Merge pull request 'AffiliationFromPublisher' (#470) from AffiliationFromPublisher into main

Reviewed-on: #470

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

@@ -44,6 +44,8 @@ public class PrepareAffiliationRelations implements Serializable {
 	public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:openaireinference";
 	public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by OpenAIRE";
 	public static final String BIP_INFERENCE_PROVENANCE = "openaire:affiliation";
+	public static final String OPENAIRE_DATASOURCE_ID = "10|infrastruct_::f66f1bd369679b5b077dcdf006089556";
+	public static final String OPENAIRE_DATASOURCE_NAME = "OpenAIRE";
 
 	public static <I extends Result> void main(String[] args) throws Exception {
 
@@ -74,6 +76,9 @@ public class PrepareAffiliationRelations implements Serializable {
 		final String webcrawlInputPath = parser.get("webCrawlInputPath");
 		log.info("webcrawlInputPath: {}", webcrawlInputPath);
 
+		final String publisherInputPath = parser.get("publisherInputPath");
+		log.info("publisherInputPath: {}", publisherInputPath);
+
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
@@ -84,7 +89,15 @@ public class PrepareAffiliationRelations implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 				Constants.removeOutputDir(spark, outputPath);
+				createActionSet(
+					spark, crossrefInputPath, pubmedInputPath, openapcInputPath, dataciteInputPath, webcrawlInputPath,
+					publisherInputPath, outputPath);
+			});
+	}
 
+	private static void createActionSet(SparkSession spark, String crossrefInputPath, String pubmedInputPath,
+		String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath,
+		String outputPath) {
 		List<KeyValue> collectedFromCrossref = OafMapperUtils
 			.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
 		JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
@@ -106,19 +119,36 @@ public class PrepareAffiliationRelations implements Serializable {
 			spark, dataciteInputPath, collectedFromDatacite);
 
 		List<KeyValue> collectedFromWebCrawl = OafMapperUtils
-					.listKeyValues(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME);
+			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 		JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
 			spark, webcrawlInputPath, collectedFromWebCrawl);
 
+		List<KeyValue> collectedfromPublisher = OafMapperUtils
+			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
+		JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisher(
+			spark, publisherlInputPath, collectedfromPublisher);
+
 		crossrefRelations
 			.union(pubmedRelations)
 			.union(openAPCRelations)
 			.union(dataciteRelations)
 			.union(webCrawlRelations)
+			.union(publisherRelations)
 			.saveAsHadoopFile(
 				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
+	}
+
+	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath,
+		List<KeyValue> collectedfrom) {
+
+		Dataset<Row> df = spark
+			.read()
+			.schema("`DOI` STRING, `Organizations` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
+			.json(inputPath)
+			.where("DOI is not null");
+
+		return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"));
 
-			});
 	}
 
 	private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
@@ -132,6 +162,10 @@ public class PrepareAffiliationRelations implements Serializable {
 			.json(inputPath)
 			.where("DOI is not null");
 
+		return getTextTextJavaPairRDD(collectedfrom, df);
+	}
+
+	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(List<KeyValue> collectedfrom, Dataset<Row> df) {
 		// unroll nested arrays
 		df = df
 			.withColumn("matching", functions.explode(new Column("Matchings")))

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

@@ -33,6 +33,11 @@
   "paramLongName": "webCrawlInputPath",
   "paramDescription": "the path to get the input data from Web Crawl",
   "paramRequired": true
+},{
+  "paramName": "pip",
+  "paramLongName": "publisherInputPath",
+  "paramDescription": "the path to get the input data from publishers",
+  "paramRequired": true
 }
 ,
   {

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

@@ -78,6 +78,10 @@ public class PrepareAffiliationRelationsTest {
 			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
 			.getPath();
 
+		String publisherAffiliationRelationPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers")
+			.getPath();
+
 		String outputPath = workingDir.toString() + "/actionSet";
 
 		PrepareAffiliationRelations
@@ -89,6 +93,7 @@ public class PrepareAffiliationRelationsTest {
 					"-openapcInputPath", crossrefAffiliationRelationPath,
 					"-dataciteInputPath", crossrefAffiliationRelationPath,
 					"-webCrawlInputPath", crossrefAffiliationRelationPath,
+					"-publisherInputPath", publisherAffiliationRelationPath,
 					"-outputPath", outputPath
 				});
 
