def test_get_tract_empty_density_map(self):
''' Sometimes a subject might not have a certain tract show up with tractography. So need
to be able to handle an empty density map. '''
self.insert_tract_test_data()
def nib_load_patch(file_path):
if md.s1_subject_id in file_path:
return md.s1_t1
elif md.s3_subject_id in file_path:
return md.empty_nifti
elif du.TEMPLATE_FILE_NAME in file_path:
return md.template_nifti
else:
raise ValueError('Invalid file path passed to nib_load_patch in test_views.')
def nib_save_patch(img, file_path):
pass
def send_file_patch(file_path, as_attachment=True, attachment_filename=None, conditional=True, add_etags=True):
'''Monkey patch flask.send_file with this function to create a response object without needing
to load a file from file system'''
global file_path_to_test
file_path_to_test = file_path
headers = Headers()
headers.add('Content-Disposition', 'attachment', filename=attachment_filename)
return Response(mimetype='application/octet-stream', headers=headers)
with monkey_patch(views, 'send_file', send_file_patch):
with monkey_patch(du.nib, 'load', nib_load_patch):
with monkey_patch(du.nib, 'save', nib_save_patch):
resp = self.client.get(f'tract/{md.t1_code}?{md.brc_atlas_males_query}&file_type=.nii.gz')
self.assert200(resp)
assert md.t1_code in file_path_to_test and 'nii.gz' in file_path_to_test
def tract_test_response(self, tract_code, query_string):
def nib_load_patch(file_path):
if md.s1_subject_id in file_path:
return md.s1_t1
elif md.s3_subject_id in file_path:
return md.s3_t1
elif du.TEMPLATE_FILE_NAME in file_path:
return md.template_nifti
else:
raise ValueError('Invalid file path passed to nib_load_patch in test_views.')
def nib_save_patch(img, file_path):
pass
def send_file_patch(file_path, as_attachment=True, attachment_filename=None, conditional=True, add_etags=True):
'''Monkey patch flask.send_file with this function to create a response object without needing
to load a file from file system'''
global file_path_to_test
file_path_to_test = file_path
headers = Headers()
headers.add('Content-Disposition', 'attachment', filename=attachment_filename)
return Response(mimetype='application/octet-stream', headers=headers)
with monkey_patch(views, 'send_file', send_file_patch):
with monkey_patch(du.nib, 'load', nib_load_patch):
with monkey_patch(du.nib, 'save', nib_save_patch):
resp = self.client.get(f'tract/{tract_code}?{query_string}&file_type=.nii.gz')
return resp
def test_get_template_file_not_found(self):
def send_file_patch(file_path, as_attachment=True, attachment_filename=None,
conditional=True, add_etags=True):
'''Monkey patch flask.send_file with this function to
generate FileNotFoundError'''
file = open('fail.nii.gz', 'rb')
with monkey_patch(views, 'send_file', send_file_patch):
resp = self.client.get('/get_template')
self.assert500(resp)
def test_get_template(self):
file_path_to_test = ''
def send_file_patch(file_path, as_attachment=True, attachment_filename=None,
conditional=True, add_etags=True):
'''Monkey patch flask.send_file with this function to create a
response object without needing to load a file from file system'''
nonlocal file_path_to_test
file_path_to_test = file_path
headers = Headers()
headers.add('Content-Disposition', 'attachment', filename=attachment_filename)
headers['Content-Length'] = 1431363
return Response(mimetype='application/octet-stream', headers=headers)
with monkey_patch(views, 'send_file', send_file_patch):
resp = self.client.get('/get_template')
assert file_path_to_test == f'../{current_app.config["DATA_FILE_PATH"]}' \
f'/{du.TEMPLATE_FILE_NAME}'
assert resp.mimetype == 'application/octet-stream'
assert resp.headers.get('Content-Disposition') == f'attachment; ' \
f'filename={du.TEMPLATE_FILE_NAME}'
assert resp.headers.get('Content-Length') == '1431363'
def test_download_tract(self):
# need to mock tract probability map + mean maps
# mock data in db
# monkey_patch nib.load, nib.save (for json file, may as well cache it for
# downloads with same query but different tract)
# monkey patch Flask.send_file? (will attempt to create zip file in memory though
# so hopefully won't need to do this)
self.insert_tract_test_data()
# insert subject_tract_metrics
s1t1m = SubjectTractMetrics(md.s1_subject_id,
md.m1_code,
md.t1_code,
0.5,
0.05,
0.5,
0.05,
3.)
db.session.add(s1t1m)
s3t1m = SubjectTractMetrics(md.s3_subject_id,
md.m1_code,
md.t1_code,
0.5,
0.05,
0.5,
0.05,
3.)
