add synonyms for equivalent nodes

SciGraph · Dec 23, 2020 · ef14285 · ef14285
1 parent 497a947
commit ef14285
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Showing 3 changed files with 13 additions and 4 deletions.
diff --git a/src/main/java/org/monarch/golr/SimpleLoader.java b/src/main/java/org/monarch/golr/SimpleLoader.java
@@ -117,9 +117,6 @@ public void generate(Writer writer,
         writeOptionalArray("definition", generator,
                 GraphUtil.getProperties(baseNode, Concept.DEFINITION, String.class));
 
-        writeOptionalArray("synonym", generator,
-                GraphUtil.getProperties(baseNode, Concept.SYNONYM, String.class));
-
         // Abbreviation (need to fix spelling in io.scigraph.frames.Concept
         writeOptionalArray("abbreviation", generator,
             GraphUtil.getProperties(baseNode, Concept.ABREVIATION, String.class));
@@ -196,9 +193,18 @@ public void generate(Writer writer,
           }
         }
 
+        Set<String> synonyms = Sets.newHashSet(
+            GraphUtil.getProperties(baseNode, Concept.SYNONYM, String.class)
+        );
+
         for (String equivalentIri : equivalences) {
           // Get curie prefix
           Optional<String> eqCurie = curieUtil.getCurie(equivalentIri);
+          Node eqNode = graphDb.getNodeById(graph.getNode(equivalentIri).get());
+          Set<String> eqSynonyms = Sets.newHashSet(
+              GraphUtil.getProperties(eqNode, Concept.SYNONYM, String.class)
+          );
+          synonyms.addAll(eqSynonyms);
           if (eqCurie.isPresent()) {
             equivalentCuries.add(eqCurie.get());
             String[] eqParts = eqCurie.get().split(":");
@@ -217,6 +223,7 @@ public void generate(Writer writer,
           }
         }
 
+        writeOptionalArray("synonym", generator, synonyms);
         writeOptionalArray("equivalent_curie", generator, equivalentCuries);
 
         // is leaf

diff --git a/src/test/java/org/monarch/golr/SimpleLoadSetup.java b/src/test/java/org/monarch/golr/SimpleLoadSetup.java
@@ -8,6 +8,7 @@
 import java.util.List;
 
 
+import io.scigraph.frames.Concept;
 import org.junit.BeforeClass;
 import org.neo4j.graphdb.GraphDatabaseService;
 import org.neo4j.graphdb.Label;
@@ -68,6 +69,7 @@ static void populateGraph(GraphDatabaseService graphDb) {
 
             Node eqGene = createNode("http://x.org/eqGeneA");
             gene.createRelationshipTo(eqGene, OwlRelationships.OWL_SAME_AS);
+            eqGene.setProperty(Concept.SYNONYM, "GeneAish");
 
             tx.success();
         }

diff --git a/src/test/resources/fixtures/searchDoc.json b/src/test/resources/fixtures/searchDoc.json
@@ -9,7 +9,7 @@
 
     ],
     "synonym":[
-
+      "GeneAish"
     ],
     "abbreviation":[