Merge pull request #102 from molgenis/fix/categorical

Fix: interpret CATEGORICAL metadata as string value
molgenis · Nov 26, 2024 · 96f5268 · 96f5268
2 parents c905eb5 + cf88f6f
commit 96f5268
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Showing 5 changed files with 19 additions and 4 deletions.
diff --git a/pom.xml b/pom.xml
@@ -13,7 +13,7 @@
 
     <groupId>org.molgenis</groupId>
     <artifactId>vip-decision-tree</artifactId>
-    <version>5.1.0</version>
+    <version>5.1.1</version>
 
     <name>vip-decision-tree</name>
     <description>Decision tree module for filtering and labelling VCF files</description>

diff --git a/src/main/java/org/molgenis/vcf/decisiontree/filter/VcfRecord.java b/src/main/java/org/molgenis/vcf/decisiontree/filter/VcfRecord.java
@@ -373,7 +373,7 @@ private Object getInfo(Field field) {
       case FLOAT:
         value = VcfUtils.getInfoAsDouble(variantContext, field);
         break;
-      case CHARACTER, STRING:
+      case CHARACTER, STRING, CATEGORICAL:
         value = VcfUtils.getInfoAsString(variantContext, field);
         break;
       default:
@@ -392,7 +392,7 @@ private List<?> getInfoList(Field field) {
       case FLOAT:
         listValues = VcfUtils.getInfoAsDoubleList(variantContext, field);
         break;
-      case CHARACTER, STRING:
+      case CHARACTER, STRING, CATEGORICAL:
         listValues = VcfUtils.getInfoAsStringList(variantContext, field);
         break;
       case FLAG:

diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/ValueValidator.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/ValueValidator.java
@@ -152,7 +152,7 @@ private static void validateValueTypes(String nodeId, Object singleValue, ValueT
                   singleValue, singleValue.getClass().getSimpleName(), valueType, nodeId));
         }
         break;
-      case STRING:
+      case STRING, CATEGORICAL:
         if (!(String.class.isAssignableFrom(singleValue.getClass()))) {
           throw new ConfigDecisionTreeValidationException(
               format(

diff --git a/src/test/java/org/molgenis/vcf/decisiontree/filter/VcfRecordTest.java b/src/test/java/org/molgenis/vcf/decisiontree/filter/VcfRecordTest.java
@@ -345,6 +345,19 @@ void getValueInfoFixedOneString() {
     assertEquals("str0", vcfRecord.getValue(field, createAllele()));
   }
 
+  @Test
+  void getValueInfoFixedOneCategorical() {
+    FieldImpl field =
+            FieldImpl.builder()
+                    .id("my_field")
+                    .fieldType(FieldType.INFO)
+                    .valueCount(ValueCount.builder().type(ValueCount.Type.FIXED).count(1).build())
+                    .valueType(ValueType.CATEGORICAL)
+                    .build();
+    when(variantContext.getAttribute("my_field")).thenReturn("str0");
+    assertEquals("str0", vcfRecord.getValue(field, createAllele()));
+  }
+
   @Test
   void getValueFormatAD() {
     FieldImpl field =

diff --git a/src/test/java/org/molgenis/vcf/decisiontree/runner/ValueValidatorTest.java b/src/test/java/org/molgenis/vcf/decisiontree/runner/ValueValidatorTest.java
@@ -62,6 +62,8 @@ private static Stream<Arguments> provideValidValues() {
             ValueCount.builder().type(ValueCount.Type.FIXED).count(1).build(), null, null)),
         Arguments.of("123", new FieldImpl("id", FieldType.INFO, ValueType.STRING,
             ValueCount.builder().type(ValueCount.Type.FIXED).count(1).build(), null, null)),
+        Arguments.of("123", new FieldImpl("id", FieldType.INFO, ValueType.CATEGORICAL,
+            ValueCount.builder().type(ValueCount.Type.FIXED).count(1).build(), null, null)),
         Arguments.of(1, new FieldImpl("id", FieldType.INFO, ValueType.FLOAT,
             ValueCount.builder().type(ValueCount.Type.FIXED).count(1).build(), null, null)),
         Arguments.of(true, new FieldImpl("id", FieldType.INFO, ValueType.FLAG,