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 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 list_avail_wfs_in_janis():
messages = []
data = []
try:
metadata = json_loads(request.form.get("meta"))
access_token = metadata["access_token"]
login_required(access_token=access_token)
# 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)
# import workflow:
avail_wfs = list_workflows_in_janis_file(
file=imported_wf_filepath,
only_return_name=True
)
# cleanup temp:
try:
rmtree(temp_dir)
except Exception as e:
pass
assert len(avail_wfs) > 0, "No workflow definition could be found in the provided Janis file."
data = {
"avail_wfs": avail_wfs
}
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 generate_param_form_sheet(): # generate param form sheet with data sent
# by the client
messages = []
data = {}
try:
data_req = request.get_json()
access_token = data_req["access_token"]
login_required(access_token=access_token)
sheet_format = data_req["sheet_format"]
job_name = data_req["job_name"]
wf_target = data_req["wf_target"]
param_modes = data_req["param_modes"]
run_names = data_req["run_names"]
batch_mode = data_req["batch_mode"]
temp_dir = make_temp_dir() # will stay, need to be cleaned up
temp_dir_name = os.path.basename(temp_dir)
output_file_path = os.path.join(temp_dir,
f"{job_name}_inputs.{sheet_format}")
gen_form_sheet(output_file_path=output_file_path,
template_config_file_path=get_path("job_templ",
wf_target=wf_target),
has_multiple_runs=batch_mode,
run_names=run_names,
param_is_run_specific=param_modes,
show_please_fill=True,
metadata={"workflow_name": wf_target})
data["get_form_sheet_href"] = url_for(
"get_param_form_sheet",
job_name=job_name,
temp_dir_name=temp_dir_name,
access_token=access_token ## should be changed
)
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_values():
messages = []
data = []
temp_dir = make_temp_dir()
try:
data_req = request.get_json()
access_token = data_req["access_token"]
username = data_req["username"]
login_required(access_token=access_token, username=username)
param_values = data_req["param_values"]
param_configs = data_req["param_configs"]
wf_target = data_req["wf_target"]
job_name = data_req["job_name"]
import_filepath = os.path.join(temp_dir, "param_sheet.xlsx")
validate_uris = data_req["validate_uris"]
search_paths = data_req["search_paths"]
search_dir = os.path.abspath(
remove_non_printable_characters(data_req["search_dir"]))
include_subdirs_for_searching = data_req[
"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.")
try:
print({
"param_values":
param_values,
"configs":
param_configs,
"output_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,
"metadata": {
"workflow_name": wf_target
}
})
generate_xls_from_param_values(
param_values=param_values,
configs=param_configs,
output_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,
metadata={"workflow_name": wf_target})
except AssertionError as e:
raise AssertionError(
"The provided form failed validation: {}".format(str(e)))
# 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="xlsx")
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})
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})
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})
