@BeforeTest
public void createEntity() {
entityType = when(mock(EntityType.class).getName()).thenReturn("Source").getMock();
Attribute idAttr = when(mock(Attribute.class).getName()).thenReturn("Identifier").getMock();
when(idAttr.getDataType()).thenReturn(INT);
Attribute intAttr = when(mock(Attribute.class).getName()).thenReturn("Int").getMock();
when(intAttr.getDataType()).thenReturn(INT);
Attribute stringAttr = when(mock(Attribute.class).getName()).thenReturn("String").getMock();
when(stringAttr.getDataType()).thenReturn(STRING);
Attribute nonNumericStringAttr =
when(mock(Attribute.class).getName()).thenReturn("NonNumericString").getMock();
when(nonNumericStringAttr.getDataType()).thenReturn(STRING);
Attribute longAttr = when(mock(Attribute.class).getName()).thenReturn("Long").getMock();
when(longAttr.getDataType()).thenReturn(LONG);
when(entityType.getIdAttribute()).thenReturn(idAttr);
when(entityType.getAttribute("Identifier")).thenReturn(idAttr);
when(entityType.getAttribute("Int")).thenReturn(intAttr);
when(entityType.getAttribute("String")).thenReturn(stringAttr);
when(entityType.getAttribute("NonNumericString")).thenReturn(nonNumericStringAttr);
when(entityType.getAttribute("Long")).thenReturn(longAttr);
entity = new DynamicEntity(entityType);
entity.set("Int", 1);
entity.set("String", "12");
entity.set("Long", 10L);
entity.set("NonNumericString", "Hello World!");
}
@Test
public void testStringEvaluatorLookupAttributeAndConvertFromIntToLong() {
Attribute amd = when(mock(Attribute.class).getName()).thenReturn("#POS").getMock();
when(amd.getDataType()).thenReturn(LONG);
when(amd.getExpression()).thenReturn("Int");
assertEquals(new StringExpressionEvaluator(amd, entityType).evaluate(entity), 1L);
}
@Test(
expectedExceptions = ConversionFailedException.class,
expectedExceptionsMessageRegExp =
"Failed to convert from type \\[java.lang.String\\] to type \\[java.lang.Long\\] for value 'Hello World!'; nested exception is java.lang.NumberFormatException: For input string: \"HelloWorld!\"")
public void testStringEvaluatorLookupAttributeAndConvertFromNonNumericStringToLongFails() {
Attribute amd = when(mock(Attribute.class).getName()).thenReturn("#POS").getMock();
when(amd.getDataType()).thenReturn(LONG);
when(amd.getExpression()).thenReturn("NonNumericString");
new StringExpressionEvaluator(amd, entityType).evaluate(entity);
}
@Test
public void testStringEvaluatorConstructorChecksIfExpressionIsMap() {
Attribute amd = when(mock(Attribute.class).getName()).thenReturn("#CHROM").getMock();
when(amd.getDataType()).thenReturn(STRING);
when(amd.getExpression()).thenReturn("{}");
try {
new StringExpressionEvaluator(amd, entityType);
fail("expected illegal state exception");
} catch (JsonSyntaxException expected) {
}
}
@Test
public void testStringEvaluatorConstructorChecksIfAttributeHasExpression() {
Attribute amd = when(mock(Attribute.class).getName()).thenReturn("#CHROM").getMock();
when(amd.getDataType()).thenReturn(STRING);
try {
new StringExpressionEvaluator(amd, entityType);
fail("Expected NPE");
} catch (NullPointerException expected) {
assertEquals(expected.getMessage(), "Attribute has no expression.");
}
}
private Object toQueryRuleValue(Object queryRuleValue, Attribute attr) {
Object value;
AttributeType attrType = attr.getDataType();
switch (attrType) {
case BOOL:
value = convertBool(attr, queryRuleValue);
break;
case EMAIL:
case HTML:
case HYPERLINK:
case SCRIPT:
case STRING:
case TEXT:
value = convertString(attr, queryRuleValue);
break;
case ENUM:
value = convertEnum(attr, queryRuleValue);
break;
case CATEGORICAL:
case XREF:
case CATEGORICAL_MREF:
case MREF:
case ONE_TO_MANY:
value = convertRef(attr, queryRuleValue);
break;
case DATE:
value = convertDate(attr, queryRuleValue);
break;
case DATE_TIME:
value = convertDateTime(attr, queryRuleValue);
break;
case DECIMAL:
value = convertDecimal(attr, queryRuleValue);
break;
case FILE:
value = convertFile(attr, queryRuleValue);
