9 changed files with 35 additions and 253 deletions
--- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/ResearchInitiative.java
+++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/ResearchInitiative.java
@ -19,7 +19,7 @@ import java.io.Serializable;
 */
 public class ResearchInitiative implements Serializable {
 	private String id; // openaireId
-	private String acronym; // context id
+	private String originalId; // context id
 	private String name; // context name
 	private String type; // context type: research initiative or research community
 	private String description;
@ -57,12 +57,12 @@ public class ResearchInitiative implements Serializable {
 		this.name = label;
 	}

-	public String getAcronym() {
-		return acronym;
+	public String getOriginalId() {
+		return originalId;
 	}

-	public void setAcronym(String acronym) {
-		this.acronym = acronym;
+	public void setOriginalId(String originalId) {
+		this.originalId = originalId;
 	}

 	public String getDescription() {
--- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java
+++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java
@ -1,6 +1,8 @@

 package eu.dnetlib.dhp.schema.oaf;

+import eu.dnetlib.dhp.schema.common.ModelSupport;
+
 import static com.google.common.base.Preconditions.checkArgument;

 import java.text.ParseException;
@ -8,8 +10,6 @@ import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;

-import eu.dnetlib.dhp.schema.common.ModelSupport;
-
 /**
 * Relation models any edge between two nodes in the OpenAIRE graph. It has a source id and a target id pointing to
 * graph node identifiers and it is further characterised by the semantic of the link through the fields relType,
@ -137,10 +137,7 @@ public class Relation extends Oaf {
 		try {
 			setValidationDate(ModelSupport.oldest(getValidationDate(), r.getValidationDate()));
 		} catch (ParseException e) {
-			throw new IllegalArgumentException(String
-				.format(
-					"invalid validation date format in relation [s:%s, t:%s]: %s", getSource(), getTarget(),
-					getValidationDate()));
+			throw new IllegalArgumentException(String.format("invalid validation date format in relation [s:%s, t:%s]: %s", getSource(), getTarget(), getValidationDate()));
 		}

 		super.mergeFrom(r);
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java
@ -4,11 +4,6 @@ package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
 import static eu.dnetlib.dhp.PropagationConstant.*;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;

-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Optional;
-
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.spark.SparkConf;
@ -27,6 +22,11 @@ import eu.dnetlib.dhp.schema.oaf.Datasource;
 import eu.dnetlib.dhp.schema.oaf.Organization;
 import eu.dnetlib.dhp.schema.oaf.Relation;

+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Optional;
+
 public class PrepareResultInstRepoAssociation {

 	private static final Logger log = LoggerFactory.getLogger(PrepareResultInstRepoAssociation.class);
@ -56,10 +56,9 @@ public class PrepareResultInstRepoAssociation {
 		final String alreadyLinkedPath = parser.get("alreadyLinkedPath");
 		log.info("alreadyLinkedPath {}: ", alreadyLinkedPath);

-		List<String> blacklist = Optional
-			.ofNullable(parser.get("blacklist"))
-			.map(v -> Arrays.asList(v.split(";")))
-			.orElse(new ArrayList<>());
+		List<String> blacklist = Optional.ofNullable(parser.get("blacklist"))
+				.map(v -> Arrays.asList(v.split(";")))
+				.orElse(new ArrayList<>());

 		SparkConf conf = new SparkConf();
 		conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
@ -92,13 +91,14 @@ public class PrepareResultInstRepoAssociation {
 	private static void prepareDatasourceOrganization(
 		SparkSession spark, String datasourceOrganizationPath, List<String> blacklist) {
 		String blacklisted = "";
-		if (blacklist.size() > 0) {
+		if(blacklist.size() > 0 ){
 			blacklisted = " AND  d.id != '" + blacklist.get(0) + "'";
 			for (int i = 1; i < blacklist.size(); i++) {
 				blacklisted += " AND d.id != '" + blacklist.get(i) + "'";
 			}
 		}

+
 		String query = "SELECT source datasourceId, target organizationId "
 			+ "FROM ( SELECT id "
 			+ "FROM datasource "
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java
@ -70,10 +70,10 @@ public class CreateContextRelation implements Serializable {
 		cce.execute(Process::getRelation, CONTEX_RELATION_DATASOURCE, ModelSupport.getIdPrefix(Datasource.class));

 		log.info("Creating relations for projects... ");
-		cce
-			.execute(
-				Process::getRelation, CONTEX_RELATION_PROJECT,
-				ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class));
+//		cce
+//			.execute(
+//				Process::getRelation, CONTEX_RELATION_PROJECT,
+//				ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class));

 		cce.close();

