Merge branch 'master' into broker

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java

@@ -62,8 +62,6 @@ public abstract class Oaf implements Serializable {
 				.distinct() // relies on KeyValue.equals
 				.collect(Collectors.toList()));
 
-		mergeOAFDataInfo(o);
-
 		setLastupdatetimestamp(
 			Math
 				.max(

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java

@@ -351,8 +351,6 @@ public class Project extends OafEntity implements Serializable {
 			? p.getFundedamount()
 			: fundedamount;
 
-		// programme = mergeLists(programme, p.getProgramme());
-
 		h2020classification = mergeLists(h2020classification, p.getH2020classification());
 
 		mergeOAFDataInfo(e);

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java

@@ -108,7 +108,7 @@ public class SparkResultToCommunityFromOrganizationJob {
 					.stream()
 					.map(con -> con.getId())
 					.collect(Collectors.toList());
-				Result res = new Result();
+				R res = (R) ret.getClass().newInstance();
 				res.setId(ret.getId());
 				List<Context> propagatedContexts = new ArrayList<>();
 				for (String cId : communitySet) {

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java

@@ -130,7 +130,7 @@ public class SparkResultToCommunityThroughSemRelJob {
 						})
 					.filter(Objects::nonNull)
 					.collect(Collectors.toList());
-				Result r = new Result();
+				R r = (R) ret.getClass().newInstance();
 				r.setId(ret.getId());
 				r.setContext(contextList);
 				ret.mergeFrom(r);

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java

@@ -24,7 +24,6 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
-import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest;
 import eu.dnetlib.dhp.schema.oaf.Dataset;
 
 public class ResultToCommunityJobTest {
@@ -66,7 +65,7 @@ public class ResultToCommunityJobTest {
 	}
 
 	@Test
-	public void test1() throws Exception {
+	public void testSparkResultToCommunityThroughSemRelJob() throws Exception {
 		SparkResultToCommunityThroughSemRelJob
 			.main(
 				new String[] {

dhp-workflows/dhp-graph-provision/pom.xml

@@ -54,6 +54,13 @@
             <artifactId>spark-solr</artifactId>
         </dependency>
 
+        <!-- the solr-test-framework requires the old junit:junit test framework -->
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.12</version>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>org.apache.solr</groupId>
             <artifactId>solr-test-framework</artifactId>
@@ -140,6 +147,12 @@
         <dependency>
             <groupId>org.apache.zookeeper</groupId>
             <artifactId>zookeeper</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>junit</groupId>
+                    <artifactId>junit</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
 
 

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

@@ -0,0 +1,52 @@
+
+package eu.dnetlib.dhp.oa.provision.utils;
+
+import java.util.Comparator;
+import java.util.Optional;
+
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
+public class AuthorPidTypeComparator implements Comparator<StructuredProperty> {
+
+	@Override
+	public int compare(StructuredProperty left, StructuredProperty right) {
+
+		String lClass = Optional
+			.ofNullable(left)
+			.map(StructuredProperty::getQualifier)
+			.map(Qualifier::getClassid)
+			.orElse(null);
+
+		String rClass = Optional
+			.ofNullable(right)
+			.map(StructuredProperty::getQualifier)
+			.map(Qualifier::getClassid)
+			.orElse(null);
+
+		if (lClass == null && rClass == null)
+			return 0;
+		if (lClass == null)
+			return 1;
+		if (rClass == null)
+			return -1;
+
+		if (lClass.equals(rClass))
+			return 0;
+
+		if (lClass.equals(ModelConstants.ORCID))
+			return -1;
+		if (rClass.equals(ModelConstants.ORCID))
+			return 1;
+
+		if (lClass.equals(ModelConstants.ORCID_PENDING))
+			return -1;
+		if (rClass.equals(ModelConstants.ORCID_PENDING))
+			return 1;
+
+		return 0;
+	}
+
+}

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

@@ -254,6 +254,18 @@ public class XmlRecordFactory implements Serializable {
 														p -> p,
 														(p1, p2) -> p1))
 											.values()
+											.stream()
+											.collect(
+												Collectors
+													.groupingBy(
+														p -> p.getValue(),
+														Collectors
+															.mapping(
+																p -> p,
+																Collectors.minBy(new AuthorPidTypeComparator()))))
+											.values()
+											.stream()
+											.map(op -> op.get())
 											.forEach(
 												sp -> {
 													String pidType = getAuthorPidType(sp.getQualifier().getClassid());

