def _process_input_zip(self, zip_arch, result_folder, remote_prefix,
file_name_base, expected_pairs, fix_number=True):
"""
Read entries in uploaded ZIP.
Raise Exception in case pairs HDR/IMG are not matched or number "expected_pairs" is not met.
:return string with HDR list (to be passed to DTI pipeline).
"""
hdr_files = []
for file_name in zip_arch.namelist():
if not file_name.startswith(file_name_base) or file_name.endswith("/"):
continue
if file_name.endswith(".hdr"):
pair_img = file_name.replace(".hdr", ".img")
if pair_img not in zip_arch.namelist():
raise ConnectException("Could not find pair for HDR file :" + str(file_name))
new_file_name = os.path.join(result_folder, file_name_base + str(len(hdr_files)) + ".hdr")
src = zip_arch.open(file_name, 'rU')
FilesHelper.copy_file(src, new_file_name)
hdr_files.append(os.path.join(remote_prefix, os.path.split(new_file_name)[1]))
new_file_name = new_file_name.replace(".hdr", ".img")
src = zip_arch.open(pair_img, 'rU')
FilesHelper.copy_file(src, new_file_name)
elif not file_name.endswith(".img"):
self.logger.warning("Ignored file :" + str(file_name))
if len(hdr_files) < expected_pairs or (fix_number and len(hdr_files) > expected_pairs):
raise ConnectException("Invalid number of files "+ str(len(hdr_files)) + " expected "+ str(expected_pairs))
result = ""
for hdr_name in hdr_files:
result = result + hdr_name + " "
return result
class DTITest(TransactionalTestCase):
"""
Test basic functionality of DTI Import Service.
"""
### First dataSet
FILE_1 = os.path.join(os.path.dirname(current_pack.__file__), "data",
"TVB_ConnectionCapacityMatrix.csv")
FILE_2 = os.path.join(os.path.dirname(current_pack.__file__), "data",
"TVB_ConnectionDistanceMatrix.csv")
### Second dataSet
FILE_3 = os.path.join(os.path.dirname(current_pack.__file__), "data",
"TVB_ConnectionCapacityMatrix_3.csv")
FILE_4 = os.path.join(os.path.dirname(current_pack.__file__), "data",
"TVB_ConnectionDistanceMatrix_3.csv")
def setUp(self):
"""
Reset the database before each test.
"""
# self.clean_database()
self.test_user = TestFactory.create_user()
self.test_project = TestFactory.create_project(self.test_user)
self.service = DTIPipelineService('127.0.0.1', 'root')
self.helper = FilesHelper()
def test_process_csv(self):
"""
Test that a CSV generated on the server is correctly processed.
"""
folder = self.helper.get_project_folder(self.test_project, "TEMP")
for file_name in [self.FILE_1, self.FILE_2, self.FILE_3, self.FILE_4]:
intermediate_file = os.path.join(folder,
os.path.split(file_name)[1])
self.helper.copy_file(file_name, intermediate_file)
result_file = 'weights.txt' if 'Capacity' in file_name else 'tracts.txt'
result_file = os.path.join(folder, result_file)
self.service._process_csv_file(intermediate_file, result_file)
matrix = read_list_data(result_file)
self.assertEqual(96, len(matrix))
self.assertEqual(96, len(matrix[0]))