--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java
@ -147,7 +147,7 @@ public class Extractor implements Serializable {
 					.map(
 						paction -> Provenance
 							.newInstance(
-								paction.getClassname(),
+								paction.getClassid(),
 								dinfo.getTrust()))
 					.orElse(
 						Provenance
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java
@ -35,7 +35,7 @@ public class Process implements Serializable {
 				ri.setType(Constants.RESEARCH_INFRASTRUCTURE);
 			}
 			ri.setId(Utils.getContextId(ci.getId()));
-			ri.setAcronym(ci.getId());
+			ri.setOriginalId(ci.getId());

 			ri.setDescription(ci.getDescription());
 			ri.setName(ci.getName());
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java
@ -12,7 +12,6 @@ import org.dom4j.Node;
 import org.dom4j.io.SAXReader;
 import org.jetbrains.annotations.NotNull;

-import eu.dnetlib.dhp.utils.DHPUtils;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;

@ -114,72 +113,14 @@ public class QueryInformationSystem {
 	@NotNull
 	private List<String> getCategoryList(Element el, String prefix) {
 		List<String> datasourceList = new ArrayList<>();
-		for (Object node : el.selectNodes(".//concept")) {
-			String oid = getOpenaireId((Node) node, prefix);
-			if (oid != null)
-				datasourceList.add(oid);
+		for (Object node : el.selectNodes(".//param")) {
+			Node n = (Node) node;
+			if (n.valueOf("./@name").equals("openaireId")) {
+				datasourceList.add(prefix + "|" + n.getText());
+			}
 		}

 		return datasourceList;
 	}

-	private String getOpenaireId(Node el, String prefix) {
-
-		for (Object node : el.selectNodes(".//param")) {
-			Node n = (Node) node;
-			if (n.valueOf("./@name").equals("openaireId")) {
-				return prefix + "|" + n.getText();
-			}
-		}
-		return makeOpenaireId(el, prefix);
-
-	}
-
-	private String makeOpenaireId(Node el, String prefix) {
-		String funder = null;
-		String grantId = null;
-		String funding = null;
-		for (Object node : el.selectNodes(".//param")) {
-			Node n = (Node) node;
-			switch (n.valueOf("./@name")) {
-				case "funding":
-					funding = n.getText();
-					break;
-				case "funder":
-					funder = n.getText();
-					break;
-				case "CD_PROJECT_NUMBER":
-					grantId = n.getText();
-					break;
-			}
-		}
-		String nsp = null;
-		switch (funder.toLowerCase()) {
-			case "ec":
-				if (funding == null) {
-					return null;
-				}
-				if (funding.toLowerCase().startsWith("h2020")) {
-					nsp = "corda__h2020::";
-				} else {
-					nsp = "corda_______::";
-				}
-				break;
-			case "tubitak":
-				nsp = "tubitakf____::";
-				break;
-			case "dfg":
-				nsp = "dfgf________::";
-				break;
-			default:
-				nsp = funder.toLowerCase();
-				for (int i = funder.length(); i < 12; i++)
-					nsp += "_";
-				nsp += "::";
-		}
-
-		return prefix + "|" + nsp + DHPUtils.md5(grantId);
-
-	}
-
 }
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java
@ -97,7 +97,7 @@ public class CreateEntityTest {
 		Assertions.assertEquals(12, riList.size());

 		riList.stream().forEach(c -> {
-			switch (c.getAcronym()) {
+			switch (c.getOriginalId()) {
 				case "mes":
 					Assertions
 						.assertTrue(c.getType().equals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_COMMUNITY));
@ -115,9 +115,9 @@ public class CreateEntityTest {
 									String
 										.format(
 											"%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX,
-											DHPUtils.md5(c.getAcronym()))));
+											DHPUtils.md5(c.getOriginalId()))));
 					Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_mes"));
-					Assertions.assertTrue("mes".equals(c.getAcronym()));
+					Assertions.assertTrue("mes".equals(c.getOriginalId()));
 					break;
 				case "clarin":
 					Assertions
@ -130,9 +130,9 @@ public class CreateEntityTest {
 									String
 										.format(
 											"%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX,
-											DHPUtils.md5(c.getAcronym()))));
+											DHPUtils.md5(c.getOriginalId()))));
 					Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_clarin"));
-					Assertions.assertTrue("clarin".equals(c.getAcronym()));
+					Assertions.assertTrue("clarin".equals(c.getOriginalId()));
 					break;
 			}
 			// TODO add check for all the others Entities
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java
@ -9,14 +9,11 @@ import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;