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java

@@ -6,15 +6,13 @@ import org.apache.solr.client.solrj.response.UpdateResponse;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
-import junit.framework.Assert;
-
 public class SolrAdminApplicationTest extends SolrTest {
 
 	@Test
 	public void testPing() throws Exception {
 		SolrPingResponse pingResponse = miniCluster.getSolrClient().ping();
 		log.info("pingResponse: '{}'", pingResponse.getStatus());
-		Assert.assertTrue(pingResponse.getStatus() == 0);
+		Assertions.assertTrue(pingResponse.getStatus() == 0);
 	}
 
 	@Test

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java

@@ -14,33 +14,33 @@ import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
+import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
 import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
 import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
+import eu.dnetlib.dhp.schema.oaf.Publication;
 
-//TODO to enable it we need to update the joined_entity.json test file
-@Disabled
 public class XmlRecordFactoryTest {
 
 	private static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource";
 
+	private static ObjectMapper OBJECT_MAPPER = new ObjectMapper()
+		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+
 	@Test
 	public void testXMLRecordFactory() throws IOException, DocumentException {
 
-		String json = IOUtils.toString(getClass().getResourceAsStream("joined_entity.json"));
-
-		assertNotNull(json);
-		JoinedEntity je = new ObjectMapper().readValue(json, JoinedEntity.class);
-		assertNotNull(je);
-
 		ContextMapper contextMapper = new ContextMapper();
 
 		XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation,
 			otherDsTypeId);
 
-		String xml = xmlRecordFactory.build(je);
+		Publication p = OBJECT_MAPPER
+			.readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class);
+
+		String xml = xmlRecordFactory.build(new JoinedEntity<>(p));
 
 		assertNotNull(xml);
 
@@ -48,6 +48,14 @@ public class XmlRecordFactoryTest {
 
 		assertNotNull(doc);
 
+		System.out.println(doc.asXML());
+
+		Assertions.assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid"));
+		Assertions.assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending"));
+
+		Assertions.assertEquals("0000-0001-9613-9956", doc.valueOf("//creator[@rank = '2']/@orcid"));
+		Assertions.assertEquals("", doc.valueOf("//creator[@rank = '2']/@orcid_pending"));
+
 		// TODO add assertions based of values extracted from the XML record
 	}
 }

dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json

@@ -0,0 +1,820 @@
+{
+  "author": [
+    {
+      "affiliation": [],
+      "fullname": "Lee, Jaehyun",
+      "name": "Jaehyun",
+      "pid": [
+        {
+          "qualifier": {
+            "classid": "orcid",
+            "classname": "Open Researcher and Contributor ID",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "0000-0001-9613-6638"
+        },
+        {
+          "qualifier": {
+            "classid": "orcid_pending",
+            "classname": "Open Researcher and Contributor ID",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "0000-0001-9613-6639"
+        }
+      ],
+      "rank": 1,
+      "surname": "Lee"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Berrada, Salim",
+      "name": "Salim",
+      "pid": [
+        {
+          "qualifier": {
+            "classid": "orcid",
+            "classname": "Open Researcher and Contributor ID",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "0000-0001-9613-9956"
+        },
+        {
+          "qualifier": {
+            "classid": "orcid_pending",
+            "classname": "Open Researcher and Contributor ID",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "0000-0001-9613-9956"
+        }
+      ],
+      "rank": 2,
+      "surname": "Berrada"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Adamu-Lema, Fikru",
+      "name": "Fikru",
+      "pid": [],
+      "rank": 3,
+      "surname": "Adamu-Lema"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Nagy, Nicole",
+      "name": "Nicole",
+      "pid": [],
+      "rank": 4,
+      "surname": "Nagy"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Georgiev, Vihar P.",
+      "name": "Vihar P.",
+      "pid": [],
+      "rank": 5,
+      "surname": "Georgiev"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Sadi, Toufik",
+      "name": "Toufik",
+      "pid": [],
+      "rank": 6,
+      "surname": "Sadi"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Liang, Jie",
+      "name": "Jie",
+      "pid": [],
+      "rank": 7,
+      "surname": "Liang"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Ramos, Raphael",
+      "name": "Raphael",
+      "pid": [],
+      "rank": 8,
+      "surname": "Ramos"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Carrillo-Nunez, Hamilton",
+      "name": "Hamilton",
+      "pid": [],
+      "rank": 9,
+      "surname": "Carrillo-Nunez"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Kalita, Dipankar",
+      "name": "Dipankar",
+      "pid": [],
+      "rank": 10,
+      "surname": "Kalita"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Lilienthal, Katharina",
+      "name": "Katharina",
+      "pid": [],
+      "rank": 11,
+      "surname": "Lilienthal"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Wislicenus, Marcus",
+      "name": "Marcus",
+      "pid": [],
+      "rank": 12,
+      "surname": "Wislicenus"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Pandey, Reeturaj",
+      "name": "Reeturaj",
+      "pid": [],
+      "rank": 13,
+      "surname": "Pandey"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Chen, Bingan",
+      "name": "Bingan",
+      "pid": [],
+      "rank": 14,
+      "surname": "Chen"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Teo, Kenneth B.K.",
+      "name": "Kenneth B. K.",
+      "pid": [],
+      "rank": 15,
+      "surname": "Teo"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Goncalves, Goncalo",
+      "name": "Goncalo",
+      "pid": [],
+      "rank": 16,
+      "surname": "Goncalves"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Okuno, Hanako",
+      "name": "Hanako",
+      "pid": [],
+      "rank": 17,
+      "surname": "Okuno"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Uhlig, Benjamin",
+      "name": "Benjamin",
+      "pid": [],
+      "rank": 18,
+      "surname": "Uhlig"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Todri-Sanial, Aida",
+      "name": "Aida",
+      "pid": [],
+      "rank": 19,
+      "surname": "Todri-Sanial"
+    },
+    {
+      "affiliation": [],
+      "fullname": "Dijon",
+      "name": "",
+      "pid": [],
+      "rank": 20,
+      "surname": ""
+    },
+    {
+      "affiliation": [],
+      "fullname": "Jean",
+      "name": "",
+      "pid": [],
+      "rank": 21,
+      "surname": ""
+    }
+  ],
+  "collectedfrom": [
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "",
+          "classname": "",
+          "schemeid": "",
+          "schemename": ""
+        },
+        "trust": ""
+      },
+      "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
+      "value": "VIRTA"
+    }
+  ],
+  "context": [],
+  "contributor": [],
+  "country": [],
+  "coverage": [],
+  "dataInfo": {
+    "deletedbyinference": false,
+    "inferenceprovenance": "",
+    "inferred": false,
+    "invisible": false,
+    "provenanceaction": {
+      "classid": "sysimport:crosswalk:datasetarchive",
+      "classname": "sysimport:crosswalk:datasetarchive",
+      "schemeid": "dnet:provenanceActions",
+      "schemename": "dnet:provenanceActions"
+    },
+    "trust": "0.9"
+  },
+  "dateofacceptance": {
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferenceprovenance": "",
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "trust": ""
+    },
+    "value": "2018-01-01"
