def test_zero_samples_igocomplete_false(self, mock_get_sample):
mock_get_sample.return_value = MockResponse(
json_data=self.data_0_fastq, status_code=200)
with self.assertRaises(MissingDataException):
fetch_sample_metadata('igoId_000', False, 'sampleName_000', {})
count_files = FileRepository.all().count()
self.assertEqual(count_files, 0)
def test_import_sample_two_fastq_files(self, mock_get_sample):
mock_get_sample.return_value = MockResponse(
json_data=self.data_2_fastq, status_code=200)
fetch_sample_metadata('igoId_002', True, 'sampleName_002', {})
count_files = FileRepository.filter(path_in=[
"/path/to/sample/08/sampleName_002-d_IGO_igoId_002_S134_L008_R2_001.fastq.gz",
"/path/to/sample/08/sampleName_002-d_IGO_igoId_002_S134_L008_R1_001.fastq.gz"
]).count()
self.assertEqual(count_files, 2)
def test_import_sample_six_fastq_files(self, mock_get_sample):
mock_get_sample.return_value = MockResponse(
json_data=self.data_6_fastq, status_code=200)
fetch_sample_metadata('igoId_006', True, 'sampleName_006', {})
count_files = FileRepository.filter(path_in=[
"/path/to/sample/01/sampleName_006_IGO_igoId_006_S64_L007_R2_001.fastq.gz",
"/path/to/sample/01/sampleName_006_IGO_igoId_006_S64_L007_R1_001.fastq.gz",
"/path/to/sample/01/sampleName_006_IGO_igoId_006_S64_L006_R1_001.fastq.gz",
"/path/to/sample/01/sampleName_006_IGO_igoId_006_S64_L006_R2_001.fastq.gz",
"/path/to/sample/02/sampleName_006_IGO_igoId_006_S54_L003_R1_001.fastq.gz",
"/path/to/sample/02/sampleName_006_IGO_igoId_006_S54_L003_R2_001.fastq.gz"
]).count()
self.assertEqual(count_files, 6)
def test_file_conflict(self, mock_get_sample):
file_conflict = File.objects.create(
path=
"/path/to/sample/08/sampleName_002-d_IGO_igoId_002_S134_L008_R2_001.fastq.gz",
file_type=self.fastq,
file_group=self.file_group,
)
file_metadata = FileMetadata.objects.create(file=file_conflict,
version=1,
metadata={})
mock_get_sample.return_value = MockResponse(
json_data=self.data_2_fastq, status_code=200)
with self.assertRaises(ErrorInconsistentDataException) as e:
fetch_sample_metadata('igoId_002', True, 'sampleName_002', {})
self.assertTrue('Conflict of fastq file(s)' in str(e))
count_files = FileRepository.filter(path_in=[
"/path/to/sample/08/sampleName_002-d_IGO_igoId_002_S134_L008_R2_001.fastq.gz",
]).count()
self.assertEqual(count_files, 1)
def test_zero_fastq_files(self, mock_get_sample):
mock_get_sample.return_value = MockResponse(
json_data=self.data_0_fastq, status_code=200)
with self.assertRaises(ErrorInconsistentDataException) as e:
fetch_sample_metadata('igoId_000', True, 'sampleName_000', {})
self.assertTrue("Missing fastq files for igcomplete: " in str(e))