Fix allowed operators for "file" values and improve exception messages.

pom.xml

@@ -13,7 +13,7 @@
 
   <groupId>org.molgenis</groupId>
   <artifactId>vip-decision-tree</artifactId>
-  <version>4.0.0</version>
+  <version>4.1.0</version>
 
   <name>vip-decision-tree</name>
   <description>Decision tree module for filtering and labelling VCF files</description>

src/main/java/org/molgenis/vcf/decisiontree/runner/QueryValidatorImpl.java

@@ -1,8 +1,5 @@
 package org.molgenis.vcf.decisiontree.runner;
 
-import static org.molgenis.vcf.decisiontree.loader.model.ConfigOperator.IN;
-import static org.molgenis.vcf.decisiontree.loader.model.ConfigOperator.NOT_IN;
-
 import java.util.Collection;
 import java.util.Set;
 import org.molgenis.vcf.decisiontree.filter.model.BoolNode;
@@ -16,10 +13,12 @@
 import org.molgenis.vcf.utils.UnexpectedEnumException;
 import org.springframework.stereotype.Component;
 
+import static org.molgenis.vcf.decisiontree.loader.model.ConfigOperator.*;
+
 @Component
 public class QueryValidatorImpl implements QueryValidator {
 
-  public static final Set<ConfigOperator> ALLOWED_FILE_OPERATORS = Set.of(IN, NOT_IN);
+  public static final Set<ConfigOperator> ALLOWED_FILE_OPERATORS = Set.of(IN, NOT_IN, CONTAINS, NOT_CONTAINS, CONTAINS_ALL, CONTAINS_ANY, CONTAINS_NONE);
 
   @Override
   public void validateBooleanNode(ConfigBoolQuery configBoolQuery, Field field) {
@@ -57,7 +56,7 @@ private void validateLesserGreater(Field field, ConfigBoolQuery query) {
     if (field.getValueType() != ValueType.FLOAT && field.getValueType() != ValueType.INTEGER) {
       throw new UnsupportedValueTypeException(field, DecisionType.BOOL);
     }
-    validateSingleOrPerAlleleCount(field, DecisionType.BOOL);
+    validateSingleOrPerAlleleCount(field, DecisionType.BOOL, IN);
   }
 
   private void validateEquals(Field field, ConfigBoolQuery configBoolQuery) {
@@ -72,7 +71,7 @@ private void validateIn(Field field) {
     if (field.getValueType() == ValueType.FLAG || field.getValueType() == ValueType.FLOAT) {
       throw new UnsupportedValueTypeException(field, DecisionType.BOOL);
     } else {
-      validateSingleOrPerAlleleCount(field, DecisionType.BOOL);
+      validateSingleOrPerAlleleCount(field, DecisionType.BOOL, IN);
     }
   }
 
@@ -82,17 +81,17 @@ private void validateContains(Field field, ConfigBoolQuery configBoolQuery) {
       throw new UnsupportedValueTypeException(field, DecisionType.BOOL);
     } else if (field.getValueCount().getType() == Type.FIXED
         && field.getValueCount().getCount() == 1) {
-      throw new UnsupportedValueCountException(field, DecisionType.BOOL);
+      throw new UnsupportedValueCountException(field, DecisionType.BOOL, CONTAINS);
     }
   }
 
-  private void validateSingleOrPerAlleleCount(Field field, DecisionType decisionType) {
+  private void validateSingleOrPerAlleleCount(Field field, DecisionType decisionType, ConfigOperator configOperator) {
     if (field.getValueCount().getType() == Type.G ||
         field.getValueCount().getType() == Type.VARIABLE) {
-      throw new UnsupportedValueCountTypeException(field, decisionType);
+      throw new UnsupportedValueCountTypeException(field, decisionType, configOperator);
     } else if (field.getValueCount().getType() == Type.FIXED
         && field.getValueCount().getCount() != 1) {
-      throw new UnsupportedValueCountException(field, decisionType);
+      throw new UnsupportedValueCountException(field, decisionType, configOperator);
     }
   }
 
@@ -102,7 +101,7 @@ public void validateCategoricalNode(Field field) {
       if (field.getValueType() == ValueType.FLAG || field.getValueType() == ValueType.FLOAT) {
         throw new UnsupportedValueTypeException(field, DecisionType.CATEGORICAL);
       }
-      validateSingleOrPerAlleleCount(field, DecisionType.CATEGORICAL);
+      validateSingleOrPerAlleleCount(field, DecisionType.CATEGORICAL, IN);
     }
   }
 }

src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountException.java

@@ -4,15 +4,16 @@
 
 import org.molgenis.vcf.decisiontree.filter.model.DecisionType;
 import org.molgenis.vcf.decisiontree.filter.model.Field;
+import org.molgenis.vcf.decisiontree.loader.model.ConfigOperator;
 
 import java.io.Serial;
 