break;
case INT:
value = convertInt(attr, queryRuleValue);
break;
case LONG:
value = convertLong(attr, queryRuleValue);
break;
case COMPOUND:
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] type [%s] is not allowed",
attr.getName(), attrType.toString())));
default:
throw new RuntimeException(format("Unknown attribute type [%s]", attrType.toString()));
}
return value;
}
@Test
public void testStringEvaluatorConstructorChecksIfAttributeMentionsExistingAttribute() {
Attribute amd = when(mock(Attribute.class).getName()).thenReturn("#CHROM").getMock();
when(amd.getDataType()).thenReturn(STRING);
when(amd.getExpression()).thenReturn("bogus");
try {
new StringExpressionEvaluator(amd, entityType);
fail("expected illegal argument exception");
} catch (IllegalArgumentException expected) {
assertEquals(
expected.getMessage(),
"Expression for attribute '#CHROM' references non-existant attribute 'bogus'.");
}
}
/**
* Validate is value is of the type defined by the attribute data type.
*
* @param attrName attribute name
* @param value value (must be of the type defined by the attribute data type.)
*/
protected void validateValueType(String attrName, Object value) {
if (value == null) {
return;
}
Attribute attr = entityType.getAttribute(attrName);
if (attr == null) {
throw new UnknownAttributeException(format("Unknown attribute [%s]", attrName));
}
AttributeType dataType = attr.getDataType();
switch (dataType) {
case BOOL:
if (!(value instanceof Boolean)) {
throw new MolgenisDataException(
format(
"Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
value.toString(),
value.getClass().getSimpleName(),
Boolean.class.getSimpleName(),
attrName));
}
break;
case CATEGORICAL:
// expected type is FileMeta. validation is not possible because molgenis-data does not
// depend on molgenis-file
case FILE:
case XREF:
if (!(value instanceof Entity)) {
throw new MolgenisDataException(
format(
"Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
value.toString(),
value.getClass().getSimpleName(),
Entity.class.getSimpleName(),
attrName));
}
break;
case CATEGORICAL_MREF:
case MREF:
case ONE_TO_MANY:
if (!(value instanceof Iterable)) {
throw new MolgenisDataException(
format(
"Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
value.toString(),
value.getClass().getSimpleName(),
Iterable.class.getSimpleName(),
attrName));
}
break;
case COMPOUND:
throw new IllegalArgumentException(
format("Unexpected data type [%s] for attribute: [%s]", dataType.toString(), attrName));
case DATE:
case DATE_TIME:
if (!(value instanceof java.util.Date)) {
throw new MolgenisDataException(
format(
"Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
value.toString(),
value.getClass().getSimpleName(),
java.util.Date.class.getSimpleName(),
attrName));
}
break;
case DECIMAL:
if (!(value instanceof Double)) {
throw new MolgenisDataException(
format(
"Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
value.toString(),
value.getClass().getSimpleName(),
Double.class.getSimpleName(),
attrName));
}
break;
case EMAIL:
case ENUM:
case HTML:
case HYPERLINK:
case SCRIPT:
case STRING:
case TEXT:
if (!(value instanceof String)) {
throw new MolgenisDataException(
format(
"Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
value.toString(),
value.getClass().getSimpleName(),
String.class.getSimpleName(),
attrName));
}
break;
case INT:
if (!(value instanceof Integer)) {
throw new MolgenisDataException(
format(
"Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
value.toString(),
value.getClass().getSimpleName(),
Integer.class.getSimpleName(),
attrName));
}
break;
case LONG:
if (!(value instanceof Long)) {
throw new MolgenisDataException(
format(
"Value [%s] is of type [%s] instead of [%s] for attribute: [%s]",
value.toString(),
value.getClass().getSimpleName(),
Long.class.getSimpleName(),
attrName));
}
break;
default:
throw new RuntimeException(format("Unknown data type [%s]", dataType.toString()));
}
}