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})