private static Double convertDecimal(Attribute attr, Object value) {
if (value instanceof Double) {
return (Double) value;
}
if (value == null) {
return null;
}
// try to convert value
Double doubleValue;
if (value instanceof String) {
try {
doubleValue = Double.valueOf((String) value);
} catch (NumberFormatException e) {
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] value [%s] cannot be converter to type [%s]",
attr.getName(), value, Double.class.getSimpleName())));
}
} else if (value instanceof Number) {
doubleValue = ((Number) value).doubleValue();
} else {
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] value is of type [%s] instead of [%s] or [%s]",
attr.getName(),
value.getClass().getSimpleName(),
String.class.getSimpleName(),
Number.class.getSimpleName())));
}
return doubleValue;
}
private static Boolean convertBool(Attribute attr, Object value) {
if (value instanceof Boolean) {
return (Boolean) value;
}
if (value == null) {
return null;
}
Boolean booleanValue;
if (value instanceof String) {
String stringValue = (String) value;
if (stringValue.equalsIgnoreCase(TRUE.toString())) {
booleanValue = true;
} else if (stringValue.equalsIgnoreCase(FALSE.toString())) {
booleanValue = false;
} else {
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] value [%s] cannot be converter to type [%s]",
attr.getName(), value, Boolean.class.getSimpleName())));
}
} else {
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] value is of type [%s] instead of [%s] or [%s]",
attr.getName(),
value.getClass().getSimpleName(),
String.class.getSimpleName(),
Boolean.class.getSimpleName())));
}
return booleanValue;
}
@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!");
}
private static Integer convertInt(Attribute attr, Object value) {
if (value instanceof Integer) {
return (Integer) value;
}
if (value == null) {
return null;
}
// try to convert value
Integer integerValue;
if (value instanceof String) {
try {
integerValue = Integer.valueOf((String) value);
} catch (NumberFormatException e) {
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] value [%s] cannot be converter to type [%s]",
attr.getName(), value, Integer.class.getSimpleName())));
}
} else if (value instanceof Number) {
integerValue = ((Number) value).intValue();
} else {
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] value is of type [%s] instead of [%s] or [%s]",
attr.getName(),
value.getClass().getSimpleName(),
String.class.getSimpleName(),
Number.class.getSimpleName())));
}
return integerValue;
}
@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);
}
private static String convertEnum(Attribute attr, Object value) {
if (value == null) {
return null;
}
String stringValue;
if (value instanceof String) {
stringValue = (String) value;
} else if (value instanceof Enum) {
stringValue = value.toString();
} else {
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] value is of type [%s] instead of [%s] or [%s]",
attr.getName(),
value.getClass().getSimpleName(),
String.class.getSimpleName(),
Enum.class.getSimpleName())));
}
if (!attr.getEnumOptions().contains(stringValue)) {
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] value [%s] is not a valid enum option",
attr.getName(), stringValue)));
}
return stringValue;
}
private static Date convertDate(Attribute attr, Object value) {
if (value instanceof Date) {
return (Date) value;
}
if (value == null) {
return null;
}
// try to convert value
Date dateValue;
if (value instanceof String) {
String paramStrValue = (String) value;
try {
dateValue = getDateFormat().parse(paramStrValue);
} catch (ParseException e) {
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] value [%s] does not match date format [%s]",
attr.getName(),
paramStrValue,
MolgenisDateFormat.getDateFormat().toPattern())));
}
} else {
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] value is of type [%s] instead of [%s]",
attr.getName(), value.getClass().getSimpleName(), String.class.getSimpleName())));
}
return dateValue;
}
@Override
public void setIdValue(Object id) {
Attribute idAttr = entityType.getIdAttribute();
if (idAttr == null) {
throw new IllegalArgumentException(
format("Entity [%s] doesn't have an id attribute", entityType.getName()));
}
set(idAttr.getName(), id);
}
@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 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 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) {
}
}
private Entity convertRef(Attribute attr, Object value) {
if (value instanceof Entity) {
return (Entity) value;
}
if (value == null) {
return null;
}
// try to convert value
Object idValue = toQueryRuleValue(value, attr.getRefEntity().getIdAttribute());
return entityManager.getReference(attr.getRefEntity(), idValue);
}
Entity getDefaultSettings() {
Entity defaultSettingsEntity = new DynamicEntity(this);
for (Attribute attr : this.getAtomicAttributes()) {
// default values are stored/retrieved as strings, so we convert them to the required type
// here.
