reintegrated changes from fcbc4ccd70

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

@@ -1,77 +0,0 @@
-package eu.dnetlib.dhp.graph;
-
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.dnetlib.dhp.schema.oaf.*;
-import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.sql.SparkSession;
-
-import java.io.IOException;
-import java.util.stream.Collectors;
-
-public class GraphMapper {
-
-
-    public void map(final SparkSession spark, final String outPath) {
-
-        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
-
-        sc.textFile(outPath + "/linked_entities")
-                .map(LinkedEntityWrapper::parse)
-                .map(GraphMapper::asLinkedEntity)
-                .map(e -> new ObjectMapper().writeValueAsString(e))
-                .saveAsTextFile(outPath + "/linked_entities_types");
-    }
-
-    private static LinkedEntity asLinkedEntity(final LinkedEntityWrapper lw) throws JsonProcessingException {
-        final LinkedEntity le = new LinkedEntity();
-
-        try {
-            le.setType(lw.getEntity().getType());
-            le.setEntity(parseEntity(lw.getEntity().getOaf(), le.getType()));
-            le.setLinks(lw.getLinks()
-                    .stream()
-                    .map(l -> new Link()
-                            .setRelation(parseRelation(l.getRelation().getOaf()))
-                            .setRelatedEntity(RelatedEntity.parse(l.getTarget().getOaf())))
-                    .collect(Collectors.toList()));
-            return le;
-        } catch (IllegalArgumentException e) {
-            throw new IllegalArgumentException(new ObjectMapper().writeValueAsString(lw), e);
-        }
-    }
-
-    private static Relation parseRelation(final String s) {
-        try {
-            return new ObjectMapper().readValue(s, Relation.class);
-        } catch (IOException e) {
-            throw new IllegalArgumentException("unable to decode Relation: " + s);
-        }
-    }
-
-    private static OafEntity parseEntity(final String json, final String type) {
-        final ObjectMapper o = new ObjectMapper();
-        try {
-            switch (type) {
-                case "publication":
-                    return o.readValue(json, Publication.class);
-                case "dataset":
-                    return o.readValue(json, Dataset.class);
-                case "otherresearchproduct":
-                    return o.readValue(json, OtherResearchProduct.class);
-                case "software":
-                    return o.readValue(json, Software.class);
-                case "datasource":
-                    return o.readValue(json, Datasource.class);
-                case "project":
-                    return o.readValue(json, Project.class);
-                case "organization":
-                    return o.readValue(json, Organization.class);
-                default:
-                    throw new IllegalArgumentException("invalid entity type: " + type);
-            }
-        } catch (IOException e) {
-            throw new IllegalArgumentException("unable to decode oaf entity: " + json);
-        }
-    }
-}

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

@@ -1,30 +0,0 @@
-package eu.dnetlib.dhp.graph;
-
-import eu.dnetlib.dhp.schema.oaf.Relation;
-
-import java.io.Serializable;
-
-public class Link implements Serializable {
-
-    private Relation relation;
-
-    private RelatedEntity relatedEntity;
-
-    public Relation getRelation() {
-        return relation;
-    }
-
-    public Link setRelation(Relation relation) {
-        this.relation = relation;
-        return this;
-    }
-
-    public RelatedEntity getRelatedEntity() {
-        return relatedEntity;
-    }
-
-    public Link setRelatedEntity(RelatedEntity relatedEntity) {
-        this.relatedEntity = relatedEntity;
-        return this;
-    }
-}

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

@@ -1,41 +1,28 @@
 package eu.dnetlib.dhp.graph;
 
-import eu.dnetlib.dhp.schema.oaf.OafEntity;
-
 import java.io.Serializable;
 import java.util.List;
 
 public class LinkedEntity implements Serializable {
 
-    private String type;
+    private TypedRow entity;
 
-    private OafEntity entity;
+    private List<Tuple> links;
 
-    private List<Link> links;
+    public TypedRow getEntity() {
-
-    public String getType() {
-        return type;
-    }
-
-    public LinkedEntity setType(String type) {
-        this.type = type;
-        return this;
-    }
-
-    public OafEntity getEntity() {
         return entity;
     }
 
-    public LinkedEntity setEntity(OafEntity entity) {
+    public LinkedEntity setEntity(TypedRow entity) {
         this.entity = entity;
         return this;
     }
 
-    public List<Link> getLinks() {
+    public List<Tuple> getLinks() {
         return links;
     }
 
-    public LinkedEntity setLinks(List<Link> links) {
+    public LinkedEntity setLinks(List<Tuple> links) {
         this.links = links;
         return this;
     }

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

@@ -1,40 +0,0 @@
-package eu.dnetlib.dhp.graph;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import java.io.IOException;
-import java.io.Serializable;
-import java.util.List;
-
-public class LinkedEntityWrapper implements Serializable {
-
-    private TypedRow entity;
-
-    private List<TupleWrapper> links;
-
-    public static LinkedEntityWrapper parse(final String s) {
-        try {
-            return new ObjectMapper().readValue(s, LinkedEntityWrapper.class);
-        } catch (IOException e) {
-            throw new IllegalArgumentException("unable to decode LinkedEntityWrapper: " + s);
-        }
-    }
-
-    public TypedRow getEntity() {
-        return entity;
-    }
-
-    public LinkedEntityWrapper setEntity(TypedRow entity) {
-        this.entity = entity;
-        return this;
-    }
-
-    public List<TupleWrapper> getLinks() {
-        return links;
-    }
-
-    public LinkedEntityWrapper setLinks(List<TupleWrapper> links) {
-        this.links = links;
-        return this;
-    }
-}

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

@@ -34,7 +34,8 @@ public class SparkXmlRecordBuilderJob {
         }
 
         new GraphJoiner(spark, inputPath, outputPath)
-                .adjacencyLists();
+                .adjacencyLists()
+                .asXML();
     }
 
 }

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

@@ -0,0 +1,29 @@
+package eu.dnetlib.dhp.graph;
+
+import java.io.Serializable;
+
+public class Tuple implements Serializable {
+
+    private TypedRow relation;
+
+    private TypedRow target;
+
+
+    public TypedRow getRelation() {
+        return relation;
+    }
+
+    public Tuple setRelation(TypedRow relation) {
+        this.relation = relation;
+        return this;
+    }
+
+    public TypedRow getTarget() {
+        return target;
+    }
+
+    public Tuple setTarget(TypedRow target) {
+        this.target = target;
+        return this;
+    }
+}