@Test
public void translateCheckConstraintViolation() {
ServerErrorMessage serverErrorMessage = mock(ServerErrorMessage.class);
when(serverErrorMessage.getTable()).thenReturn("entity");
when(serverErrorMessage.getConstraint()).thenReturn("entity_column_chk");
//noinspection ThrowableResultOfMethodCallIgnored
MolgenisValidationException e =
PostgreSqlExceptionTranslator.translateCheckConstraintViolation(
new PSQLException(serverErrorMessage));
assertEquals(e.getMessage(), "Unknown enum value for attribute 'column' of entity 'entity'.");
}
@Test
public void translateInvalidIntegerExceptionDate() {
ServerErrorMessage serverErrorMessage = mock(ServerErrorMessage.class);
when(serverErrorMessage.getMessage())
.thenReturn("invalid input syntax for type date: \"str1\"");
//noinspection ThrowableResultOfMethodCallIgnored
MolgenisValidationException e =
PostgreSqlExceptionTranslator.translateInvalidIntegerException(
new PSQLException(serverErrorMessage));
assertEquals(e.getMessage(), "Value [str1] of this entity attribute is not of type [DATE].");
}
@Test
public void translateDependentObjectsStillExistNoDoubleQuotes() {
ServerErrorMessage serverErrorMessage = mock(ServerErrorMessage.class);
when(serverErrorMessage.getSQLState()).thenReturn("2BP01");
when(serverErrorMessage.getDetail())
.thenReturn("constraint my_foreign_key_constraint on table xxx depends on table yyy");
//noinspection ThrowableResultOfMethodCallIgnored
MolgenisValidationException e =
PostgreSqlExceptionTranslator.translateDependentObjectsStillExist(
new PSQLException(serverErrorMessage));
assertEquals(e.getMessage(), "Cannot delete entity 'xxx' because entity 'yyy' depends on it.");
}
@Test
public void translateUndefinedColumnException() {
ServerErrorMessage serverErrorMessage = mock(ServerErrorMessage.class);
when(serverErrorMessage.getSQLState()).thenReturn("42703");
when(serverErrorMessage.getMessage())
.thenReturn("Undefined column: 7 ERROR: column \"test\" does not exist");
//noinspection ThrowableResultOfMethodCallIgnored
MolgenisValidationException e =
PostgreSqlExceptionTranslator.translateUndefinedColumnException(
new PSQLException(serverErrorMessage));
assertEquals(e.getMessage(), "Undefined column: 7 ERROR: column \"test\" does not exist");
}
@Test
public void testWrongIntValue() throws IOException {
try {
importer.importEntities(
loadTestFile("wrong-int-type.xlsx"), DatabaseAction.ADD_UPDATE_EXISTING);
fail("Should have thrown MolgenisValidationException");
} catch (MolgenisValidationException e) {
assertEquals(e.getViolations().size(), 1);
assertEquals(e.getViolations().iterator().next().getViolatedAttribute().getName(), "age");
assertEquals(e.getViolations().iterator().next().getRownr(), 1);
}
}
@Test
public void testXrefCircular() throws IOException {
try {
importer.importEntities(
loadTestFile("xref-circular.xlsx"), DatabaseAction.ADD_UPDATE_EXISTING);
fail("Should have thrown MolgenisValidationException");
} catch (MolgenisValidationException e) {
assertEquals(e.getViolations().size(), 2);
assertEquals(e.getViolations().iterator().next().getViolatedAttribute().getName(), "father");
assertEquals(e.getViolations().iterator().next().getRownr(), 1);
}
}
@Test
public void translateReadonlyViolationNoDoubleQuotes() {
ServerErrorMessage serverErrorMessage = mock(ServerErrorMessage.class);
when(serverErrorMessage.getMessage())
.thenReturn("Updating read-only column attr of table entity with id [abc] is not allowed");
//noinspection ThrowableResultOfMethodCallIgnored
MolgenisValidationException e =
PostgreSqlExceptionTranslator.translateReadonlyViolation(
new PSQLException(serverErrorMessage));
assertEquals(
e.getMessage(),
"Updating read-only attribute 'attr' of entity 'entity' with id 'abc' is not allowed.");
