def test_query_report(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)
db.session.commit()
# initial request
resp = self.client.get(f'/query_report?{md.brc_atlas_females_query}')
data = json.loads(resp.get_data())
assert isinstance(data, dict)
assert isinstance(data['dataset'], dict)
assert len(data['dataset'].keys()) == 1
assert list(data['dataset'].keys())[0] == md.d1_code
assert int(data['dataset'][md.d1_code]) == 1 # query string is for females in BRC_ATLAS dataset
def insert_tract_test_data(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(md.d1_code, md.d1_name, md.d1_file_path, md.d1_query_params)
db.session.add(d1)
t1 = Tract(md.t1_code, md.t1_name, md.t1_file_path, md.t1_description)
db.session.add(t1)
t2 = Tract(md.t2_code, md.t2_name, md.t2_file_path, md.t2_description)
db.session.add(t2)
db.session.commit()
def test_get_static_tract_info_no_subjects(self):
''' Test 404 returned when no subjects in query. '''
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)
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(md.d1_code, md.d1_name, md.d1_file_path, md.d1_query_params)
db.session.add(d1)
t1 = Tract(md.t1_code, md.t1_name, md.t1_file_path, md.t1_description)
db.session.add(t1)
t2 = Tract(md.t2_code, md.t2_name, md.t2_file_path, md.t2_description)
db.session.add(t2)
db.session.commit()
resp = self.client.get(f'/get_tract_info/{md.t1_code}?{md.brc_atlas_males_query}')
self.assert404(resp)
def test_get_tract_no_subjects(self):
''' Test behaviour when there are no subjects returned by the selected query. '''
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)
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(md.d1_code, md.d1_name, md.d1_file_path, md.d1_query_params)
db.session.add(d1)
t1 = Tract(md.t1_code, md.t1_name, md.t1_file_path, md.t1_description)
db.session.add(t1)
t2 = Tract(md.t2_code, md.t2_name, md.t2_file_path, md.t2_description)
db.session.add(t2)
db.session.commit()
resp = self.tract_test_response(md.t1_code, md.brc_atlas_males_query)
self.assert404(resp)
def test_query_report_nonexistent_dataset(self):
# only add subject from TESTDATASET
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)
db.session.commit()
# query for females in BRC_ATLAS
resp = self.client.get(f'/query_report?{md.brc_atlas_females_query}')
data = json.loads(resp.get_data())
assert isinstance(data, dict)
assert isinstance(data['dataset'], dict)
assert len(data['dataset'].keys()) == 1
assert list(data['dataset'].keys())[0] == md.d1_code
assert int(data['dataset'][md.d1_code]) == 0
def test_subject_tract_metrics(self):
# insert subjects
sbjct1 = Subject(subject_id=DatabaseUtilsTestCase.sbjct1_subject_id,
gender=DatabaseUtilsTestCase.sbjct1_gender,
age=DatabaseUtilsTestCase.sbjct1_age,
handedness=DatabaseUtilsTestCase.sbjct1_handedness,
edinburgh_handedness_raw=DatabaseUtilsTestCase.sbjct1_edinburgh_handedness_raw,
ravens_iq_raw=DatabaseUtilsTestCase.sbjct1_ravens_iq_raw,
dataset_code=DatabaseUtilsTestCase.sbjct1_dataset_code,
file_path=DatabaseUtilsTestCase.sbjct1_file_path,
