[OC New] last fix

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

@@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
 
 		return projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> {
 			Project project = new Project();
-			project.setId(bipProjectScores.getProjectId());
+			// project.setId(bipProjectScores.getProjectId());
 			project.setMeasures(bipProjectScores.toMeasures());
 			return project;
 		}, Encoders.bean(Project.class))

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

@@ -22,6 +22,7 @@ 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;
@@ -41,7 +42,9 @@ public class CreateActionSetSparkJob implements Serializable {
 	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);
@@ -74,25 +77,18 @@ 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,
-		boolean shouldDuplicateRels) {
+	private static void extractContent(SparkSession spark, String inputPath, String outputPath) {
 
 		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) {
@@ -115,7 +111,7 @@ public class CreateActionSetSparkJob implements Serializable {
 					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
 	}
 
-	private static List<Relation> createRelation(COCI value) {
+	private static List<Relation> createRelation(COCI value) throws JsonProcessingException {
 
 		List<Relation> relationList = new ArrayList<>();
 
@@ -131,25 +127,52 @@ public class CreateActionSetSparkJob implements Serializable {
 			case "pmid":
 				citing = PMID_PREFIX
 					+ IdentifierFactory
-						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
+						.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: " + value.getCiting_pid());
+				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.getCiting()));
+						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited()));
 				break;
 			case "pmid":
 				cited = PMID_PREFIX
 					+ IdentifierFactory
-						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
+						.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: " + value.getCited_pid());
+				throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
 		}
 
 		if (!citing.equals(cited)) {

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

@@ -9,11 +9,19 @@ 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;
@@ -62,6 +70,10 @@ public class MapOCIdsInPids implements Serializable {
 		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,
@@ -70,6 +82,41 @@ public class MapOCIdsInPids implements Serializable {
 
 	}
 
+	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()
@@ -85,7 +132,7 @@ public class MapOCIdsInPids implements Serializable {
 			.option("inferSchema", "true")
 			.option("header", "true")
 			.option("quotes", "\"")
-			.load(inputPath + "/correspondence/omid.zip")
+			.load(inputPath + "/correspondence/omid.csv")
 			.repartition(5000)
 			.flatMap((FlatMapFunction<Row, Tuple2<String, String>>) r -> {
 				String ocIdentifier = r.getAs("omid");
@@ -98,7 +145,7 @@ public class MapOCIdsInPids implements Serializable {
 			}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
 
 		Dataset<COCI> mappedCitingDataset = coci
-			.joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1")), "left")
+			.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(":")));
@@ -118,6 +165,16 @@ public class MapOCIdsInPids implements Serializable {
 			.mode(SaveMode.Append)
 			.option("compression", "gzip")
 			.json(outputPath);
+
+		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))
+			.foreach((ForeachFunction<COCI>) c -> System.out.println(OBJECT_MAPPER.writeValueAsString(c)));
 	}
 
 }

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

@@ -14,6 +14,7 @@ import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.*;
 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;
@@ -79,7 +80,7 @@ public class ReadCOCI implements Serializable {
 				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")
@@ -91,6 +92,7 @@ public class ReadCOCI implements Serializable {
 				.repartition(100);
 
 			cociData.map((MapFunction<Row, COCI>) row -> {
+
 				COCI coci = new COCI();
 
 				coci.setCiting(row.getString(1));
@@ -100,10 +102,12 @@ public class ReadCOCI implements Serializable {
 
 				return coci;
 			}, Encoders.bean(COCI.class))
+				.filter((FilterFunction<COCI>) c -> c != null)
 				.write()
 				.mode(SaveMode.Append)
 				.option("compression", "gzip")
 				.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

@@ -27,6 +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;
 	}
 
@@ -35,6 +37,8 @@ public class COCI implements Serializable {
 	}
 
 	public void setCited(String cited) {
+		if (cited != null && cited.startsWith("omid:"))
+			cited = cited.substring(5);
 		this.cited = cited;
 	}
 

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

@@ -27,6 +27,7 @@
             <case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
             <case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case>
             <case to="read">${wf:conf('resumeFrom') eq 'ReadContent'}</case>
+            <case to="remap">${wf:conf('resumeFrom') eq 'MapContent'}</case>
             <case to="create_actionset">${wf:conf('resumeFrom') eq 'CreateAS'}</case>
             <default to="deleteoutputpath"/> <!-- first action to be done when downloadDump is to be performed -->
         </switch>
@@ -154,6 +155,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}</arg>
             <arg>--outputPath</arg><arg>${outputPathExtraction}</arg>
+            <arg>--nameNode</arg><arg>${nameNode}</arg>
         </spark>
         <ok to="create_actionset"/>
         <error to="Kill"/>

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

@@ -16,5 +16,10 @@
     "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
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