@@ -105,7 +110,7 @@ public class PrepareAffiliationRelationsTest {
 //            );
 //        }
 		// count the number of relations
-		assertEquals(120, tmp.count());
+		assertEquals(138, tmp.count());
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
@@ -116,7 +121,7 @@ public class PrepareAffiliationRelationsTest {
 		// verify that we have equal number of bi-directional relations
 		Assertions
 			.assertEquals(
-				60, execVerification
+				69, execVerification
 					.filter(
 						"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
 					.collectAsList()
@@ -124,7 +129,7 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				60, execVerification
+				69, execVerification
 					.filter(
 						"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
 					.collectAsList()
@@ -145,5 +150,11 @@ public class PrepareAffiliationRelationsTest {
 					.get(0)
 					.getString(4));
 
+
+		final String publisherid = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s00217-010-1268-9"));
+		final String rorId = "20|ror_________::" + IdentifierFactory.md5("https://ror.org/03265fv13");
+
+		Assertions.assertEquals(1, execVerification.filter("source = '" + publisherid + "' and target = '" + rorId +"'").count()
+				);
 	}
 }

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers/publisher

@@ -0,0 +1,6 @@
+{"DOI": "10.1007/s00217-010-1268-9", "Authors": [{"Name": {"Full": "Martin Zarnkow", "First": null, "Last": null}, "Raw_affiliations": ["TU M\u00fcnchen, Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Andrea Faltermaier", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Werner Back", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Technologie der Brauerei I"], "Organization_PIDs": []}, {"Name": {"Full": "Martina Gastl", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Elkek K. Arendt", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}
+{"DOI": "10.1007/BF01154707", "Authors": [{"Name": {"Full": "Buggy, M.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]}, {"Name": {"Full": "Carew, A.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]}
+{"DOI": "10.1007/s10237-017-0974-7", "Authors": [{"Name": {"Full": "Donnacha J. McGrath", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Anja Lena Thiebes", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Christian G. Cornelissen", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Barry O\u2019Brien", "First": null, "Last": null}, "Raw_affiliations": ["Department for Internal Medicine \u2013 Section for Pneumology, Medical Faculty, RWTH Aachen University, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/04xfq0f34", "Confidence": 1}]}, {"Name": {"Full": "Stefan Jockenhoevel", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Mark Bruzzi", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Peter E. McHugh", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}, {"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 1}]}
+{"DOI": "10.1007/BF03168973", "Authors": [{"Name": {"Full": "Sheehan, G.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}, {"Name": {"Full": "Chew, N.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}], "Organizations": []}
+{"DOI": "10.1007/s00338-009-0480-1", "Authors": [{"Name": {"Full": "Gleason, D. F.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Danilowicz, B. S.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Nolan, C. J.", "First": null, "Last": null}, "Raw_affiliations": ["School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/05m7pjf47", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}, {"RORid": "https://ror.org/05m7pjf47", "Confidence": 1}]}
+{"DOI": "10.1007/s10993-010-9187-y", "Authors": [{"Name": {"Full": "Martin Howard", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}

dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcidTest.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.broker.oa.matchers.simple;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -16,7 +17,8 @@ class EnrichMissingAuthorOrcidTest {
 	final EnrichMissingAuthorOrcid matcher = new EnrichMissingAuthorOrcid();
 
 	@BeforeEach
-	void setUp() throws Exception {}
+	void setUp() throws Exception {
+	}
 
 	@Test
 	void testFindDifferences_1() {

dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java

@@ -23,7 +23,8 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 public class ConversionUtilsTest {
 
 	@BeforeEach
-	public void setUp() throws Exception {}
+	public void setUp() throws Exception {
+	}
 
 	@Test
 	public void testAllResultPids() {

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java

@@ -20,7 +20,6 @@ import javax.xml.transform.*;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 
-import eu.dnetlib.dhp.oa.provision.model.*;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
@@ -42,6 +41,7 @@ import com.google.common.collect.Sets;
 import com.mycila.xmltool.XMLDoc;
 import com.mycila.xmltool.XMLTag;
 
+import eu.dnetlib.dhp.oa.provision.model.*;
 import eu.dnetlib.dhp.schema.common.*;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.Result;