mmse=DatabaseUtilsTestCase.sbjct1_mmse)
db.session.add(sbjct1)
sbjct2 = Subject(subject_id=DatabaseUtilsTestCase.sbjct2_subject_id,
gender=DatabaseUtilsTestCase.sbjct2_gender,
age=DatabaseUtilsTestCase.sbjct2_age,
handedness=DatabaseUtilsTestCase.sbjct2_handedness,
edinburgh_handedness_raw=DatabaseUtilsTestCase.sbjct2_edinburgh_handedness_raw,
ravens_iq_raw=DatabaseUtilsTestCase.sbjct2_ravens_iq_raw,
dataset_code=DatabaseUtilsTestCase.sbjct2_dataset_code,
file_path=DatabaseUtilsTestCase.sbjct2_file_path,
mmse=DatabaseUtilsTestCase.sbjct2_mmse)
db.session.add(sbjct2)
sbjct3 = Subject(subject_id=DatabaseUtilsTestCase.sbjct3_subject_id,
gender=DatabaseUtilsTestCase.sbjct3_gender,
age=DatabaseUtilsTestCase.sbjct3_age,
handedness=DatabaseUtilsTestCase.sbjct3_handedness,
edinburgh_handedness_raw=DatabaseUtilsTestCase.sbjct3_edinburgh_handedness_raw,
ravens_iq_raw=DatabaseUtilsTestCase.sbjct3_ravens_iq_raw,
dataset_code=DatabaseUtilsTestCase.sbjct3_dataset_code,
file_path=DatabaseUtilsTestCase.sbjct3_file_path,
mmse=DatabaseUtilsTestCase.sbjct3_mmse)
db.session.add(sbjct3)
# insert test tract
tract1 = Tract(code=DatabaseUtilsTestCase.tract1_code,
name=DatabaseUtilsTestCase.tract1_name,
file_path=DatabaseUtilsTestCase.tract1_file_path,
description=DatabaseUtilsTestCase.tract1_description)
db.session.add(tract1)
# insert subject metrics
sbjct1_mets = SubjectTractMetrics(subject_id=DatabaseUtilsTestCase.sbjct1_subject_id,
tract_code=DatabaseUtilsTestCase.tract1_code,
method_code=DatabaseUtilsTestCase.method1_code,
mean_MD=0.5,
std_MD=0.01,
mean_FA=0.5,
std_FA=0.01,
volume=10)
db.session.add(sbjct1_mets)
sbjct2_mets = SubjectTractMetrics(subject_id=DatabaseUtilsTestCase.sbjct2_subject_id,
tract_code=DatabaseUtilsTestCase.tract1_code,
method_code=DatabaseUtilsTestCase.method1_code,
mean_MD=0.5,
std_MD=0.01,
mean_FA=0.5,
std_FA=0.01,
volume=10)
db.session.add(sbjct2_mets)
sbjct3_mets = SubjectTractMetrics(subject_id=DatabaseUtilsTestCase.sbjct3_subject_id,
tract_code=DatabaseUtilsTestCase.tract1_code,
method_code=DatabaseUtilsTestCase.method1_code,
mean_MD=0.5,
std_MD=0.01,
mean_FA=0.5,
std_FA=0.01,
volume=10)
db.session.add(sbjct3_mets)
db.session.commit()
test_query = {
"TESTDATASET1": {
"method": "DTI",
"constraints": {
"handedness": {"type": "checkbox", "values": ["R","L"]}
}
}
}
metrics = dbu.subject_tract_metrics(test_query, DatabaseUtilsTestCase.tract1_code)
assert type(metrics) == np.ndarray
assert metrics.shape == (3,5)
assert np.sum(metrics) == 33.06
def test_subject_id_dataset_file_path(self):
# insert 2 test datasets
dataset1 = Dataset(code=DatabaseUtilsTestCase.dataset1_code,
name=DatabaseUtilsTestCase.dataset1_name,
file_path=DatabaseUtilsTestCase.dataset1_file_path,
query_params=DatabaseUtilsTestCase.dataset1_query_params)
db.session.add(dataset1)
dataset2 = Dataset(code=DatabaseUtilsTestCase.dataset2_code,
name=DatabaseUtilsTestCase.dataset2_name,
file_path=DatabaseUtilsTestCase.dataset2_file_path,
query_params=DatabaseUtilsTestCase.dataset2_query_params)
db.session.add(dataset2)
