660549063-0610398792","citing":"10.3390/nano10040644","citing_pid":"doi","cited":"10.1007/bf00470411","cited_pid":"doi"}
+{"oci":"oci:0660549063-0610398792","citing":"32235596","citing_pid":"pmid","cited":"10.1007/bf00470411","cited_pid":"doi"}
+{"oci":"oci:06420189324-06301543046","citing":"10.1098/rspa.2006.1747","citing_pid":"doi","cited":"10.1007/bf00470411","cited_pid":"doi"}
+{"oci":"oci:06380130275-061502004367","citing":"16104945","citing_pid":"pmid","cited":"10.1007/978-3-642-38844-6_25","cited_pid":"doi"}
+{"oci":"oci:06380130275-061502004367","citing":"10.1111/j.1523-5378.2005.00327.x","citing_pid":"doi","cited":"10.1007/978-3-642-38844-6_25","cited_pid":"doi"}
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