merge with dump

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

@@ -4,7 +4,7 @@ package eu.dnetlib.dhp.schema.dump.oaf;
 import java.io.Serializable;
 
 /**
- * Used to refer to the Article Processing Charge information. Not dumped in this release. It contains two parameters: -
+ * Used to refer to the Article Processing Charge information. It contains two parameters: -
  * currency of type String to store the currency of the APC - amount of type String to stores the charged amount
  */
 public class APC implements Serializable {

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

@@ -12,9 +12,11 @@ import java.util.List;
  * type of type String to store the type of the instance as defined in the corresponding dnet vocabulary
  * (dnet:pubication_resource). It corresponds to the instancetype.classname of the instance to be mapped - url of type
  * List<String> list of locations where the instance is accessible. It corresponds to url of the instance to be dumped -
- * publicationdate of type String to store the publication date of the instance ;// dateofacceptance; - refereed of type
+ * publicationdate of type String to store the publication date of the instance ;// dateofacceptance;
- * String to store information abour tthe review status of the instance. Possible values are 'Unknown',
+ * - refereed of type
+ * String to store information abour the review status of the instance. Possible values are 'Unknown',
  * 'nonPeerReviewed', 'peerReviewed'. It corresponds to refereed.classname of the instance to be dumped
+ * - articleprocessingcharge of type APC to store the article processing charges possibly associated to the instance
  */
 public class Instance implements Serializable {
 
@@ -28,6 +30,8 @@ public class Instance implements Serializable {
 
 	private String publicationdate;// dateofacceptance;
 
+	private APC articleprocessingcharge;
+
 	private String refereed; // peer-review status
 
 	public String getLicense() {
@@ -78,4 +82,11 @@ public class Instance implements Serializable {
 		this.refereed = refereed;
 	}
 
+	public APC getArticleprocessingcharge() {
+		return articleprocessingcharge;
+	}
+
+	public void setArticleprocessingcharge(APC articleprocessingcharge) {
+		this.articleprocessingcharge = articleprocessingcharge;
+	}
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java

@@ -24,8 +24,6 @@ public class Constants {
 
 	public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative";
 
-	public static String ORCID = "orcid";
-
 	static {
 		accessRightsCoarMap.put("OPEN", "c_abf2");
 		accessRightsCoarMap.put("RESTRICTED", "c_16ec");

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java

@@ -424,6 +424,14 @@ public class ResultMapper implements Serializable {
 			.ifPresent(value -> instance.setType(value.getClassname()));
 		Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
 
+		Optional<Field<String>> oPca = Optional.ofNullable(i.getProcessingchargeamount());
+		Optional<Field<String>> oPcc = Optional.ofNullable(i.getProcessingchargecurrency());
+		if (oPca.isPresent() && oPcc.isPresent()) {
+			APC apc = new APC();
+			apc.setCurrency(oPcc.get().getValue());
+			apc.setAmount(oPca.get().getValue());
+			instance.setArticleprocessingcharge(apc);
+		}
 	}
 
 	private static List<Provenance> getUniqueProvenance(List<Provenance> provenance) {
@@ -503,7 +511,7 @@ public class ResultMapper implements Serializable {
 
 	private static Pid getOrcid(List<StructuredProperty> p) {
 		for (StructuredProperty pid : p) {
-			if (pid.getQualifier().getClassid().equals(Constants.ORCID)) {
+			if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) {
 				Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
 				if (di.isPresent()) {
 					return Pid

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java

@@ -57,16 +57,12 @@ public class CommunitySplit implements Serializable {
 		Dataset<CommunityResult> community_products = result
 			.filter((FilterFunction<CommunityResult>) r -> containsCommunity(r, c));
 
-		try {
-			community_products.first();
-			community_products
-				.write()
-				.option("compression", "gzip")
-				.mode(SaveMode.Overwrite)
-				.json(outputPath + "/" + c);
-		} catch (Exception e) {
 
-		}
+		community_products
+			.write()
+			.option("compression", "gzip")
+			.mode(SaveMode.Overwrite)
+			.json(outputPath + "/" + c);
 
 	}
 
@@ -75,9 +71,9 @@ public class CommunitySplit implements Serializable {
 			return r
 				.getContext()
 				.stream()
-				.filter(con -> con.getCode().equals(c))
+				.map(con -> con.getCode())
 				.collect(Collectors.toList())
-				.size() > 0;
+				.contains(c);
 		}
 		return false;
 	}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java

