def upload_cwl_zip():
messages = []
data = {}
try:
metadata = json_loads(request.form.get("meta"))
access_token = metadata["access_token"]
login_required(access_token=access_token)
assert 'file' in request.files, 'No file received.'
import_wf_file = request.files['file']
assert import_wf_file.filename != '', "No file specified."
assert is_allowed_file(import_wf_file.filename, type="zip"), (
"Wrong file type. Only files with following extensions are allowed: "
+ ", ".join(allowed_extensions_by_type["CWL"]))
# save the file to the CWL directory:
import_wf_filename = secure_filename(import_wf_file.filename)
temp_upload_dir = make_temp_dir()
imported_filepath = os.path.join(temp_upload_dir, import_wf_filename)
import_wf_file.save(imported_filepath)
temp_extract_dir = make_temp_dir()
unzip_dir(imported_filepath, temp_extract_dir)
try:
rmtree(temp_upload_dir)
except Exception as e:
pass
data["temp_dir"] = temp_extract_dir
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
import_wf_file.filename +
" was successfully uploaded and extracted."
})
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 create_job_from_param_form_sheet():
messages = []
data = []
temp_dir = make_temp_dir()
try:
metadata = json_loads(request.form.get("meta"))
access_token = metadata["access_token"]
username = metadata["username"]
login_required(access_token=access_token, username=username)
assert 'file' in request.files, 'No file received.'
import_file = request.files['file']
assert import_file.filename != '', "No file specified."
assert is_allowed_file(import_file.filename, type="spreadsheet"), "Wrong file type. Only files with following extensions are allowed: " + \
", ".join(allowed_extensions_by_type["spreadsheet"])
sheet_format = os.path.splitext(
import_file.filename)[1].strip(".").lower()
job_name = metadata["job_name"]
import_filepath = os.path.join(temp_dir, f"param_sheet.{sheet_format}")
import_file.save(import_filepath)
validate_uris = metadata["validate_uris"]
search_paths = metadata["search_paths"]
search_dir = os.path.abspath(
remove_non_printable_characters(metadata["search_dir"]))
include_subdirs_for_searching = metadata[
"include_subdirs_for_searching"]
if search_paths:
# test if search dir exists:
assert os.path.isdir(search_dir), (
"The specified search dir \"" + search_dir +
"\" does not exist or is not a directory.")
# validate the uploaded form sheet:
validation_result = only_validate_xls(
sheet_file=import_filepath,
validate_uris=validate_uris,
search_paths=search_paths,
search_subdirs=include_subdirs_for_searching,
allow_remote_uri=app.config["INPUT_SOURCES"]["URL"],
allow_local_path=app.config["INPUT_SOURCES"]["local_file_system"],
input_dir=search_dir)
assert validation_result == "VALID", "The provided form failed validation: {}".format(
validation_result)
# create job:
make_job_dir_tree(job_name)
create_job_(job_name=job_name,
username=username,
job_param_sheet=import_filepath,
validate_uris=validate_uris,
search_paths=search_paths,
search_subdirs=include_subdirs_for_searching,
search_dir=search_dir,
sheet_format=sheet_format)
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))
if len(messages) == 0:
messages.append({
"type":
"success",
"text":
f"Job {job_name} was successfully created. Please head over to \"Job Execution and Results\""
})
try:
rmtree(temp_dir)
except Exception:
pass
return jsonify({"data": data, "messages": messages})