-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.gson.Gson;

 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
 import eu.dnetlib.dhp.schema.oaf.Datasource;
-import eu.dnetlib.dhp.schema.oaf.Project;
 import eu.dnetlib.dhp.utils.DHPUtils;

 public class CreateRelationTest {
@ -206,7 +203,6 @@ public class CreateRelationTest {
 				"    <param name=\"suggestedAcknowledgement\"/>\n" +
 				"    <param name=\"zenodoCommunity\">oac_ni</param>\n" +
 				"    <param name=\"creationdate\">2018-03-01T12:00:00</param>\n" +
-				"    <category claim=\"false\" id=\"ni::projects\" label=\"NI Content providers\"/>\n" +
 				"    <category claim=\"false\" id=\"ni::contentproviders\" label=\"NI Content providers\">\n" +
 				"        <concept claim=\"false\" id=\"ni::contentproviders::1\" label=\"OpenNeuro\">\n" +
 				"            <param name=\"openaireId\">re3data_____::5b9bf9171d92df854cf3c520692e9122</param>\n" +
@ -441,65 +437,7 @@ public class CreateRelationTest {
 				"    <param name=\"suggestedAcknowledgement\"/>\n" +
 				"    <param name=\"zenodoCommunity\">oaa_elixir-gr</param>\n" +
 				"    <param name=\"creationdate\">2018-03-01T12:00:00</param>\n" +
-				"    <category claim=\"false\" id=\"elixir-gr::projects\" label=\"ELIXIR GR Projects\">\n" +
-				"                    <concept claim=\"false\" id=\"ni::projects::12\" label=\"\">\n" +
-				"                        <param name=\"projectfullname\">BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)</param>\n"
-				+
-				"                        <param name=\"acronym\"/>\n" +
-				"                        <param name=\"CD_PROJECT_NUMBER\">1U24RR025736-01</param>\n" +
-				"                        <param name=\"funder\">NIH</param>\n" +
-				"                    </concept>\n" +
-				"                    <concept claim=\"false\" id=\"ni::projects::13\" label=\"\">\n" +
-				"                        <param name=\"projectfullname\">COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning</param>\n"
-				+
-				"                        <param name=\"acronym\"/>\n" +
-				"                        <param name=\"CD_PROJECT_NUMBER\">0223843</param>\n" +
-				"                        <param name=\"funder\">NSF</param>\n" +
-				"                    </concept>\n" +
-				"                    <concept claim=\"false\" id=\"ni::projects::14\" label=\"\">\n" +
-				"                        <param name=\"projectfullname\">The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia</param>\n"
-				+
-				"                        <param name=\"acronym\"/>\n" +
-				"                        <param name=\"CD_PROJECT_NUMBER\">5R01MH082795-05</param>\n" +
-				"                        <param name=\"funder\">NIH</param>\n" +
-				"                    </concept>\n" +
-				"                    <concept claim=\"false\" id=\"ni::projects::15\" label=\"\">\n" +
-				"                        <param name=\"projectfullname\">Fragmented early life environmental and emotional / cognitive vulnerabilities</param>\n"
-				+
-				"                        <param name=\"acronym\"/>\n" +
-				"                        <param name=\"CD_PROJECT_NUMBER\">1P50MH096889-01A1</param>\n" +
-				"                        <param name=\"funder\">NIH</param>\n" +
-				"                    </concept>\n" +
-				"                    <concept claim=\"false\" id=\"ni::projects::16\" label=\"\">\n" +
-				"                        <param name=\"projectfullname\">Enhancement of the 1000 Functional Connectome Project</param>\n"
-				+
-				"                        <param name=\"acronym\"/>\n" +
-				"                        <param name=\"CD_PROJECT_NUMBER\">1R03MH096321-01A1</param>\n" +
-				"                        <param name=\"funder\">TUBITAK</param>\n" +
-				"                    </concept>\n" +
-				"                    <concept claim=\"false\" id=\"ni::projects::17\" label=\"\">\n" +
-				"                        <param name=\"projectfullname\">CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project</param>\n"
-				+
-				"                        <param name=\"acronym\"/>\n" +
-				"                        <param name=\"CD_PROJECT_NUMBER\">1131441</param>\n" +
-				"                        <param name=\"funder\">NSF</param>\n" +
-				"                    </concept>\n" +
-				"                    <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" +
-				"                        <param name=\"projectfullname\">Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI</param>\n"
-				+
-				"                        <param name=\"acronym\"/>\n" +
-				"                        <param name=\"CD_PROJECT_NUMBER\">0121950</param>\n" +
-				"                        <param name=\"funder\">NSF</param>\n" +
-				"                    </concept>\n" +
-				"                    <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" +
-				"                        <param name=\"projectfullname\">Transforming statistical methodology for neuroimaging meta-analysis.</param>\n"
-				+
-				"                        <param name=\"acronym\"/>\n" +
-				"                        <param name=\"CD_PROJECT_NUMBER\">100309</param>\n" +
-				"                        <param name=\"funder\">WT</param>\n" +
-				"                    </concept>\n" +
-				"                </category>" +
-
+				"    <category claim=\"false\" id=\"elixir-gr::projects\" label=\"ELIXIR GR Projects\"/>\n" +
 				"    <category claim=\"false\" id=\"elixir-gr::contentproviders\" label=\"Elixir-GR Content providers\">\n"
 				+
 				"        <concept claim=\"false\" id=\"elixir-gr::contentproviders::1\" label=\"bio.tools\">\n" +
@ -628,98 +566,4 @@ public class CreateRelationTest {
 					tmp.contains("10|doajarticles::2899208a99aa7d142646e0a80bfeef05"));