+  },
+  "dateofcollection": "2020-01-27T11:32:33.729Z",
+  "dateoftransformation": "2020-01-27T12:03:59.662Z",
+  "description": [],
+  "embargoenddate": {
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferenceprovenance": "",
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "trust": ""
+    },
+    "value": ""
+  },
+  "extraInfo": [],
+  "format": [],
+  "fulltext": [],
+  "id": "50|CSC_________::0000ec4dd9df012feaafa77e71a0fb4c",
+  "instance": [
+    {
+      "accessright": {
+        "classid": "OPEN",
+        "classname": "Open Access",
+        "schemeid": "dnet:access_modes",
+        "schemename": "dnet:access_modes"
+      },
+      "collectedfrom": {
+        "dataInfo": {
+          "deletedbyinference": false,
+          "inferenceprovenance": "",
+          "inferred": false,
+          "invisible": false,
+          "provenanceaction": {
+            "classid": "",
+            "classname": "",
+            "schemeid": "",
+            "schemename": ""
+          },
+          "trust": ""
+        },
+        "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
+        "value": "VIRTA"
+      },
+      "dateofacceptance": {
+        "dataInfo": {
+          "deletedbyinference": false,
+          "inferenceprovenance": "",
+          "inferred": false,
+          "invisible": false,
+          "provenanceaction": {
+            "classid": "",
+            "classname": "",
+            "schemeid": "",
+            "schemename": ""
+          },
+          "trust": ""
+        },
+        "value": "2018-01-01"
+      },
+      "distributionlocation": "",
+      "hostedby": {
+        "dataInfo": {
+          "deletedbyinference": false,
+          "inferenceprovenance": "",
+          "inferred": false,
+          "invisible": false,
+          "provenanceaction": {
+            "classid": "",
+            "classname": "",
+            "schemeid": "",
+            "schemename": ""
+          },
+          "trust": ""
+        },
+        "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
+        "value": "VIRTA"
+      },
+      "instancetype": {
+        "classid": "0001",
+        "classname": "Article",
+        "schemeid": "dnet:dataCite_resource",
+        "schemename": "dnet:dataCite_resource"
+      },
+      "license": {
+        "dataInfo": {
+          "deletedbyinference": false,
+          "inferenceprovenance": "",
+          "inferred": false,
+          "invisible": false,
+          "provenanceaction": {
+            "classid": "",
+            "classname": "",
+            "schemeid": "",
+            "schemename": ""
+          },
+          "trust": ""
+        },
+        "value": ""
+      },
+      "url": [
+        "http://juuli.fi/Record/0331473718",
+        "http://dx.doi.org/10.1109/TED.2018.2853550"
+      ]
+    }
+  ],
+  "journal": {
+    "conferencedate": "",
+    "conferenceplace": "",
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferenceprovenance": "",
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "trust": ""
+    },
+    "edition": "",
+    "ep": "3892",
+    "iss": "9",
+    "issnLinking": "",
+    "issnOnline": "",
+    "issnPrinted": "0018-9383",
+    "name": "IEEE Transactions on Electron Devices",
+    "sp": "3884",
+    "vol": "65"
+  },
+  "language": {
+    "classid": "en",
+    "classname": "en",
+    "schemeid": "dnet:languages",
+    "schemename": "dnet:languages"
+  },
+  "lastupdatetimestamp": 0,
+  "originalId": [
+    "0331473718",
+    "10.1109/TED.2018.2853550",
+    "http://juuli.fi/Record/0331473718"
+  ],
+  "pid": [
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "",
+          "classname": "",
+          "schemeid": "",
+          "schemename": ""
+        },
+        "trust": ""
+      },
+      "qualifier": {
+        "classid": "doi",
+        "classname": "doi",
+        "schemeid": "dnet:pid_types",
+        "schemename": "dnet:pid_types"
+      },
+      "value": "10.1109/TED.2018.2853550"
+    }
+  ],
+  "publisher": {
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferenceprovenance": "",
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "",
+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
+      },
+      "trust": ""
+    },
+    "value": ""
+  },
+  "relevantdate": [],
+  "resourcetype": {
+    "classid": "0001",
+    "classname": "Article",
+    "schemeid": "dnet:dataCite_resource",
+    "schemename": "dnet:dataCite_resource"
+  },
+  "resulttype": {
+    "classid": "publication",
+    "classname": "publication",
+    "schemeid": "dnet:result_typologies",
+    "schemename": "dnet:result_typologies"
+  },
+  "source": [],
+  "subject": [
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "",
+          "classname": "",
+          "schemeid": "",
+          "schemename": ""
+        },
+        "trust": ""
+      },
+      "qualifier": {
+        "classid": "http://finto.fi/okm-tieteenala/en/",
+        "classname": "finto",
+        "schemeid": "dnet:subject_classification_typologies",
+        "schemename": "dnet:subject_classification_typologies"
+      },
+      "value": "ta114"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "",
+          "classname": "",
+          "schemeid": "",
+          "schemename": ""
+        },
+        "trust": ""
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+}