def test_import_invalid_json(
tmp_path: Path,
user,
project_factory,
samples_dir: Path,
sample_scans,
):
json_file = str(tmp_path / 'import.json')
json_content = generate_import_json(samples_dir, sample_scans)
# deliberately invalidate the data
json_content['scans'][0]['site_id'] = 666
with open(json_file, 'w') as fd:
fd.write(json.dumps(json_content))
project = project_factory(import_path=json_file)
with pytest.raises(
ValidationError,
match=re.escape(
"666 is not of type 'string'\n\nFailed validating 'type' in schema['properties']['scans']['items']['properties']['site_id']:\n {'type': 'string'}\n\nOn instance['scans'][0]['site_id']:\n 666" # noqa: E501
),
):
import_data(user.id, project.id)
def import_(self, request, **kwargs):
project: Project = self.get_object()
# tasks sent to celery must use serializable arguments
import_data(project.id)
return Response(status=status.HTTP_204_NO_CONTENT)
def test_import_invalid_csv(tmp_path: Path, user, project_factory, sample_scans):
csv_file = str(tmp_path / 'import.csv')
output, writer = generate_import_csv(sample_scans)
# deliberately invalidate the data
writer.writerow(
{
'xnat_experiment_id': 'NCANDA_DUMMY',
# This value with no common prefix with the other scans will cause a ValueError
'nifti_folder': 'NOT_A_REAL_FOLDER',
'scan_id': '123',
'scan_type': 'foobar',
'experiment_note': '',
'decision': '',
'scan_note': '',
}
)
with open(csv_file, 'w') as fd:
fd.write(output.getvalue())
project = project_factory(import_path=csv_file)
with pytest.raises(ValueError, match='empty separator'):
import_data(user.id, project.id)
def test_import_with_relative_path(project_factory):
rel_import_csv = Path(__file__).parent / 'data' / 'relative_import.csv'
project = project_factory(import_path=rel_import_csv)
import_data(project.id)
frame = Frame.objects.first()
assert frame.raw_path == str(
Path(__file__).parent / 'data' / 'example.nii.gz')
def test_import_s3_preserves_path(project_factory):
s3_import_csv = Path(__file__).parent / 'data' / 's3_import.csv'
project = project_factory(import_path=s3_import_csv)
import_data(project.id)
frame = Frame.objects.first()
assert (
frame.raw_path ==
's3://miqa-sample/IXI_small/Guys/IXI002/0828-DTI/IXI002-Guys-0828-DTI-00.nii.gz'
)
def test_import_csv(tmp_path, user, project_factory, sample_scans, authenticated_api_client):
csv_file = str(tmp_path / 'import.csv')
with open(csv_file, 'w') as fd:
output, _writer = generate_import_csv(sample_scans)
fd.write(output.getvalue())
project = project_factory(import_path=csv_file)
import_data(user.id, project.id)
# Test that the API import succeeds
resp = authenticated_api_client.post(f'/api/v1/projects/{project.id}/import')
assert resp.status_code == 204
def test_import_json(
tmp_path: Path,
user,
project_factory,
samples_dir: Path,
sample_scans,
authenticated_api_client,
):
json_file = str(tmp_path / 'import.json')
with open(json_file, 'w') as fd:
fd.write(json.dumps(generate_import_json(samples_dir, sample_scans)))
project = project_factory(import_path=json_file)
import_data(user.id, project.id)
# Test that the API import succeeds
resp = authenticated_api_client.post(f'/api/v1/projects/{project.id}/import')
assert resp.status_code == 204
def test_import_invalid_csv(tmp_path: Path, user, project_factory,
sample_scans):
csv_file = str(tmp_path / 'import.csv')
output, writer = generate_import_csv(sample_scans)
# deliberately invalidate the data
writer.writerow({
'project_name': 'testProject',
'experiment_name': 'testExperiment',
'scan_name': 'testScan',
'scan_type': 'foobar',
'frame_number': 0,
'file_location': '/not/a/real/file.nii.gz',
})
with open(csv_file, 'w') as fd:
fd.write(output.getvalue())
project = project_factory(import_path=csv_file)
with pytest.raises(APIException, match='Could not locate file'):
import_data(user.id, project.id)
def test_import_invalid_json(
tmp_path: Path,
user,
project_factory,
samples_dir: Path,
sample_scans,
):
json_file = str(tmp_path / 'import.json')
json_content = generate_import_json(samples_dir, sample_scans)
# deliberately invalidate the data
json_content['fake_key'] = 'foo'
with open(json_file, 'w') as fd:
fd.write(json.dumps(json_content))
project = project_factory(import_path=json_file)
with pytest.raises(
APIException,
match=re.escape('Invalid format of import file'),
):
import_data(user.id, project.id)
def test_import_invalid_extension(user, project_factory):
invalid_file = '/foo/bar.txt'
project = project_factory(import_path=invalid_file)
with pytest.raises(ValidationError, match=f'Invalid import file {invalid_file}'):
import_data(user.id, project.id)
def import_(self, request, **kwargs):
import_data(None)
return Response(status=status.HTTP_204_NO_CONTENT)