def test_sample_relationship_issue(self):
"""Testing an error with related alias. Not sure if it can happen or
not"""
# get record from sample
record = self.sample_record
# change alias in relationship in order to have no a related obj
record["sampleRelationships"] = [{
"alias": "IMAGEA999999999",
"relationshipNature": "derived from"
}]
# create a fake ValidationResultRecord
record_result = ValidationResultRecord(record_id=record['title'])
# check relationship method
related, result = self.metadata.check_relationship(
record, record_result)
# this is an error in results
self.assertEqual(related, [])
self.assertEqual(result.get_overall_status(), 'Error')
self.assertIn("Could not locate the referenced record",
result.get_messages()[0])
def check_biosample_id(self, mock_get, status_code):
"""Base method for checking biosample id"""
# paching response
response = Mock()
response.status_code = status_code
mock_get.return_value = response
# create a fake ValidationResultRecord
record_result = ValidationResultRecord(record_id="test")
# get a metadata object
metadata = MetaDataValidation()
# check biosample object
record_result = metadata.check_biosample_id_target(
"FAKEA123456", "test", record_result)
# assert my methods called
self.assertTrue(self.check_ruleset.called)
self.assertTrue(self.read_in_ruleset.called)
self.assertTrue(mock_get.called)
return record_result
def test_validate_submission_errors(self, my_validate, my_check):
"""A submission with errors is a NEED_REVISION submission"""
# setting check_usi_structure result. now is a ValidateResultRecord
result = PickableMock()
result.get_overall_status.return_value = "Pass"
result.get_messages.return_value = []
my_check.return_value = result
# setting a return value for check_with_ruleset
result1 = ValidationResultRecord("animal_1")
result1.add_validation_result_column(
ValidationResultColumn("warning", "warn message", "animal_1",
"warn column"))
result2 = ValidationResultRecord("animal_2")
result2.add_validation_result_column(
ValidationResultColumn("pass", "a message", "animal_2", ""))
result3 = ValidationResultRecord("animal_3")
result3.add_validation_result_column(
ValidationResultColumn("pass", "a message", "animal_3", ""))
result4 = ValidationResultRecord("sample_1")
result4.add_validation_result_column(
ValidationResultColumn("error", "error message", "sample_1",
"error column"))
# add results to result set
responses = [result1, result2, result3, result4]
my_validate.side_effect = responses
# call task
res = self.my_task.run(submission_id=self.submission_id)
# assert a success with validation taks
self.assertEqual(res, "success")
# check submission status and message
self.submission.refresh_from_db()
# check submission.state changed
self.assertEqual(self.submission.status, NEED_REVISION)
self.assertIn("Error in metadata", self.submission.message)
# check Animal (they are all ok)
self.check_model_status(self.animal_qs, responses, READY)
# sample has need revision
self.check_model_status(self.sample_qs,
responses[self.animal_qs.count():],
NEED_REVISION)
# test for my methods called
self.assertTrue(my_check.called)
self.assertTrue(my_validate.called)
# asserting my mock objects
self.assertTrue(self.read_in_ruleset.called)
self.assertTrue(self.check_ruleset.called)
self.assertFalse(self.validate_retry.called)
self.check_message(
message='Need Revision',
notification_message=('Validation got errors: Error in '
'metadata. Need revisions before submit'),
validation_message={
'animals': self.n_animals,
'samples': self.n_samples,
'animal_unkn': 0,
'sample_unkn': 0,
'animal_issues': 0,
'sample_issues': 1
},
pk=1)
def test_validate_submission_wrong_json(self, my_validate, my_check):
"""Test an error in JSON format"""
# setting check_usi_structure result. now is a ValidateResultRecord
messages = [('Wrong JSON structure: no title field for record with '
'alias as animal_1'),
('Wrong JSON structure: the values for attribute Person '
'role needs to be in an array for record animal_1')]
usi_result = ValidationResultRecord("animal_1")
usi_result.add_validation_result_column(
ValidationResultColumn("error", messages[0], "animal_1", ""))
usi_result.add_validation_result_column(
ValidationResultColumn("error", messages[1], "animal_1", ""))
# track 4 object to call check_model_status
responses = [usi_result] * 4
my_check.side_effect = responses
# setting a return value for check_with_ruleset
rule_result = Mock()
rule_result.get_overall_status.return_value = "Pass"
my_validate.return_value = rule_result
# call task
res = self.my_task.run(submission_id=self.submission_id)
# assert a success with validation taks
self.assertEqual(res, "success")
# check submission status and message
self.submission.refresh_from_db()
# check submission.state changed
self.assertEqual(self.submission.status, NEED_REVISION)
self.assertIn("Validation got errors", self.submission.message)
# Animals and samples have issues
self.check_model_status(self.animal_qs, responses, NEED_REVISION)
# sample has need revision
self.check_model_status(self.sample_qs,
responses[self.animal_qs.count():],
NEED_REVISION)
# if JSON is not valid, I don't check for ruleset
self.assertTrue(my_check.called)
self.assertFalse(my_validate.called)
# asserting my mock objects
self.assertTrue(self.read_in_ruleset.called)
self.assertTrue(self.check_ruleset.called)
self.assertFalse(self.validate_retry.called)
# all sample and animals have issues
self.check_message(
'Need Revision', ('Validation got errors: Error in metadata. '
'Need revisions before submit'), {
'animals': self.n_animals,
'samples': self.n_samples,
'animal_unkn': 0,
'sample_unkn': 0,
'animal_issues': self.n_animals,
'sample_issues': self.n_samples
}, 1)