def upload_wf():
messages = []
data = []
try:
login_required()
assert 'file' in request.files, 'No file received.'
import_file = request.files['file']
assert import_file.filename != '', "No file specified."
# save the file to the CWL directory:
metadata = json_loads(request.form.get("meta"))
import_filename = secure_filename(import_file.filename)
wf_type = metadata["wf_type"] if "wf_type" in metadata.keys() else None
temp_dir = make_temp_dir()
imported_filepath = os.path.join(temp_dir, import_filename)
import_file.save(imported_filepath)
import_name = secure_filename(metadata["import_name"]) \
if "import_name" in metadata.keys() and metadata["import_name"] != "" \
else import_filename
import_wf_(wf_path=imported_filepath, name=import_name, wf_type=wf_type)
try:
rmtree(temp_dir)
except Exception as e:
pass
messages.append( {
"time": get_time_string(),
"type":"success",
"text": import_file.filename + " successfully imported."
} )
except AssertionError as e:
messages.append( handle_known_error(e, return_front_end_message=True))
except Exception as e:
messages.append(handle_unknown_error(e, return_front_end_message=True))
return jsonify({"data":data,"messages":messages})
def import_wf_by_path_or_url():
messages = []
data = []
try:
data_req = request.get_json()
access_token = data_req["access_token"]
login_required(access_token=access_token)
wf_path = data_req["wf_path"]
is_url = data_req["is_url"] if "is_url" in data_req.keys() else None
import_name = data_req["import_name"]
wf_type = data_req["wf_type"] if "wf_type" in data_req.keys() else None
if is_url:
validate_url(wf_path)
else:
allowed_dirs = get_allowed_base_dirs(
allow_input=True,
allow_upload=True,
allow_download=False,
include_tmp_dir=True
)
assert os.path.isfile(wf_path) and \
check_if_path_in_dirs(wf_path, allowed_dirs) is not None, \
"Path does not exist or you have no permission to enter it."
import_wf_(wf_path=wf_path, name=import_name, wf_type=wf_type)
messages.append( {
"time": get_time_string(),
"type":"success",
"text": import_name + " successfully imported."
} )
except AssertionError as e:
messages.append( handle_known_error(e, return_front_end_message=True))
except Exception as e:
messages.append(handle_unknown_error(e, return_front_end_message=True))
return jsonify({"data":data,"messages":messages})
def upload_wf():
messages = []
data = []
try:
metadata = json_loads(request.form.get("meta"))
access_token = metadata["access_token"]
login_required(access_token=access_token)
# load metadata:
wf_type = metadata["wf_type"] if "wf_type" in metadata.keys() else None
# only relavant for janis:
translate_to_cwl = metadata["translate_to_cwl"] \
if "translate_to_cwl" in metadata.keys() else True
translate_to_wdl = metadata["translate_to_wdl"] \
if "translate_to_wdl" in metadata.keys() else True
wf_name_in_script = metadata["wf_name_in_script"] \
if "wf_name_in_script" in metadata.keys() else None
# save the file to the CWL directory:
assert 'wf_file' in request.files, 'No file received.'
import_wf_file = request.files['wf_file']
assert import_wf_file.filename != '', "No file specified."
import_wf_filename = secure_filename(import_wf_file.filename)
temp_dir = make_temp_dir()
imported_wf_filepath = os.path.join(temp_dir, import_wf_filename)
import_wf_file.save(imported_wf_filepath)
# if existent, save imports.zip:
wf_imports_zip_filepath = None
if 'wf_imports_zip' in request.files.keys():
wf_imports_zip_file = request.files['wf_imports_zip']
wf_imports_zip_filepath = os.path.join(temp_dir, "imports.zip")
wf_imports_zip_file.save(wf_imports_zip_filepath)
# import workflow:
import_name = secure_filename(metadata["import_name"]) \
if "import_name" in metadata.keys() and metadata["import_name"] != "" \
else import_wf_filename
import_wf_(wf_path=imported_wf_filepath,
name=os.path.splitext(import_name)[0],
wf_type=wf_type,
wf_imports_zip_path=wf_imports_zip_filepath,
translate_to_cwl=translate_to_cwl,
translate_to_wdl=translate_to_wdl,
wf_name_in_script=wf_name_in_script)
# cleanup temp:
try:
rmtree(temp_dir)
except Exception as e:
pass
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
import_wf_file.filename + " successfully imported."
})
except AssertionError as e:
messages.append(handle_known_error(e, return_front_end_message=True))
except Exception as e:
messages.append(handle_unknown_error(e, return_front_end_message=True))
return jsonify({"data": data, "messages": messages})