def make_patients_data(parameters):
if parameters.outcomes[0] != '':
patient_data_name = tools.read_excel(
os.path.join(parameters.path_files,
'data_files_and_project_names.xlsx')).get_value(1, 0)
if patient_data_name == "no file":
return None
patient_data = tools.read_excel(os.path.join(parameters.data_files,
patient_data_name),
indexCol=0)
patient_data.dropna(axis='index', how='all', inplace=True)
return patient_data
return None
def make_cyto_data(parameters):
cy_data_name = tools.read_excel(
os.path.join(parameters.path_files,
'data_files_and_project_names.xlsx')).get_value(0, 0)
cy_data = tools.read_excel(os.path.join(parameters.data_files, cy_data_name), skiprows=[4, 5, 6, 7], indexCol=0, header = 3) if parameters.luminex \
else tools.read_excel(os.path.join(parameters.data_files, cy_data_name), indexCol=0)
cy_data.dropna(axis='index', how='all', inplace=True)
parameters.cytokines = list(
cy_data.columns) if parameters.cytokines[0] == '' and len(
parameters.cytokines) == 1 else parameters.cytokines # None
cy_data = cy_data[
parameters.
cytokines] # Only cytokines contained in parameters.cytokines list
# TODO: ADD convertLevel
return cy_data
def assert_column_exists_in_path(file_path, col_name, sheet=0):
df = tools.read_excel(file_path, sheet=sheet, nrows=3)
if col_name not in df.columns:
message = f'column {col_name} does not exist in file {file_path}'
logging.error(message)
return False, message
return True, "success"
def time_to_delete(project):
project_metadata = tools.read_excel(
os.path.join('static/', project, 'process_id_status.xlsx'))
project_status = project_metadata['value'][1]
project_time = project_metadata['value'][2]
current_time = time.time()
return (project_status
== 'DONE') and (current_time - project_time > DELETION_TIME)
def check_input(parameters):
assert type(parameters.name_data) is str
assert type(parameters.name_compartment) is str
assert type(parameters.log_transform) is bool
assert type(parameters.max_testing_k) is int
assert type(parameters.outcomes) is list
assert type(parameters.covariates) is list
if parameters.cytokines != "":
cytokines_file_name = tools.read_excel(
os.path.join(parameters.path_files,
'data_files_and_project_names.xlsx')).get_value(0, 0)
path = os.path.join(parameters.data_files, cytokines_file_name)
cytokines_columns_exists, message = check_columns(
parameters.cytokines, path)
if not cytokines_columns_exists:
return False, message
outcomes_file_name = tools.read_excel(
os.path.join(parameters.path_files,
'data_files_and_project_names.xlsx')).get_value(1, 0)
if outcomes_file_name == "no file":
return True, "no outcome file"
if parameters.outcomes != ['']:
file_name = tools.read_excel(
os.path.join(parameters.path_files,
'data_files_and_project_names.xlsx')).get_value(1, 0)
if type(file_name) is float:
return False, "file does not match"
path = os.path.join(parameters.data_files, file_name)
outcome_columns_exists, message = check_columns(
parameters.outcomes, path)
if not outcome_columns_exists:
return False, message
covariates_columns_exists, message = check_columns(
parameters.covariates, path)
if not covariates_columns_exists:
return False, message
log_columns_names_exists, message = check_columns(
parameters.log_column_names, path)
if not log_columns_names_exists:
return False, message
# TODO: INSERT CHECK FILE
return True, "success"
def encode_images(id):
if not os.path.exists(os.path.join('static', id, 'all_results.xlsx')):
return
xls_results = tools.read_excel(
os.path.join('static/', id, 'all_results.xlsx')).set_index('index')
index = 1
for image in xls_results['image']:
if image != 'not':
with open(image, "rb") as image_file:
encoded_string = base64.b64encode(image_file.read())
xls_results['image'][f'row_{index}'] = f'{encoded_string}'
index = index + 1
return xls_results
def error_status(project):
project_metadata = tools.read_excel(
os.path.join('static/', project, 'process_id_status.xlsx'))
project_status = project_metadata['value'][1]
return project_status == 'DATA ERROR' or project_status == 'RUN TIME ERROR'