Merge pull request 'validatedLinksToProjects' (#93) from validatedLinksToProjects into master

LGTM

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java

@@ -334,6 +334,7 @@ public class MappersTest {
 		assertValidId(p.getCollectedfrom().get(0).getKey());
 		System.out.println(p.getTitle().get(0).getValue());
 		assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
+
 	}
 
 	@Test

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_claim_crossref.xml

@@ -46,6 +46,7 @@
         <oaf:collectedFrom id="openaire____::crossref" name="Crossref"/>
         <oaf:identifier identifierType="doi">10.1080/23744235.2020.1774644</oaf:identifier>
         <oaf:journal eissn="2374-4243" ep="3" iss="" issn="2374-4235" sp="1" vol="">Infectious Diseases</oaf:journal>
+        <oaf:projectid validationDate="2020-12-07T11:15:59.627Z">corda__h2020::814530</oaf:projectid>
     </metadata>
     <about xmlns:oai="http://www.openarchives.org/OAI/2.0/">
         <provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java

@@ -8,7 +8,6 @@ import java.util.Objects;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.common.ModelConstants;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.spark.SparkConf;
@@ -28,6 +27,7 @@ import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
 import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
 import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 import scala.Tuple2;

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

@@ -14,7 +14,8 @@ public class GraphMappingUtils {
 
 	public static final String SEPARATOR = "_";
 
-	public static Set<String> authorPidTypes = Sets.newHashSet(
+	public static Set<String> authorPidTypes = Sets
+		.newHashSet(
 			ModelConstants.ORCID, ModelConstants.ORCID_PENDING, "magidentifier");
 
 	public static String removePrefix(final String s) {

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

@@ -73,7 +73,9 @@ public class TemplateFactory {
 		final Collection<String> fields,
 		final String semanticclass,
 		final String semantischeme,
-		final DataInfo info) {
+		final DataInfo info,
+		final boolean validated,
+		final String validationDate) {
 		return getTemplate(resources.getRel())
 			.add("type", type)
 			.add("objIdentifier", escapeXml(removePrefix(objIdentifier)))
@@ -86,6 +88,8 @@ public class TemplateFactory {
 			.add(
 				"provenanceaction",
 				info.getProvenanceaction() != null ? info.getProvenanceaction().getClassid() : "")
+			.add("validated", validated)
+			.add("validationdate", validationDate)
 			.render();
 	}
 

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

@@ -1096,7 +1096,8 @@ public class XmlRecordFactory implements Serializable {
 		final HashSet<String> fields = Sets.newHashSet(mapFields(link, contexts));
 		return templateFactory
 			.getRel(
-				targetType, rel.getTarget(), fields, rel.getRelClass(), scheme, rel.getDataInfo());
+				targetType, rel.getTarget(), fields, rel.getRelClass(), scheme, rel.getDataInfo(), rel.getValidated(),
+				rel.getValidationDate());
 	}
 
 	private List<String> listChildren(

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/rel.st

@@ -1,4 +1,5 @@
 <rel inferred="$inferred$" trust="$trust$" inferenceprovenance="$inferenceprovenance$" provenanceaction="$provenanceaction$">
-  <to class="$class$" scheme="$scheme$" type="$type$">$objIdentifier$</to>
+$if(validated)$<validated date="$validationdate$"/>$else$$endif$
+<to class="$class$" scheme="$scheme$" type="$type$">$objIdentifier$</to>
     $metadata:{ it | $it$ }$
 </rel>

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

@@ -5,22 +5,27 @@ import static org.junit.jupiter.api.Assertions.*;
 
 import java.io.IOException;
 import java.io.StringReader;
+import java.util.List;
 
 import org.apache.commons.io.IOUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
 import org.dom4j.io.SAXReader;
 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 com.google.common.collect.Lists;
 
 import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
+import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
+import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
 import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
 import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
+import eu.dnetlib.dhp.schema.oaf.Project;
 import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.Relation;
 
