fixed conflict

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

@@ -10,54 +10,60 @@ public class DataInfo implements Serializable {
     private Boolean deletedbyinference;
     private String trust;
     private String inferenceprovenance;
-    private List<Qualifier> provenanceaction;
+    private Qualifier provenanceaction;
 
 
     public Boolean getInvisible() {
         return invisible;
     }
 
-    public void setInvisible(Boolean invisible) {
+    public DataInfo setInvisible(Boolean invisible) {
         this.invisible = invisible;
+        return this;
     }
 
     public Boolean getInferred() {
         return inferred;
     }
 
-    public void setInferred(Boolean inferred) {
+    public DataInfo setInferred(Boolean inferred) {
         this.inferred = inferred;
+        return this;
     }
 
     public Boolean getDeletedbyinference() {
         return deletedbyinference;
     }
 
-    public void setDeletedbyinference(Boolean deletedbyinference) {
+    public DataInfo setDeletedbyinference(Boolean deletedbyinference) {
         this.deletedbyinference = deletedbyinference;
+        return this;
     }
 
     public String getTrust() {
         return trust;
     }
 
-    public void setTrust(String trust) {
+    public DataInfo setTrust(String trust) {
         this.trust = trust;
+        return this;
     }
 
     public String getInferenceprovenance() {
         return inferenceprovenance;
     }
 
-    public void setInferenceprovenance(String inferenceprovenance) {
+    public DataInfo setInferenceprovenance(String inferenceprovenance) {
         this.inferenceprovenance = inferenceprovenance;
+        return this;
     }
 
-    public List<Qualifier> getProvenanceaction() {
+    public Qualifier getProvenanceaction() {
         return provenanceaction;
     }
 
-    public void setProvenanceaction(List<Qualifier> provenanceaction) {
+    public DataInfo setProvenanceaction(Qualifier provenanceaction) {
         this.provenanceaction = provenanceaction;
+        return this;
     }
 }

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

@@ -14,23 +14,26 @@ public class KeyValue implements Serializable {
         return key;
     }
 
-    public void setKey(String key) {
+    public KeyValue setKey(String key) {
         this.key = key;
+        return this;
     }
 
     public String getValue() {
         return value;
     }
 
-    public void setValue(String value) {
+    public KeyValue setValue(String value) {
         this.value = value;
+        return this;
     }
 
     public DataInfo getDataInfo() {
         return dataInfo;
     }
 
-    public void setDataInfo(DataInfo dataInfo) {
+    public KeyValue setDataInfo(DataInfo dataInfo) {
         this.dataInfo = dataInfo;
+        return this;
     }
 }

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

@@ -15,39 +15,44 @@ public class Qualifier implements Serializable {
         return classid;
     }
 
-    public void setClassid(String classid) {
+    public Qualifier setClassid(String classid) {
         this.classid = classid;
+        return this;
     }
 
     public String getClassname() {
         return classname;
     }
 
-    public void setClassname(String classname) {
+    public Qualifier setClassname(String classname) {
         this.classname = classname;
+        return this;
     }
 
     public String getSchemeid() {
         return schemeid;
     }
 
-    public void setSchemeid(String schemeid) {
+    public Qualifier setSchemeid(String schemeid) {
         this.schemeid = schemeid;
+        return this;
     }
 
     public String getSchemename() {
         return schemename;
     }
 
-    public void setSchemename(String schemename) {
+    public Qualifier setSchemename(String schemename) {
         this.schemename = schemename;
+        return this;
     }
 
     public DataInfo getDataInfo() {
         return dataInfo;
     }
 
-    public void setDataInfo(DataInfo dataInfo) {
+    public Qualifier setDataInfo(DataInfo dataInfo) {
         this.dataInfo = dataInfo;
+        return this;
     }
 }

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

@@ -20,47 +20,53 @@ public class Relation extends Oaf {
         return relType;
     }
 