db.session.add(s3t1m)
db.session.commit()
# mock cached file paths and added completed jobs to the cache
prob_map_file_path = f'{md.t1_code}_some_time.nii.gz'
MD_file_path = 'MD_some_time.nii.gz'
FA_file_path = 'FA_some_time.nii.gz'
current_app.cache.set(md.brc_atlas_males_query, {
md.t1_code: {
'status': 'COMPLETE',
'result': prob_map_file_path
},
'mean_maps': {
'status': 'COMPLETE',
'result': {
'MD': MD_file_path,
'FA': FA_file_path
}
}
})
def nib_load_patch(file_path):
if file_path == prob_map_file_path:
return md.s1_t1
elif file_path == MD_file_path:
return md.s1_MD
elif file_path == FA_file_path:
return md.sd_FA
else:
raise ValueError(f'Unexpected file path {file_path} passed to nib_load_patch!')
def nib_save_patch(img, file_path):
# pretend to do something with the nifti img
pass
def zipfile_write_patch(self, file_path, arcname=''):
pass
with monkey_patch(du.nib, 'load', nib_load_patch), \
monkey_patch(du.nib, 'save', nib_save_patch), \
monkey_patch(zipfile.ZipFile, 'write', zipfile_write_patch):
resp = self.client.get(f'/download/tract/{md.t1_code}?{md.brc_atlas_males_query}')
self.assert200(resp)
zipped_bytes = resp.get_data()
zipped_file = zipfile.ZipFile(io.BytesIO(zipped_bytes), 'r')
with zipped_file.open('data.json') as data_json:
data = json.loads(data_json.read())
assert len(data['subjects']) == 2
assert len(data['demographic_data']) == 2
def test_generate_mean_maps(self):
s1 = Subject(subject_id=md.s1_subject_id,
gender=md.s1_gender,
age=md.s1_age,
handedness=md.s1_handedness,
edinburgh_handedness_raw=md.s1_edinburgh_handedness_raw,
ravens_iq_raw=md.s1_ravens_iq_raw,
dataset_code=md.s1_dataset_code,
file_path=md.s1_file_path,
mmse=md.s1_mmse)
db.session.add(s1)
s2 = Subject(subject_id=md.s2_subject_id,
gender=md.s2_gender,
age=md.s2_age,
handedness=md.s2_handedness,
edinburgh_handedness_raw=md.s2_edinburgh_handedness_raw,
ravens_iq_raw=md.s2_ravens_iq_raw,
dataset_code=md.s2_dataset_code,
file_path=md.s2_file_path,
mmse=md.s2_mmse)
db.session.add(s2)
s3 = Subject(subject_id=md.s3_subject_id,
gender=md.s3_gender,
age=md.s3_age,
handedness=md.s3_handedness,
edinburgh_handedness_raw=md.s3_edinburgh_handedness_raw,
ravens_iq_raw=md.s3_ravens_iq_raw,
dataset_code=md.s3_dataset_code,
file_path=md.s3_file_path,
mmse=md.s3_mmse)
db.session.add(s3)
s4 = Subject(subject_id=md.s4_subject_id,
gender=md.s4_gender,
age=md.s4_age,
handedness=md.s4_handedness,
edinburgh_handedness_raw=md.s4_edinburgh_handedness_raw,
ravens_iq_raw=md.s4_ravens_iq_raw,
dataset_code=md.s4_dataset_code,
file_path=md.s4_file_path,
mmse=md.s4_mmse)
db.session.add(s4)
d1 = Dataset(code=md.d1_code, name=md.d1_name, file_path=md.d1_file_path, query_params=md.d1_query_params)
db.session.add(d1)
d2 = Dataset(code=md.d2_code, name=md.d2_name, file_path=md.d2_file_path, query_params=md.d1_query_params)
db.session.add(d2)
db.session.commit()
self.saved_file_path = ''
self.saved_img = None
def nib_save_patch(img, file_path):
self.saved_file_path = file_path
self.saved_img = img
data = img.get_data()
assert np.all(data == 1.)
def nib_load_patch(file_path):
if du.TEMPLATE_FILE_NAME in file_path:
return md.template_nifti
elif md.s1_subject_id in file_path:
return md.s1_MD if 'MD' in file_path else md.s1_FA
elif md.s3_subject_id in file_path:
return md.s3_MD if 'MD' in file_path else md.s3_FA
else:
print('Unexpected file path passed to nib_load_path in test_views.test_generate_maps')
print(file_path)
return
# assert the cache is empty for query string before response
assert not current_app.cache.get(md.brc_atlas_males_query)
# first request
with monkey_patch(du.nib, 'save', nib_save_patch):
with monkey_patch(du.nib, 'load', nib_load_patch):
resp = self.client.get(f'/generate_mean_maps?{md.brc_atlas_males_query}')
self.assertStatus(resp, 204)
assert current_app.cache.get(md.brc_atlas_males_query) # check data has been cached