 public class XmlRecordFactoryTest {
 
@@ -58,4 +63,67 @@ public class XmlRecordFactoryTest {
 
 		// TODO add assertions based of values extracted from the XML record
 	}
+
+	@Test
+	public void testXMLRecordFactoryWithValidatedProject() throws IOException, DocumentException {
+
+		ContextMapper contextMapper = new ContextMapper();
+
+		XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation,
+			otherDsTypeId);
+
+		Publication p = OBJECT_MAPPER
+			.readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class);
+		Project pj = OBJECT_MAPPER
+			.readValue(IOUtils.toString(getClass().getResourceAsStream("project.json")), Project.class);
+		Relation rel = OBJECT_MAPPER
+			.readValue(
+				(IOUtils.toString(getClass().getResourceAsStream("relToValidatedProject.json"))), Relation.class);
+		RelatedEntity relatedProject = CreateRelatedEntitiesJob_phase1.asRelatedEntity(pj, Project.class);
+		List<RelatedEntityWrapper> links = Lists.newArrayList();
+		RelatedEntityWrapper rew = new RelatedEntityWrapper(rel, relatedProject);
+		links.add(rew);
+		JoinedEntity je = new JoinedEntity<>(p);
+		je.setLinks(links);
+
+		String xml = xmlRecordFactory.build(je);
+
+		assertNotNull(xml);
+
+		Document doc = new SAXReader().read(new StringReader(xml));
+		assertNotNull(doc);
+		System.out.println(doc.asXML());
+		Assertions.assertEquals("2021-01-01", doc.valueOf("//validated/@date"));
+	}
+
+	@Test
+	public void testXMLRecordFactoryWithNonValidatedProject() throws IOException, DocumentException {
+
+		ContextMapper contextMapper = new ContextMapper();
+
+		XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation,
+			otherDsTypeId);
+
+		Publication p = OBJECT_MAPPER
+			.readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class);
+		Project pj = OBJECT_MAPPER
+			.readValue(IOUtils.toString(getClass().getResourceAsStream("project.json")), Project.class);
+		Relation rel = OBJECT_MAPPER
+			.readValue((IOUtils.toString(getClass().getResourceAsStream("relToProject.json"))), Relation.class);
+		RelatedEntity relatedProject = CreateRelatedEntitiesJob_phase1.asRelatedEntity(pj, Project.class);
+		List<RelatedEntityWrapper> links = Lists.newArrayList();
+		RelatedEntityWrapper rew = new RelatedEntityWrapper(rel, relatedProject);
+		links.add(rew);
+		JoinedEntity je = new JoinedEntity<>(p);
+		je.setLinks(links);
+
+		String xml = xmlRecordFactory.build(je);
+
+		assertNotNull(xml);
+
+		Document doc = new SAXReader().read(new StringReader(xml));
+		assertNotNull(doc);
+		System.out.println(doc.asXML());
+		assertEquals("", doc.valueOf("//rel/validated"));
+	}
 }

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

@@ -0,0 +1,109 @@
+{
+  "id": "40|corda__h2020::79a0e16c122c9a18eb60e4a5e64b620d",
+  "originalId": [],
+  "pid": [],
+  "dateofcollection": "2020-01-01",
+  "dateoftransformation": "2020-01-01",
+  "extraInfo": [],
+  "oaiprovenance": null,
+  "websiteurl": {
+    "value": "https://web.site",
+    "datainfo": null
+  },
+  "code": {
+    "value": "79a0e",
+    "datainfo": null
+  },
+  "acronym": {
+    "value": "79a0e_acronym",
+    "datainfo": null
+  },
+  "title": {
+    "value": "79a0e_title",
+    "datainfo": null
+  },
+  "startdate": {
+    "value": "2019-02-01",
+    "datainfo": null
+  },
+  "enddate": {
+    "value": "2021-01-09",
+    "datainfo": null
+  },
+  "callidentifier": {
+    "value": "79a0e_callID",
+    "datainfo": null
+  },
+  "keywords": {
+    "value": "",
+    "datainfo": null
+  },
+  "duration": {
+    "value": "",
+    "datainfo": null
+  },
+  "ecsc39": {
+    "value": "true",
+    "datainfo": null
+  },
+  "oamandatepublications": {
+    "value": "true",
+    "datainfo": null
+  },
+  "ecarticle29_3": {
+    "value": "false",
+    "datainfo": null
+  },
+  "optional1": {
+    "value": "",
+    "datainfo": null
+  },
+  "optional2": {
+    "value": "",
+    "datainfo": null
+  },
+  "jsonextrainfo":{
+    "value": "",
+    "datainfo": null
+  },
+  "contactfullname":{
+    "value": "",
+    "datainfo": null
+  },
+  "contactfax": {
+    "value": "",
+    "datainfo": null
+  },
+  "contactphone": {
+    "value": "",
+    "datainfo": null
+  },
+  "contactemail": {
+    "value": "",
+    "datainfo": null
+  },
+  "summary": {
+    "value": "79a0e_description",
+    "datainfo": null
+  },
+  "currency": {
+    "value": "EUR",
+    "datainfo": null
+  },
+  "totalcost": 120000,
+  "fundedamount": 18000,
+  "h2020topiccode": "",
+  "h2020topicdescription": "",
+  "h2020classification": [],
+  "subjects": [
+    {
+      "value": "",
+      "qualifier": null,
+      "datainfo": null
+    }
+  ],
+  "fundingtree": []
+
+}
+
+

dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/record.xml

@@ -294,6 +294,28 @@
                         >rcuk________::23feba2a5ca7f6b6016bf3a45180da50</to>
                         <legalname>University of Delhi</legalname>
                     </rel>
+                    <rel inferred="false" trust="0.9" inferenceprovenance="" provenanceaction="sysimport:crosswalk:repository">
+                       <validated date="2021-01-01">true</validated>
+                        <to class="isProducedBy" scheme="dnet:result_project_relations" type="project">corda_______::30c6b5ab90f30666de1d112fb93d8c77</to>
+                        <code>227878</code>
+                        <funding>
+                            <funder id="ec__________::EC" shortname="EC" name="European Commission" jurisdiction="EU" />
+                            <funding_level_0 name="FP7">ec__________::EC::FP7</funding_level_0>
+                            <funding_level_1 name="SP2">ec__________::EC::FP7::SP2</funding_level_1>
+                            <funding_level_2 name="ERC">ec__________::EC::FP7::SP2::ERC</funding_level_2>
+                        </funding>
+                        <title>Complex structure and dynamics of collective motion</title>
+                        <acronym>COLLMOT</acronym>
+                        <contracttype classid="ERC" classname="Support for frontier research (ERC)" schemeid="ec:FP7contractTypes" schemename="ec:FP7contractTypes" />
+                    </rel>
+                    <rel inferred="true" trust="0.72" inferenceprovenance="iis::document_referencedProjects" provenanceaction="iis">
+                        <to class="isProducedBy" scheme="dnet:result_project_relations" type="project">irb_hr______::2330a1d0dac71ffbe15fbcbc807288d4</to>
+                        <code>108-1083570-3635</code>
+                        <funding>
+                            <funder id="irb_hr______::MZOS" shortname="MZOS" name="Ministry of Science, Education and Sports of the Republic of Croatia (MSES)" jurisdiction="HR" />
+                        </funding>
+                        <title>Pentadecapeptide BPC 157 - further investigations</title>
+                    </rel>
                 </rels>
                 <children>
                     <instance id="openaire____::55045bd2a65019fd8e6741a755395c8c">

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

@@ -0,0 +1,31 @@
+{
+"collectedfrom": [
+{
+"key": "10|opendoar____::eccbc87e4b5ce2fe28308fd9f2a7baf3",
+"value": "AMS Acta",
+"dataInfo": null
+}
+],
+"dataInfo": {
+"invisible": false,
+"inferred": false,
+"deletedbyinference": false,
+"trust": "0.9",
+"inferenceprovenance": "",
+"provenanceaction": {
+"classid": "sysimport:crosswalk:repository",
+"classname": "sysimport:crosswalk:repository",
+"schemeid": "dnet:provenanceActions",
+"schemename": "dnet:provenanceActions"
+}
+},
+"lastupdatetimestamp": 1606898557407,
+"relType": "resultProject",
+"subRelType": "outcome",
+"relClass": "isProducedBy",
+"source": "50|CSC_________::0000ec4dd9df012feaafa77e71a0fb4c",
+"target": "40|corda__h2020::79a0e16c122c9a18eb60e4a5e64b620d",
+"validated": false,
+"validationDate": null,
+"properties": []
+}

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

@@ -0,0 +1,31 @@
+{
+"collectedfrom": [
+{
+"key": "10|opendoar____::eccbc87e4b5ce2fe28308fd9f2a7baf3",
+"value": "AMS Acta",
+"dataInfo": null
+}
+],
+"dataInfo": {
+"invisible": false,
+"inferred": false,
+"deletedbyinference": false,
+"trust": "0.9",
+"inferenceprovenance": "",
+"provenanceaction": {
+"classid": "sysimport:crosswalk:repository",
+"classname": "sysimport:crosswalk:repository",
+"schemeid": "dnet:provenanceActions",
+"schemename": "dnet:provenanceActions"
+}
+},
+"lastupdatetimestamp": 1606898557407,
+"relType": "resultProject",
+"subRelType": "outcome",
+"relClass": "isProducedBy",
+"source": "50|CSC_________::0000ec4dd9df012feaafa77e71a0fb4c",
+"target": "40|corda__h2020::79a0e16c122c9a18eb60e4a5e64b620d",
+"validated": true,
+"validationDate": "2021-01-01",
+"properties": []
+}