-    public void setRelType(String relType) {
+    public Relation setRelType(String relType) {
         this.relType = relType;
+        return this;
     }
 
     public String getSubRelType() {
         return subRelType;
     }
 
-    public void setSubRelType(String subRelType) {
+    public Relation setSubRelType(String subRelType) {
         this.subRelType = subRelType;
+        return this;
     }
 
     public String getRelClass() {
         return relClass;
     }
 
-    public void setRelClass(String relClass) {
+    public Relation setRelClass(String relClass) {
         this.relClass = relClass;
+        return this;
     }
 
     public String getSource() {
         return source;
     }
 
-    public void setSource(String source) {
+    public Relation setSource(String source) {
         this.source = source;
+        return this;
     }
 
     public String getTarget() {
         return target;
     }
 
-    public void setTarget(String target) {
+    public Relation setTarget(String target) {
         this.target = target;
+        return this;
     }
 
     public List<KeyValue> getCollectedFrom() {
         return collectedFrom;
     }
 
-    public void setCollectedFrom(List<KeyValue> collectedFrom) {
+    public Relation setCollectedFrom(List<KeyValue> collectedFrom) {
         this.collectedFrom = collectedFrom;
+        return this;
     }
 }

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

@@ -10,28 +10,30 @@ public class StructuredProperty implements Serializable {
 
     private DataInfo dataInfo;
 
-
     public String getValue() {
         return value;
     }
 
-    public void setValue(String value) {
+    public StructuredProperty setValue(String value) {
         this.value = value;
+        return this;
     }
 
     public Qualifier getQualifier() {
         return qualifier;
     }
 
-    public void setQualifier(Qualifier qualifier) {
+    public StructuredProperty setQualifier(Qualifier qualifier) {
         this.qualifier = qualifier;
+        return this;
     }
 
     public DataInfo getDataInfo() {
         return dataInfo;
     }
 
-    public void setDataInfo(DataInfo dataInfo) {
+    public StructuredProperty setDataInfo(DataInfo dataInfo) {
         this.dataInfo = dataInfo;
+        return this;
     }
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoConverter.java

@@ -1,7 +1,5 @@
 package eu.dnetlib.dhp.graph;
 
-
-import com.googlecode.protobuf.format.JsonFormat;
 import eu.dnetlib.data.proto.KindProtos;
 import eu.dnetlib.data.proto.OafProtos;
 import eu.dnetlib.dhp.schema.oaf.*;
@@ -9,30 +7,39 @@ import eu.dnetlib.dhp.schema.oaf.*;
 import java.io.Serializable;
 import java.util.stream.Collectors;
 
+import static eu.dnetlib.dhp.graph.ProtoUtils.mapKV;
 
 public class ProtoConverter implements Serializable {
 
-
     public static Oaf convert(String s) {
         try {
-            final OafProtos.Oaf.Builder builder =  OafProtos.Oaf.newBuilder();
+            OafProtos.Oaf oaf = ProtoUtils.parse(s);
-            JsonFormat.merge(s, builder);
 
-            if (builder.getKind() == KindProtos.Kind.entity)
+            if (oaf.getKind() == KindProtos.Kind.entity)
-                return convertEntity(builder);
+                return convertEntity(oaf);
             else {
-               return convertRelation(builder);
+               return convertRelation(oaf);
             }
         } catch (Throwable e) {
             throw new RuntimeException(e);
         }
     }
 
-    private static Relation convertRelation(OafProtos.Oaf.Builder oaf) {
+    private static Relation convertRelation(OafProtos.Oaf oaf) {
-        return new Relation();
+        final Relation rel = new Relation();
+        final OafProtos.OafRel r = oaf.getRel();
+        return rel
+                .setSource(r.getSource())
+                .setTarget(r.getTarget())
+                .setRelType(r.getRelType().toString())
+                .setSubRelType(r.getSubRelType().toString())
+                .setRelClass(r.getRelClass())
+                .setCollectedFrom(r.getCollectedfromList().stream()
+                        .map(kv -> mapKV(kv))
+                        .collect(Collectors.toList()));
     }
 
-    private static OafEntity convertEntity(OafProtos.Oaf.Builder oaf) {
+    private static OafEntity convertEntity(OafProtos.Oaf oaf) {
 
         switch (oaf.getEntity().getType()) {
             case result:
@@ -48,11 +55,12 @@ public class ProtoConverter implements Serializable {
         }
     }
 