# insert subjects
sbjct1 = Subject(subject_id=DatabaseUtilsTestCase.sbjct1_subject_id,
gender=DatabaseUtilsTestCase.sbjct1_gender,
age=DatabaseUtilsTestCase.sbjct1_age,
handedness=DatabaseUtilsTestCase.sbjct1_handedness,
edinburgh_handedness_raw=DatabaseUtilsTestCase.sbjct1_edinburgh_handedness_raw,
ravens_iq_raw=DatabaseUtilsTestCase.sbjct1_ravens_iq_raw,
dataset_code=DatabaseUtilsTestCase.sbjct1_dataset_code,
file_path=DatabaseUtilsTestCase.sbjct1_file_path,
mmse=DatabaseUtilsTestCase.sbjct1_mmse)
db.session.add(sbjct1)
sbjct2 = Subject(subject_id=DatabaseUtilsTestCase.sbjct2_subject_id,
gender=DatabaseUtilsTestCase.sbjct2_gender,
age=DatabaseUtilsTestCase.sbjct2_age,
handedness=DatabaseUtilsTestCase.sbjct2_handedness,
edinburgh_handedness_raw=DatabaseUtilsTestCase.sbjct2_edinburgh_handedness_raw,
ravens_iq_raw=DatabaseUtilsTestCase.sbjct2_ravens_iq_raw,
dataset_code=DatabaseUtilsTestCase.sbjct2_dataset_code,
file_path=DatabaseUtilsTestCase.sbjct2_file_path,
mmse=DatabaseUtilsTestCase.sbjct2_mmse)
db.session.add(sbjct2)
sbjct3 = Subject(subject_id=DatabaseUtilsTestCase.sbjct3_subject_id,
gender=DatabaseUtilsTestCase.sbjct3_gender,
age=DatabaseUtilsTestCase.sbjct3_age,
handedness=DatabaseUtilsTestCase.sbjct3_handedness,
edinburgh_handedness_raw=DatabaseUtilsTestCase.sbjct3_edinburgh_handedness_raw,
ravens_iq_raw=DatabaseUtilsTestCase.sbjct3_ravens_iq_raw,
dataset_code=DatabaseUtilsTestCase.sbjct3_dataset_code,
file_path=DatabaseUtilsTestCase.sbjct3_file_path,
mmse=DatabaseUtilsTestCase.sbjct3_mmse)
db.session.add(sbjct3)
sbjct4 = Subject(subject_id=DatabaseUtilsTestCase.sbjct4_subject_id,
gender=DatabaseUtilsTestCase.sbjct4_gender,
age=DatabaseUtilsTestCase.sbjct4_age,
handedness=DatabaseUtilsTestCase.sbjct4_handedness,
edinburgh_handedness_raw=DatabaseUtilsTestCase.sbjct4_edinburgh_handedness_raw,
ravens_iq_raw=DatabaseUtilsTestCase.sbjct4_ravens_iq_raw,
dataset_code=DatabaseUtilsTestCase.sbjct4_dataset_code,
file_path=DatabaseUtilsTestCase.sbjct4_file_path,
mmse=DatabaseUtilsTestCase.sbjct4_mmse)
db.session.add(sbjct4)
db.session.commit()
test_query = {
"TESTDATASET1": {
"method": "DTI",
"constraints": {
"handedness": {"type": "checkbox", "values": ["R","L"]}
}
},
"TESTDATASET2": {
"method": "DTI",
"constraints": {
"handedness": {"type": "checkbox", "values": ["R","L"]}
}
}
}
result = dbu.subject_id_dataset_file_path(test_query)
assert len(result) == 4
sorted_result = sorted(result, key=lambda subject: subject[0])
assert sorted_result[0][0] == DatabaseUtilsTestCase.sbjct1_subject_id
assert sorted_result[0][1] == DatabaseUtilsTestCase.dataset1_file_path
assert sorted_result[1][0] == DatabaseUtilsTestCase.sbjct2_subject_id
assert sorted_result[1][1] == DatabaseUtilsTestCase.dataset1_file_path
assert sorted_result[2][0] == DatabaseUtilsTestCase.sbjct3_subject_id
assert sorted_result[2][1] == DatabaseUtilsTestCase.dataset1_file_path
assert sorted_result[3][0] == DatabaseUtilsTestCase.sbjct4_subject_id
assert sorted_result[3][1] == DatabaseUtilsTestCase.dataset2_file_path
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