Refactor PrepareAffiliationRelations.java to use OafMapperUtils common functions

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java

@@ -1,19 +1,14 @@
 
 package eu.dnetlib.dhp.actionmanager.bipaffiliations;
 
-import static eu.dnetlib.dhp.actionmanager.Constants.*;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
 import java.util.stream.Collectors;
-import java.util.stream.Stream;
 
 import eu.dnetlib.dhp.actionmanager.Constants;
 import eu.dnetlib.dhp.actionmanager.bipaffiliations.model.*;
+import eu.dnetlib.dhp.actionmanager.ror.GenerateRorActionSetJob;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
@@ -25,7 +20,6 @@ import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -33,16 +27,14 @@ import org.apache.spark.sql.Dataset;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
-import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import scala.Tuple2;
 
 /**
- * created the Atomic Action for each tipe of results
+ * Creates action sets for Crossref affiliation relations inferred by BIP!
  */
 public class PrepareAffiliationRelations implements Serializable {
 
@@ -50,19 +42,17 @@ public class PrepareAffiliationRelations implements Serializable {
     private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelations.class);
     private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
     private static final String ID_PREFIX = "50|doi_________::";
-
+    public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
-    private static final String TRUST = "0.91";
+    public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
-
+    public static final String BIP_INFERENCE_PROVENANCE = "bip_affiliation";
-    public static final String BIP_AFFILIATIONS_CLASSID = "sysimport:crosswalk:bipaffiliations";
-    public static final String BIP_AFFILIATIONS_CLASSNAME = "Imported from BIP! Affiliations";
 
     public static <I extends Result> void main(String[] args) throws Exception {
 
         String jsonConfiguration = IOUtils
-                .toString(
+            .toString(
-                        PrepareAffiliationRelations.class
+                PrepareAffiliationRelations.class
-                                .getResourceAsStream(
+                .getResourceAsStream(
-                                        "/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json"));
+                    "/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json"));
 
         final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
         parser.parseArgument(args);
@@ -91,14 +81,12 @@ public class PrepareAffiliationRelations implements Serializable {
 
         final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
+        // load and parse affiliation relations from HDFS
         JavaRDD<AffiliationRelationDeserializer> affiliationRelationsDeserializeRDD = sc
             .textFile(inputPath)
             .map(item -> OBJECT_MAPPER.readValue(item, AffiliationRelationDeserializer.class));
 
-//        for(AffiliationRelationDeserializer rel: bipDeserializeJavaRDD.collect()){
+        // convert affiliation to an internal representation
-//            System.out.println(rel);
-//        }
-
         Dataset<AffiliationRelationModel> affiliationRelations =
             spark.createDataset(
                 affiliationRelationsDeserializeRDD.flatMap(entry ->
@@ -112,15 +100,40 @@ public class PrepareAffiliationRelations implements Serializable {
                 .rdd(),
                 Encoders.bean(AffiliationRelationModel.class));
 
+        // prepare action sets for affiliation relations
         affiliationRelations
             .map((MapFunction<AffiliationRelationModel, Relation>) affRel -> {
 
-                String paperId = ID_PREFIX
+                // DOI to OpenAIRE id
-                        + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", affRel.getDoi()));
+                final String paperId = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", affRel.getDoi()));
-                final String affId = ID_PREFIX
-                        + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("ror", affRel.getRorId()));
 
-                return getRelation(paperId, affId, ModelConstants.HAS_AUTHOR_INSTITUTION);
+                // ROR id to OpenAIRE id
+                final String affId = GenerateRorActionSetJob.calculateOpenaireId(affRel.getRorId());
+
+                Qualifier qualifier = OafMapperUtils.qualifier(
+                    BIP_AFFILIATIONS_CLASSID,
+                    BIP_AFFILIATIONS_CLASSNAME,
+                    ModelConstants.DNET_PROVENANCE_ACTIONS,
+                    ModelConstants.DNET_PROVENANCE_ACTIONS);
+
+                // format data info; setting `confidence` into relation's `trust`
+                DataInfo dataInfo = OafMapperUtils.dataInfo(
+                   false,
+                   BIP_INFERENCE_PROVENANCE,
+                   true,
+                   false,
+                   qualifier,
+                   Double.toString(affRel.getConfidence()));
+
+                return OafMapperUtils.getRelation(
+                    paperId,
+                    affId,
+                    ModelConstants.RESULT_ORGANIZATION,
+                    ModelConstants.AFFILIATION,
+                    ModelConstants.HAS_AUTHOR_INSTITUTION,
+                    null,
+                    dataInfo,
+                    null);
 
             }, Encoders.bean(Relation.class))
             .toJavaRDD()
@@ -131,50 +144,4 @@ public class PrepareAffiliationRelations implements Serializable {
             .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
 
     }
-
-    public static Relation getRelation(String source, String target, String relclass) {
-        Relation r = new Relation();
-
-        r.setCollectedfrom(getCollectedFrom());
-        r.setSource(source);
-        r.setTarget(target);
-        r.setRelClass(relclass);
-        r.setRelType(ModelConstants.RESULT_ORGANIZATION);
-        r.setSubRelType(ModelConstants.AFFILIATION);
-        r.setDataInfo(getDataInfo());
-        return r;
-    }
-
-    public static List<KeyValue> getCollectedFrom() {
-        KeyValue kv = new KeyValue();
-        kv.setKey(ModelConstants.DNET_PROVENANCE_ACTIONS);
-        kv.setValue(ModelConstants.DNET_PROVENANCE_ACTIONS);
-
-        return Collections.singletonList(kv);
-    }
-
-    public static DataInfo getDataInfo() {
-        DataInfo di = new DataInfo();
-        di.setInferred(false);
-        di.setDeletedbyinference(false);
-        di.setTrust(TRUST);
-        di.setProvenanceaction(
-            getQualifier(
-                BIP_AFFILIATIONS_CLASSID,
-                BIP_AFFILIATIONS_CLASSNAME,
-                ModelConstants.DNET_PROVENANCE_ACTIONS
-            ));
-        return di;
-    }
-
-    public static Qualifier getQualifier(String class_id, String class_name,
-                                         String qualifierSchema) {
-        Qualifier pa = new Qualifier();
-        pa.setClassid(class_id);
-        pa.setClassname(class_name);
-        pa.setSchemeid(qualifierSchema);
-        pa.setSchemename(qualifierSchema);
-        return pa;
-    }
-
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java

@@ -168,7 +168,7 @@ public class GenerateRorActionSetJob {
 
 	}
 
-	private static String calculateOpenaireId(final String rorId) {
+	public static String calculateOpenaireId(final String rorId) {
 		return String.format("20|%s::%s", Constants.ROR_NS_PREFIX, DHPUtils.md5(rorId));
 	}