-    private static Organization convertOrganization(OafProtos.Oaf.Builder oaf) {
+    private static Organization convertOrganization(OafProtos.Oaf oaf) {
         return new Organization();
     }
 
-    private static Datasource convertDataSource(OafProtos.Oaf.Builder oaf) {
+
+    private static Datasource convertDataSource(OafProtos.Oaf oaf) {
         final Datasource result = new Datasource();
 
         //setting oaf field
@@ -75,11 +83,11 @@ public class ProtoConverter implements Serializable {
         return result;
     }
 
-    private static Project convertProject(OafProtos.Oaf.Builder oaf) {
+    private static Project convertProject(OafProtos.Oaf oaf) {
         return new Project();
     }
 
-    private static Result convertResult(OafProtos.Oaf.Builder oaf) {
+    private static Result convertResult(OafProtos.Oaf oaf) {
         switch (oaf.getEntity().getResult().getMetadata().getResulttype().getClassid()) {
             case "dataset":
                 return createDataset(oaf);
@@ -94,19 +102,19 @@ public class ProtoConverter implements Serializable {
         }
     }
 
-    private static Software createSoftware(OafProtos.Oaf.Builder oaf) {
+    private static Software createSoftware(OafProtos.Oaf oaf) {
         return new Software();
     }
 
-    private static OtherResearchProducts createORP(OafProtos.Oaf.Builder oaf) {
+    private static OtherResearchProducts createORP(OafProtos.Oaf oaf) {
         return new OtherResearchProducts();
     }
 
-    private static Publication createPublication(OafProtos.Oaf.Builder oaf) {
+    private static Publication createPublication(OafProtos.Oaf oaf) {
         return new Publication();
     }
 
-    private static Dataset createDataset(OafProtos.Oaf.Builder oaf) {
+    private static Dataset createDataset(OafProtos.Oaf oaf) {
         return new Dataset();
     }
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoUtils.java

@@ -0,0 +1,53 @@
+package eu.dnetlib.dhp.graph;
+
+import com.googlecode.protobuf.format.JsonFormat;
+import eu.dnetlib.data.proto.FieldTypeProtos;
+import eu.dnetlib.data.proto.OafProtos;
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
+import java.util.List;
+
+public class ProtoUtils {
+
+    public static OafProtos.Oaf parse(String json) throws JsonFormat.ParseException {
+        final OafProtos.Oaf.Builder builder =  OafProtos.Oaf.newBuilder();
+        JsonFormat.merge(json, builder);
+        return builder.build();
+    }
+
+    public static KeyValue mapKV(FieldTypeProtos.KeyValue kv) {
+        return new KeyValue()
+                .setKey(kv.getKey())
+                .setValue(kv.getValue())
+                .setDataInfo(mapDataInfo(kv.getDataInfo()));
+    }
+
+    public static DataInfo mapDataInfo(FieldTypeProtos.DataInfo d) {
+        return new DataInfo()
+                .setDeletedbyinference(d.getDeletedbyinference())
+                .setInferenceprovenance(d.getInferenceprovenance())
+                .setInferred(d.getInferred())
+                .setInvisible(d.getInvisible())
+                .setProvenanceaction(mapQualifier(d.getProvenanceaction()));
+    }
+
+    public static Qualifier mapQualifier(FieldTypeProtos.Qualifier q) {
+        return new Qualifier()
+                .setClassid(q.getClassid())
+                .setClassname(q.getClassname())
+                .setSchemeid(q.getSchemeid())
+                .setSchemename(q.getSchemename())
+                .setDataInfo(q.hasDataInfo() ? mapDataInfo(q.getDataInfo()) : null);
+    }
+
+    public static StructuredProperty mapStructuredProperty(FieldTypeProtos.StructuredProperty sp) {
+        return new StructuredProperty()
+                .setValue(sp.getValue())
+                .setQualifier(mapQualifier(sp.getQualifier()))
+                .setDataInfo(sp.hasDataInfo() ? mapDataInfo(sp.getDataInfo()) : null);
+    }
+
+}