Merge pull request 'bipFinder: unresolved entities' (#174) from bipFinder into beta

Reviewed-on: #174

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java

@@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.actionmanager.bipmodel.Constants.UPDATE_CLASS_NAME;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;
@@ -28,6 +29,7 @@ import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Instance;
 import eu.dnetlib.dhp.schema.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.oaf.Measure;
 import eu.dnetlib.dhp.schema.oaf.Result;
@@ -39,7 +41,7 @@ public class PrepareBipFinder implements Serializable {
 	private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.class);
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	public static <I extends Result> void main(String[] args) throws Exception {
+	public static void main(String[] args) throws Exception {
 
 		String jsonConfiguration = IOUtils
 			.toString(
@@ -75,7 +77,7 @@ public class PrepareBipFinder implements Serializable {
 			});
 	}
 
-	private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath) {
+	private static void prepareResults(SparkSession spark, String inputPath, String outputPath) {
 
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
@@ -95,7 +97,9 @@ public class PrepareBipFinder implements Serializable {
 				Result r = new Result();
 
 				r.setId(DHPUtils.generateUnresolvedIdentifier(v.getId(), DOI));
-				r.setMeasures(getMeasure(v));
+				Instance inst = new Instance();
+				inst.setMeasures(getMeasure(v));
+				r.setInstance(Arrays.asList(inst));
 				return r;
 			}, Encoders.bean(Result.class))
 			.write()

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java

@@ -20,7 +20,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.Result;
 
 public class SparkSaveUnresolved implements Serializable {
-	private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class);
+	private static final Logger log = LoggerFactory.getLogger(SparkSaveUnresolved.class);
 
 	public static void main(String[] args) throws Exception {
 
@@ -64,7 +64,7 @@ public class SparkSaveUnresolved implements Serializable {
 			.map(
 				(MapFunction<String, Result>) l -> OBJECT_MAPPER.readValue(l, Result.class),
 				Encoders.bean(Result.class))
-			.groupByKey((MapFunction<Result, String>) r -> r.getId(), Encoders.STRING())
+			.groupByKey((MapFunction<Result, String>) Result::getId, Encoders.STRING())
 			.mapGroups((MapGroupsFunction<String, Result, Result>) (k, it) -> {
 				Result ret = it.next();
 				it.forEachRemaining(r -> ret.mergeFrom(r));

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml

@@ -1,9 +1,5 @@
 <workflow-app name="BipFinderScore" xmlns="uri:oozie:workflow:0.5">
     <parameters>
-        <property>
-            <name>inputPath</name>
-            <description>the input path of the resources to be extended</description>
-        </property>
 
         <property>
             <name>bipScorePath</name>
@@ -108,7 +104,5 @@
         <error to="Kill"/>
     </action>
 
-
-
     <end name="End"/>
 </workflow-app>

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java

@@ -96,13 +96,18 @@ public class PrepareTest {
 		String doi1 = "unresolved::10.0000/096020199389707::doi";
 
 		Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count());
-		Assertions.assertEquals(3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getMeasures().size());
+		Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().size());
+		Assertions
+			.assertEquals(
+				3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().get(0).getMeasures().size());
 		Assertions
 			.assertEquals(
 				"6.34596412687e-09", tmp
 					.filter(r -> r.getId().equals(doi1))
 					.collect()
 					.get(0)
+					.getInstance()
+					.get(0)
 					.getMeasures()
 					.stream()
 					.filter(sl -> sl.getId().equals("influence"))
@@ -117,6 +122,8 @@ public class PrepareTest {
 					.filter(r -> r.getId().equals(doi1))
 					.collect()
 					.get(0)
+					.getInstance()
+					.get(0)
 					.getMeasures()
 					.stream()
 					.filter(sl -> sl.getId().equals("popularity_alt"))
@@ -131,6 +138,8 @@ public class PrepareTest {
 					.filter(r -> r.getId().equals(doi1))
 					.collect()
 					.get(0)
+					.getInstance()
+					.get(0)
 					.getMeasures()
 					.stream()
 					.filter(sl -> sl.getId().equals("popularity"))

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java

@@ -126,6 +126,8 @@ public class ProduceTest {
 					.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
 					.collect()
 					.get(0)
+					.getInstance()
+					.get(0)
 					.getMeasures()
 					.size());
 
@@ -179,7 +181,8 @@ public class ProduceTest {
 
 		List<Measure> measures = tmp
 			.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
-			.flatMap(row -> row.getMeasures().iterator())
+			.flatMap(row -> row.getInstance().iterator())
+			.flatMap(inst -> inst.getMeasures().iterator())
 			.collect();
 		Assertions
 			.assertEquals(
@@ -226,7 +229,7 @@ public class ProduceTest {
 				85,
 				tmp
 					.filter(row -> !row.getId().equals("unresolved::10.3390/s18072310::doi"))
-					.filter(r -> r.getMeasures() != null)
+					.filter(r -> r.getInstance() != null)
 					.count());
 
 	}