}
@Test
public void translateNotNullViolationNoDoubleQuotes() {
ServerErrorMessage serverErrorMessage = mock(ServerErrorMessage.class);
when(serverErrorMessage.getSQLState()).thenReturn("23502");
when(serverErrorMessage.getTable()).thenReturn("xxx");
when(serverErrorMessage.getMessage())
.thenReturn("null value in column yyy violates not-null constraint");
//noinspection ThrowableResultOfMethodCallIgnored
MolgenisValidationException e =
PostgreSqlExceptionTranslator.translateNotNullViolation(
new PSQLException(serverErrorMessage));
assertEquals(e.getMessage(), "The attribute 'yyy' of entity 'xxx' can not be null.");
}
@Test
public void translateUniqueKeyViolation() {
ServerErrorMessage serverErrorMessage = mock(ServerErrorMessage.class);
when(serverErrorMessage.getSQLState()).thenReturn("23505");
when(serverErrorMessage.getTable()).thenReturn("mytable");
when(serverErrorMessage.getDetail()).thenReturn("Key (mycolumn)=(myvalue) already exists.");
//noinspection ThrowableResultOfMethodCallIgnored
MolgenisValidationException e =
PostgreSqlExceptionTranslator.translateUniqueKeyViolation(
new PSQLException(serverErrorMessage));
assertEquals(
e.getMessage(),
"Duplicate value 'myvalue' for unique attribute 'mycolumn' from entity 'mytable'.");
}
@Test
public void translateForeignKeyViolation() {
ServerErrorMessage serverErrorMessage = mock(ServerErrorMessage.class);
when(serverErrorMessage.getSQLState()).thenReturn("23503");
when(serverErrorMessage.getTable()).thenReturn("mytable");
when(serverErrorMessage.getDetail()).thenReturn("... (mycolumn) ... (myvalue) ...");
//noinspection ThrowableResultOfMethodCallIgnored
MolgenisValidationException e =
PostgreSqlExceptionTranslator.translateForeignKeyViolation(
new PSQLException(serverErrorMessage));
assertEquals(
e.getMessage(),
"Unknown xref value 'myvalue' for attribute 'mycolumn' of entity 'mytable'.");
}
@Test
public void translateDependentObjectsStillExistMultipleDependentTables() {
ServerErrorMessage serverErrorMessage = mock(ServerErrorMessage.class);
when(serverErrorMessage.getSQLState()).thenReturn("2BP01");
when(serverErrorMessage.getDetail())
.thenReturn(
"constraint my_foreign_key_constraint on table \"myTable\" depends on table \"myDependentTable\"\nconstraint myOther_foreign_key_constraint on table \"myTable\" depends on table \"myOtherDependentTable\"");
//noinspection ThrowableResultOfMethodCallIgnored
MolgenisValidationException e =
PostgreSqlExceptionTranslator.translateDependentObjectsStillExist(
new PSQLException(serverErrorMessage));
assertEquals(
e.getMessage(),
"Cannot delete entity 'myTable' because entities 'myDependentTable, myOtherDependentTable' depend on it.");
}
@Test
public void translateForeignKeyViolationStillReferenced() {
ServerErrorMessage serverErrorMessage = mock(ServerErrorMessage.class);
when(serverErrorMessage.getSQLState()).thenReturn("23503");
when(serverErrorMessage.getTable()).thenReturn("mytable");
when(serverErrorMessage.getDetail())
.thenReturn("Key (mycolumn)=(myvalue) is still referenced from table \"mytable\"");
//noinspection ThrowableResultOfMethodCallIgnored
MolgenisValidationException e =
PostgreSqlExceptionTranslator.translateForeignKeyViolation(
new PSQLException(serverErrorMessage));
assertEquals(
e.getMessage(),
"Value 'myvalue' for attribute 'mycolumn' is referenced by entity 'mytable'.");
}
@ExceptionHandler(MolgenisValidationException.class)
@ResponseStatus(BAD_REQUEST)
@ResponseBody
public ErrorMessageResponse handleValidationException(MolgenisValidationException e) {
LOG.info("Validation exception occurred.", e);
return new ErrorMessageResponse(new ErrorMessage(e.getMessage()));
}
@Override
@Transactional(rollbackFor = IOException.class)
