fix(rdf): non-required refLink caused RDF API to fail (#4688)

* fixed refLink being processed when actually null * minor fix to test code * minor test change
molgenis · Feb 11, 2025 · 0fb3ef1 · 0fb3ef1
1 parent f09c1ff
commit 0fb3ef1
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Showing 3 changed files with 34 additions and 3 deletions.
diff --git a/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapper.java b/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapper.java
@@ -221,8 +221,10 @@ Set<Value> retrieveValues(String baseURL, Row row, Column column) {
 
       @Override
       boolean isEmpty(Row row, Column column) {
-        // Composite key requires all fields to be filled. If one is null, all should be null.
-        return row.getString(column.getReferences().get(0).getName()) == null;
+        // Composite key requires all fields to be filled. Using refLink from a non-required field
+        // could cause a part of the composite key to be defined.
+        // Therefore, if a composite key is partly defined, assume it is not defined.
+        return column.getReferences().stream().anyMatch(i -> row.getString(i.getName()) == null);
       }
     },
     REFBACK(CoreDatatype.XSD.ANYURI) {

diff --git a/backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/RDFTest.java b/backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/RDFTest.java
@@ -70,6 +70,7 @@ public class RDFTest {
   static Schema tableInherExtTest;
   static Schema fileTest;
   static Schema refBackTest;
+  static Schema refLinkTest;
 
   final Set<Namespace> DEFAULT_NAMESPACES =
       new HashSet<>() {
@@ -317,6 +318,25 @@ public static void setup() {
 
     refBackTest.getTable("tableRefBack").insert(row("id", "a"));
     refBackTest.getTable("tableRef").insert(row("id", "1", "link", "a"));
+
+    // refLink test
+    refLinkTest = database.dropCreateSchema("refLinkTest");
+
+    refLinkTest.create(
+        table("table1", column("id").setType(ColumnType.STRING).setPkey()),
+        table(
+            "table2",
+            column("id1").setPkey().setType(ColumnType.REF).setRefTable("table1"),
+            column("id2").setType(ColumnType.STRING).setPkey()),
+        table(
+            "table3",
+            column("p1").setPkey().setType(ColumnType.REF).setRefTable("table1"),
+            column("p2").setPkey().setType(ColumnType.REF).setRefTable("table2").setRefLink("p1"),
+            column("ref").setType(ColumnType.REF).setRefTable("table2").setRefLink("p1")));
+
+    refLinkTest.getTable("table1").insert(row("id", "t1First"));
+    refLinkTest.getTable("table2").insert(row("id1", "t1First", "id2", "t2First"));
+    refLinkTest.getTable("table3").insert(row("p1", "t1First", "p2", "t2First"));
   }
 
   private static String getApi(Schema schema) {
@@ -334,6 +354,7 @@ public static void tearDown() {
     database.dropSchema(tableInherTest.getName());
     database.dropSchema(fileTest.getName());
     database.dropSchema(refBackTest.getName());
+    database.dropSchema(refLinkTest.getName());
   }
 
   @Test
@@ -1260,6 +1281,13 @@ void refBackInRdf() throws IOException {
     assertEquals(Set.of(Values.iri(getApi(refBackTest) + "TableRef?id=1")), refBacks);
   }
 
+  @Test
+  void testRefLinkWorks() throws IOException {
+    var handler = new InMemoryRDFHandler() {};
+    assertDoesNotThrow(() -> getAndParseRDF(Selection.of(refLinkTest), handler));
+
+  }
+
   /**
    * Helper test method to compare namespaces of 2 schemas.
    *

diff --git a/backend/molgenis-emx2/src/main/java/org/molgenis/emx2/Column.java b/backend/molgenis-emx2/src/main/java/org/molgenis/emx2/Column.java
@@ -627,8 +627,9 @@ public String getRefLink() {
     return refLink;
   }
 
-  public void setRefLink(String refLink) {
+  public Column setRefLink(String refLink) {
     this.refLink = refLink;
+    return this;
   }
 
   public Column getRefLinkColumn() {