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Fix: interpret CATEGORICAL metadata as string value #102

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merged 1 commit into from
Nov 26, 2024
Merged

Fix: interpret CATEGORICAL metadata as string value #102

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2 changes: 1 addition & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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>
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4 changes: 2 additions & 2 deletions src/main/java/org/molgenis/vcf/decisiontree/filter/VcfRecord.java
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Expand Up @@ -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:
Expand All @@ -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:
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2 changes: 1 addition & 1 deletion src/main/java/org/molgenis/vcf/decisiontree/runner/ValueValidator.java
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Expand Up @@ -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(
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13 changes: 13 additions & 0 deletions src/test/java/org/molgenis/vcf/decisiontree/filter/VcfRecordTest.java
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Expand Up @@ -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 =
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2 changes: 2 additions & 0 deletions src/test/java/org/molgenis/vcf/decisiontree/runner/ValueValidatorTest.java
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Expand Up @@ -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,
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