public EntityImportReport doImport(
RepositoryCollection repositories, DatabaseAction databaseAction) throws IOException {
// All new repository identifiers
List<String> newRepoIdentifiers = new ArrayList<String>();
// First import entities, the data sheets are ignored in the entitiesimporter
EntityImportReport importReport = entitiesImporter.importEntities(repositories, databaseAction);
// RULE: Feature can only belong to one Protocol in a DataSet. Check it (see issue #1136)
checkFeatureCanOnlyBelongToOneProtocolForOneDataSet();
// Import data sheets
for (String name : repositories.getEntityNames()) {
Repository repository = repositories.getRepositoryByEntityName(name);
if (repository.getName().startsWith(DATASET_SHEET_PREFIX)) {
// Import DataSet sheet, create new OmxRepository
String identifier = repository.getName().substring(DATASET_SHEET_PREFIX.length());
if (!dataService.hasRepository(identifier)) {
dataService.addRepository(
new AggregateableCrudRepositorySecurityDecorator(
new OmxRepository(dataService, searchService, identifier, entityValidator)));
newRepoIdentifiers.add(identifier);
DataSet dataSet =
dataService.findOne(
DataSet.ENTITY_NAME,
new QueryImpl().eq(DataSet.IDENTIFIER, identifier),
DataSet.class);
List<Protocol> protocols =
ProtocolUtils.getProtocolDescendants(dataSet.getProtocolUsed());
List<ObservableFeature> categoricalFeatures = new ArrayList<ObservableFeature>();
for (Protocol protocol : protocols) {
List<ObservableFeature> observableFeatures = protocol.getFeatures();
if (observableFeatures != null) {
for (ObservableFeature observableFeature : observableFeatures) {
String dataType = observableFeature.getDataType();
FieldType type = MolgenisFieldTypes.getType(dataType);
if (type.getEnumType() == FieldTypeEnum.CATEGORICAL) {
categoricalFeatures.add(observableFeature);
}
}
}
}
for (ObservableFeature categoricalFeature : categoricalFeatures) {
if (!dataService.hasRepository(
OmxLookupTableEntityMetaData.createOmxLookupTableEntityMetaDataName(
categoricalFeature.getIdentifier()))) {
dataService.addRepository(
new OmxLookupTableRepository(
dataService, categoricalFeature.getIdentifier(), queryResolver));
newRepoIdentifiers.add(
OmxLookupTableEntityMetaData.createOmxLookupTableEntityMetaDataName(
categoricalFeature.getIdentifier()));
}
}
}
// Check if all column names in the excel sheet exist as attributes of the entity
Set<ConstraintViolation> violations = Sets.newLinkedHashSet();
EntityMetaData meta = dataService.getEntityMetaData(identifier);
for (AttributeMetaData attr : repository.getEntityMetaData().getAttributes()) {
if (meta.getAttribute(attr.getName()) == null) {
String message =
String.format(
"Unknown attributename '%s' for entity '%s'. Sheet: '%s'",
attr.getName(), meta.getName(), repository.getName());
violations.add(new ConstraintViolation(message, attr.getName(), null, null, meta, 0));
}
}
if (!violations.isEmpty()) {
throw new MolgenisValidationException(violations);
}
// Import data into new OmxRepository
try {
dataService.add(identifier, repository);
} catch (MolgenisValidationException e) {
// Add sheet info
for (ConstraintViolation violation : e.getViolations()) {
if (violation.getRownr() > 0) {
// Rownr +1 for header
violation.setImportInfo(
String.format(
"Sheet: '%s', row: %d", repository.getName(), violation.getRownr() + 1));
} else {
violation.setImportInfo(String.format("Sheet: '%s'", repository.getName()));
}
}
for (String newRepoIdentifier : newRepoIdentifiers) {
dataService.removeRepository(newRepoIdentifier);
}
throw e;
}
int count = (int) RepositoryUtils.count(repository);
importReport.addEntityCount(identifier, count);
importReport.addNrImported(count);
}
}
return importReport;
}