String defaultValue = attr.getDefaultValue();
if (defaultValue != null) {
Object typedDefaultValue = getTypedValue(defaultValue, attr, entityManager);
defaultSettingsEntity.set(attr.getName(), typedDefaultValue);
}
}
return defaultSettingsEntity;
}
@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'.");
}
}
@Test
public void testGenerateRules() {
EntityType targetRefEntityType = createCategoricalRefEntityType("HOP_HYPERTENSION");
Entity targetEntity1 =
new DynamicEntity(
targetRefEntityType, of("code", 0, "label", "Never had high blood pressure "));
Entity targetEntity2 =
new DynamicEntity(
targetRefEntityType, of("code", 1, "label", "Ever had high blood pressure "));
Entity targetEntity3 =
new DynamicEntity(targetRefEntityType, of("code", 9, "label", "Missing"));
Mockito.when(dataService.findAll(targetRefEntityType.getName()))
.thenReturn(Stream.of(targetEntity1, targetEntity2, targetEntity3));
targetAttribute =
attrMetaFactory.create().setName("History of Hypertension").setDataType(CATEGORICAL);
targetAttribute.setRefEntity(targetRefEntityType);
EntityType sourceRefEntityType = createCategoricalRefEntityType("High_blood_pressure_ref");
Entity sourceEntity1 = new DynamicEntity(targetRefEntityType, of("code", 1, "label", "yes"));
Entity sourceEntity2 = new DynamicEntity(targetRefEntityType, of("code", 2, "label", "no"));
Entity sourceEntity3 =
new DynamicEntity(targetRefEntityType, of("code", 3, "label", "I do not know"));
Mockito.when(dataService.findAll(sourceRefEntityType.getName()))
.thenReturn(Stream.of(sourceEntity1, sourceEntity2, sourceEntity3));
sourceAttribute =
attrMetaFactory.create().setName("High_blood_pressure").setDataType(CATEGORICAL);
sourceAttribute.setRefEntity(sourceRefEntityType);
String generatedAlgorithm =
categoryAlgorithmGenerator.generate(
targetAttribute, singletonList(sourceAttribute), targetEntityType, sourceEntityType);
String expectedAlgorithm =
"$('High_blood_pressure').map({\"1\":\"1\",\"2\":\"0\",\"3\":\"9\"}, null, null).value();";
Assert.assertEquals(generatedAlgorithm, expectedAlgorithm);
}
private FileMeta convertFile(Attribute attr, Object paramValue) {
Entity entity = convertRef(attr, paramValue);
if (entity == null) {
return null;
}
if (!(entity instanceof FileMeta)) {
throw new MolgenisValidationException(
new ConstraintViolation(
format(
"Attribute [%s] value is of type [%s] instead of [%s]",
attr.getName(),
entity.getClass().getSimpleName(),
FileMeta.class.getSimpleName())));
}
return (FileMeta) entity;
}
@BeforeMethod
public void init() {
dataService = Mockito.mock(DataService.class);
categoryAlgorithmGenerator = new OneToOneCategoryAlgorithmGenerator(dataService);
EntityType targetRefEntityType = createCategoricalRefEntityType("POTATO_REF");
Entity targetEntity1 =
new DynamicEntity(targetRefEntityType, of("code", 1, "label", "Almost daily + daily"));
Entity targetEntity2 =
new DynamicEntity(targetRefEntityType, of("code", 2, "label", "Several times a week"));
Entity targetEntity3 =
new DynamicEntity(targetRefEntityType, of("code", 3, "label", "About once a week"));
Entity targetEntity4 =
new DynamicEntity(
targetRefEntityType, of("code", 4, "label", "Never + fewer than once a week"));
Entity targetEntity5 =
new DynamicEntity(targetRefEntityType, of("code", 9, "label", "missing"));
targetAttribute =
attrMetaFactory
.create()
.setName("Current Consumption Frequency of Potatoes")
.setDataType(CATEGORICAL);
targetAttribute.setRefEntity(targetRefEntityType);
Mockito.when(dataService.findAll(targetRefEntityType.getName()))
.thenReturn(
Stream.of(targetEntity1, targetEntity2, targetEntity3, targetEntity4, targetEntity5));
targetEntityType = entityTypeFactory.create("target");
targetEntityType.addAttribute(targetAttribute);
EntityType sourceRefEntityType = createCategoricalRefEntityType("LifeLines_POTATO_REF");
Entity sourceEntity1 =
new DynamicEntity(targetRefEntityType, of("code", 1, "label", "Not this month"));
Entity sourceEntity2 =
new DynamicEntity(targetRefEntityType, of("code", 2, "label", "1 day per month"));
Entity sourceEntity3 =
new DynamicEntity(targetRefEntityType, of("code", 3, "label", "2-3 days per month"));
Entity sourceEntity4 =
new DynamicEntity(targetRefEntityType, of("code", 4, "label", "1 day per week"));
Entity sourceEntity5 =
new DynamicEntity(targetRefEntityType, of("code", 5, "label", "2-3 days per week"));
Entity sourceEntity6 =
new DynamicEntity(targetRefEntityType, of("code", 6, "label", "4-5 days per week"));
Entity sourceEntity7 =
new DynamicEntity(targetRefEntityType, of("code", 7, "label", "6-7 days per week"));
Entity sourceEntity8 =
new DynamicEntity(targetRefEntityType, of("code", 8, "label", "9 days per week"));
sourceAttribute = attrMetaFactory.create().setName("MESHED_POTATO").setDataType(CATEGORICAL);
sourceAttribute.setLabel(
"How often did you eat boiled or mashed potatoes (also in stew) in the past month? Baked potatoes are asked later");
sourceAttribute.setRefEntity(sourceRefEntityType);
Mockito.when(dataService.findAll(sourceRefEntityType.getName()))
.thenReturn(
Stream.of(
sourceEntity1,
sourceEntity2,
sourceEntity3,
sourceEntity4,
sourceEntity5,
sourceEntity6,
sourceEntity7,
sourceEntity8));
sourceEntityType = entityTypeFactory.create("source");
sourceEntityType.addAttributes(Lists.newArrayList(sourceAttribute));
}
@Override
public Object getIdValue() {
// abstract entities might not have an id attribute
Attribute idAttr = entityType.getIdAttribute();
return idAttr != null ? get(idAttr.getName()) : null;
}
@Override
public Object getLabelValue() {
// abstract entities might not have an label attribute
Attribute labelAttr = entityType.getLabelAttribute();
return labelAttr != null ? get(labelAttr.getName()) : null;
}
/**
* 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()));
}
}