 public class UnsupportedValueCountException extends RuntimeException {
   @Serial
   private static final long serialVersionUID = 1L;
-  public UnsupportedValueCountException(Field field, DecisionType decisionType) {
+  public UnsupportedValueCountException(Field field, DecisionType decisionType, ConfigOperator configOperator) {
     super(
         format(
-            "Unsupported number of values (%d) for field '%s' for decision type '%s'.", field.getValueCount().getCount(), field.getId(), decisionType));
+            "Unsupported number of values (%d) for field '%s' for combination of decision type '%s' and operator of type '%s'.", field.getValueCount().getCount(), field.getId(), decisionType, configOperator));
   }
 }

src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountTypeException.java

@@ -4,16 +4,17 @@
 
 import org.molgenis.vcf.decisiontree.filter.model.DecisionType;
 import org.molgenis.vcf.decisiontree.filter.model.Field;
+import org.molgenis.vcf.decisiontree.loader.model.ConfigOperator;
 
 import java.io.Serial;
 
 public class UnsupportedValueCountTypeException extends RuntimeException {
   @Serial
   private static final long serialVersionUID = 1L;
-  public UnsupportedValueCountTypeException(Field field, DecisionType decisionType) {
+  public UnsupportedValueCountTypeException(Field field, DecisionType decisionType, ConfigOperator configOperator) {
     super(
         format(
-            "Unsupported value count type '%s' of field '%s' for decision type '%s'.",
-            field.getValueCount().getType(), field.getId(), decisionType));
+            "Unsupported value count type '%s' of field '%s' for combination of decision type '%s' and operator of type '%s'.",
+            field.getValueCount().getType(), field.getId(), decisionType, configOperator.toString()));
   }
 }

src/test/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountExceptionTest.java

@@ -9,15 +9,16 @@
 import org.molgenis.vcf.decisiontree.filter.model.ValueCount;
 import org.molgenis.vcf.decisiontree.filter.model.ValueCount.Type;
 import org.molgenis.vcf.decisiontree.filter.model.ValueType;
+import org.molgenis.vcf.decisiontree.loader.model.ConfigOperator;
 
 class UnsupportedValueCountExceptionTest {
   @Test
   void getMessage() {
     assertEquals(
-        "Unsupported number of values (3) for field 'test' for decision type 'CATEGORICAL'.",
+        "Unsupported number of values (3) for field 'test' for combination of decision type 'CATEGORICAL' and operator of type 'CONTAINS'.",
         new UnsupportedValueCountException(
             FieldImpl.builder().id("test").fieldType(FieldType.INFO).valueType(ValueType.FLOAT)
                 .valueCount(
-                    ValueCount.builder().type(Type.FIXED).count(3).build()).build(), DecisionType.CATEGORICAL).getMessage());
+                    ValueCount.builder().type(Type.FIXED).count(3).build()).build(), DecisionType.CATEGORICAL, ConfigOperator.CONTAINS).getMessage());
   }
 }

src/test/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountTypeExceptionTest.java

@@ -9,15 +9,16 @@
 import org.molgenis.vcf.decisiontree.filter.model.ValueCount;
 import org.molgenis.vcf.decisiontree.filter.model.ValueCount.Type;
 import org.molgenis.vcf.decisiontree.filter.model.ValueType;
+import org.molgenis.vcf.decisiontree.loader.model.ConfigOperator;
 
 class UnsupportedValueCountTypeExceptionTest {
   @Test
   void getMessage() {
     assertEquals(
-        "Unsupported value count type 'G' of field 'test' for decision type 'CATEGORICAL'.",
+        "Unsupported value count type 'G' of field 'test' for combination of decision type 'CATEGORICAL' and operator of type 'IN'.",
         new UnsupportedValueCountTypeException(
             FieldImpl.builder().id("test").fieldType(FieldType.INFO).valueType(ValueType.FLOAT)
                 .valueCount(
-                    ValueCount.builder().type(Type.G).build()).build(), DecisionType.CATEGORICAL).getMessage());
+                    ValueCount.builder().type(Type.G).build()).build(), DecisionType.CATEGORICAL, ConfigOperator.IN).getMessage());
   }
 }

src/test/resources/clinvar.txt

@@ -0,0 +1,3 @@
+conflicting_interpretations_of_pathogenicity
+conflicting_data_from_submitters
+uncertain_significance

src/test/resources/example.json

@@ -1,4 +1,9 @@
 {
+  "files": {
+    "clinvar" : {
+      "path" : "src/test/resources/clinvar.txt"
+    }
+  },
   "rootNode": "filter",
   "nodes": {
     "filter": {
@@ -163,11 +168,7 @@
             {
               "field": "INFO/CLINVAR",
               "operator": "contains_any",
-              "value": [
-                "conflicting_interpretations_of_pathogenicity",
-                "conflicting_data_from_submitters",
-                "uncertain_significance"
-              ]
+              "value": "file:clinvar"
             }
           ],
           "outcomeTrue": {