@@ -102,19 +102,26 @@ public class SparkDumpFunderResults implements Serializable {
 			} else {
 				funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase();
 			}
-			writeFunderResult(funder, result, outputPath + "/" + funderdump);
+			writeFunderResult(funder, result, outputPath, funderdump);
 		});
 
 	}
 
-	private static void writeFunderResult(String funder, Dataset<CommunityResult> results, String outputPath) {
+	private static void dumpResults(String nsp, Dataset<CommunityResult> results, String outputPath,
+		String funderName) {
 
 		results.map((MapFunction<CommunityResult, CommunityResult>) r -> {
 			if (!Optional.ofNullable(r.getProjects()).isPresent()) {
 				return null;
 			}
 			for (Project p : r.getProjects()) {
-				if (p.getId().startsWith(funder)) {
+				if (p.getId().startsWith(nsp)) {
+					if (nsp.startsWith("40|irb")) {
+						if (p.getFunder().getShortName().equals(funderName))
+							return r;
+						else
+							return null;
+					}
 					return r;
 				}
 			}
@@ -124,7 +131,18 @@ public class SparkDumpFunderResults implements Serializable {
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
-			.json(outputPath);
+			.json(outputPath + "/" + funderName);
+	}
+
+	private static void writeFunderResult(String funder, Dataset<CommunityResult> results, String outputPath,
+		String funderDump) {
+
+		if (funder.startsWith("40|irb")) {
+			dumpResults(funder, results, outputPath, "HRZZ");
+			dumpResults(funder, results, outputPath, "MZOS");
+		} else
+			dumpResults(funder, results, outputPath, funderDump);
+
 	}
 
 }

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funderresults/oozie_app/workflow.xml

@@ -1,9 +1,8 @@
 <workflow-app name="dump_funder_results" xmlns="uri:oozie:workflow:0.5">
-
     <parameters>
         <property>
             <name>upload</name>
-            <value>false</value>
+            <value>true</value>
             <description>true to upload the dump for the funders in Zenodo</description>
         </property>
         <property>

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java

@@ -13,6 +13,7 @@ import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.ForeachFunction;
 import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
 import org.junit.jupiter.api.*;
 import org.slf4j.Logger;
@@ -408,4 +409,54 @@ public class DumpJobTest {
 
 	}
 
+	@Test
+	public void testArticlePCA() {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca")
+			.getPath();
+
+		final String communityMapPath = getClass()
+			.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
+			.getPath();
+
+		DumpProducts dump = new DumpProducts();
+		dump
+			.run(
+				// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
+				false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
+				GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<GraphResult> tmp = sc
+			.textFile(workingDir.toString() + "/result")
+			.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
+
+		org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
+			.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
+
+		Assertions.assertEquals(23, verificationDataset.count());
+		// verificationDataset.show(false);
+
+		Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count());
+
+		verificationDataset.createOrReplaceTempView("check");
+
+		org.apache.spark.sql.Dataset<Row> temp = spark
+			.sql(
+				"select id " +
+					"from check " +
+					"lateral view explode (instance) i as inst " +
+					"where inst.articleprocessingcharge is not null");
+
+		Assertions.assertTrue(temp.count() == 2);
+
+		Assertions.assertTrue(temp.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'").count() == 1);
+
+		Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1);
+
+
+//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
+	}
+
 }

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java

@@ -137,5 +137,10 @@ public class SplitPerFunderTest {
 			.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
 		Assertions.assertEquals(3, tmp.count());
 
+		// H2020 3
+		tmp = sc
+			.textFile(workingDir.toString() + "/split/MZOS")
+			.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
+		Assertions.assertEquals(1, tmp.count());
 	}
 }

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation

@@ -5,4 +5,5 @@
 {"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::8b75543067b50076e70764917e188178","subRelType":"provision","target":"40|snsf________::50cb15ff7a6a3f8531f063770179e346"}
 {"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::9f3ff882f023209d9ffb4dc32b77d376","subRelType":"provision","target":"40|corda_______::ffc1811633b3222e4764c7b0517f83e8"}
 {"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::b566fa319c3923454e1e8eb886ab62d2","subRelType":"provision","target":"40|nhmrc_______::4e6c928fef9851b37ec73f4f6daca35b"}
-{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::e0554fb004a155bc23cfb43ee9fc8eae","subRelType":"provision","target":"40|corda__h2020::846b777af165fef7c904a81712a83b66"}
+{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::e0554fb004a155bc23cfb43ee9fc8eae","subRelType":"provision","target":"40|corda__h2020::846b777af165fef7c904a81712a83b66"}
+{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"40|irb_hr______::1e5e62235d094afd01cd56e65112fc63"}