Merge pull request 'Add Pubmed affiliations (inferred by BIP) as actionsets' (#353) from 9117_pubmed_affiliations into beta

Reviewed-on: #353

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

@@ -12,6 +12,7 @@ import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.compress.GzipCodec;
 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.FlatMapFunction;
 import org.apache.spark.sql.*;
 import org.apache.spark.sql.Dataset;
@@ -57,11 +58,14 @@ public class PrepareAffiliationRelations implements Serializable {
 		Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-		final String inputPath = parser.get("inputPath");
+		final String crossrefInputPath = parser.get("crossrefInputPath");
-		log.info("inputPath {}: ", inputPath);
+		log.info("crossrefInputPath: {}", crossrefInputPath);
+
+		final String pubmedInputPath = parser.get("pubmedInputPath");
+		log.info("pubmedInputPath: {}", pubmedInputPath);
 
 		final String outputPath = parser.get("outputPath");
-		log.info("outputPath {}: ", outputPath);
+		log.info("outputPath: {}", outputPath);
 
 		SparkConf conf = new SparkConf();
 
@@ -70,12 +74,28 @@ public class PrepareAffiliationRelations implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 				Constants.removeOutputDir(spark, outputPath);
-				prepareAffiliationRelations(spark, inputPath, outputPath);
+
+				List<KeyValue> collectedFromCrossref = OafMapperUtils
+					.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
+				JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
+					spark, crossrefInputPath, collectedFromCrossref);
+
+				List<KeyValue> collectedFromPubmed = OafMapperUtils
+					.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
+				JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
+					spark, pubmedInputPath, collectedFromPubmed);
+
+				crossrefRelations
+					.union(pubmedRelations)
+					.saveAsHadoopFile(
+						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+
 			});
 	}
 
-	private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath,
+	private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
-		String outputPath) {
+		String inputPath,
+		List<KeyValue> collectedfrom) {
 
 		// load and parse affiliation relations from HDFS
 		Dataset<Row> df = spark
@@ -92,7 +112,7 @@ public class PrepareAffiliationRelations implements Serializable {
 				new Column("matching.Confidence").as("confidence"));
 
 		// prepare action sets for affiliation relations
-		df
+		return df
 			.toJavaRDD()
 			.flatMap((FlatMapFunction<Row, Relation>) row -> {
 
@@ -120,8 +140,6 @@ public class PrepareAffiliationRelations implements Serializable {
 						qualifier,
 						Double.toString(row.getAs("confidence")));
 
-				List<KeyValue> collectedfrom = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
-
 				// return bi-directional relations
 				return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
 
@@ -129,9 +147,7 @@ public class PrepareAffiliationRelations implements Serializable {
 			.map(p -> new AtomicAction(Relation.class, p))
 			.mapToPair(
 				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
-			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
-
 	}
 
 	private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json

@@ -6,9 +6,15 @@
     "paramRequired": false
   },
   {
-    "paramName": "ip",
+    "paramName": "cip",
-    "paramLongName": "inputPath",
+    "paramLongName": "crossrefInputPath",
-    "paramDescription": "the URL from where to get the programme file",
+    "paramDescription": "the path to get the input data from Crossref",
+    "paramRequired": true
+  },
+  {
+    "paramName": "pip",
+    "paramLongName": "pubmedInputPath",
+    "paramDescription": "the path to get the input data from Pubmed",
     "paramRequired": true
   },
   {

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties

@@ -31,5 +31,6 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
 # The following is needed as a property of a workflow
 oozie.wf.application.path=${oozieTopWfApplicationPath}
 
-inputPath=/data/bip-affiliations/data.json
+crossrefInputPath=/data/bip-affiliations/data.json
+pubmedInputPath=/data/bip-affiliations/pubmed-data.json
 outputPath=/tmp/crossref-affiliations-output-v5

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

@@ -2,8 +2,12 @@
     <parameters>
 
         <property>
-            <name>inputPath</name>
+            <name>crossrefInputPath</name>
-            <description>the path where to find the inferred affiliation relations</description>
+            <description>the path where to find the inferred affiliation relations from Crossref</description>
+        </property>
+        <property>
+            <name>pubmedInputPath</name>
+            <description>the path where to find the inferred affiliation relations from Pubmed</description>
         </property>
         <property>
             <name>outputPath</name>
@@ -83,7 +87,7 @@
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
-            <name>Produces the atomic action with the inferred by BIP! affiliation relations from Crossref</name>
+            <name>Produces the atomic action with the inferred by BIP! affiliation relations (from Crossref and Pubmed)</name>
             <class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations</class>
             <jar>dhp-aggregation-${projectVersion}.jar</jar>
             <spark-opts>
@@ -96,7 +100,8 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--inputPath</arg><arg>${inputPath}</arg>
+            <arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg>
+            <arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java

@@ -74,7 +74,11 @@ public class PrepareAffiliationRelationsTest {
 	@Test
 	void testMatch() throws Exception {
 
-		String affiliationRelationsPath = getClass()
+		String crossrefAffiliationRelationPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
+			.getPath();
+
+		String pubmedAffiliationRelationsPath = getClass()
 				.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
 				.getPath();
 
@@ -84,7 +88,8 @@ public class PrepareAffiliationRelationsTest {
 			.main(
 				new String[] {
 					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-inputPath", affiliationRelationsPath,
+					"-crossrefInputPath", crossrefAffiliationRelationPath,
+					"-pubmedInputPath", pubmedAffiliationRelationsPath,
 					"-outputPath", outputPath
 				});
 
@@ -101,7 +106,7 @@ public class PrepareAffiliationRelationsTest {
 //            );
 //        }
 		// count the number of relations
-		assertEquals(20, tmp.count());
+		assertEquals(40, tmp.count());
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
@@ -112,7 +117,7 @@ public class PrepareAffiliationRelationsTest {
 		// verify that we have equal number of bi-directional relations
 		Assertions
 			.assertEquals(
-				10, execVerification
+				20, execVerification
 					.filter(
 						"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
 					.collectAsList()
@@ -120,7 +125,7 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				10, execVerification
+				20, execVerification
 					.filter(
 						"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
 					.collectAsList()