 	}
-
-	@Test
-	public void test2() {
-		List<ContextInfo> cInfoList = new ArrayList<>();
-		final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci);
-
-		queryInformationSystem
-			.getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class));
-
-		cInfoList.forEach(c -> System.out.println(new Gson().toJson(c)));
-
-		List<Relation> rList = new ArrayList<>();
-
-		cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add));
-
-		Assertions.assertEquals(44, rList.size());
-
-		Assertions
-			.assertFalse(
-				rList
-					.stream()
-					.map(r -> r.getSource().getId())
-					.collect(Collectors.toSet())
-					.contains(
-						String
-							.format(
-								"%s|%s::%s", Constants.CONTEXT_ID,
-								Constants.CONTEXT_NS_PREFIX,
-								DHPUtils.md5("dh-ch"))));
-
-		Assertions
-			.assertEquals(
-				2,
-				rList
-					.stream()
-					.filter(
-						r -> r
-							.getSource()
-							.getId()
-							.equals(
-								String
-									.format(
-										"%s|%s::%s", Constants.CONTEXT_ID,
-										Constants.CONTEXT_NS_PREFIX,
-										DHPUtils.md5("clarin"))))
-					.collect(Collectors.toList())
-					.size());
-
-		Assertions
-			.assertEquals(
-				2,
-				rList
-					.stream()
-					.filter(
-						r -> r
-							.getTarget()
-							.getId()
-							.equals(
-								String
-									.format(
-										"%s|%s::%s", Constants.CONTEXT_ID,
-										Constants.CONTEXT_NS_PREFIX,
-										DHPUtils.md5("clarin"))))
-					.collect(Collectors.toList())
-					.size());
-
-		Set<String> tmp = rList
-			.stream()
-			.filter(
-				r -> r
-					.getSource()
-					.getId()
-					.equals(
-						String
-							.format(
-								"%s|%s::%s", Constants.CONTEXT_ID,
-								Constants.CONTEXT_NS_PREFIX,
-								DHPUtils.md5("clarin"))))
-			.map(r -> r.getTarget().getId())
-			.collect(Collectors.toSet());
-
-		Assertions
-			.assertTrue(
-				tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") &&
-					tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4"));
-
-		rList.forEach(rel -> {
-			if (rel.getSource().getId().startsWith("40|")) {
-				String proj = rel.getSource().getId().substring(3);
-				Assertions.assertTrue(proj.substring(0, proj.indexOf("::")).length() == 12);
-			}
-		});
-
-	}
 }