def register():
messages = []
data = {"success": False}
try:
data_req = request.get_json()
username = data_req["username"]
email = data_req["email"]
password = data_req["password"]
rep_password = data_req["rep_password"]
valid_format = check_all_format_conformance(username, email, password,
rep_password)
if valid_format != "valid":
messages.append({
"time": get_time_string(),
"type": "error",
"text": valid_format
})
else:
add_user(username, email, "user", password, "need_approval")
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
"Successfully send. An administrator will need to approve your account."
})
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 login():
messages = []
data = {}
try:
data_req = request.get_json()
username = data_req["username"]
password = data_req["password"]
remember_me = data_req["remember_me"]
validated_user = check_user_credentials(username,
password,
return_user_if_valid=True)
if validated_user is None:
messages.append({
"time": get_time_string(),
"type": "error",
"text": "Username or password is not valid."
})
else:
login_user(validated_user, remember=remember_me)
messages.append({
"time": get_time_string(),
"type": "success",
"text": "Successfully validated."
})
data = {"success": True}
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 modify_or_delete_users():
messages = []
data = []
try:
validate_local_login_enabled()
data_req = request.get_json()
access_token = data_req["access_token"]
login_required(access_token=access_token, admin=True)
action = data_req["action"]
user_selection = data_req["user_selection"]
value = data_req["value"]
if action == "delete":
for username in user_selection:
user_manager.delete(username)
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
"Successfully deleted users: \"" + ", ".join(user_selection) +
"\""
})
if action == "set_status":
for user in user_selection:
change_user_status_or_level(get_user_by_username(user).id,
new_status=value)
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
"Successfully set status on users: \"" +
", ".join(user_selection) + "\""
})
if action == "set_level":
for user in user_selection:
change_user_status_or_level(get_user_by_username(user).id,
new_level=value)
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
"Successfully set level on users: \"" +
", ".join(user_selection) + "\""
})
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 start_exec(
): # returns all parmeter and its default mode (global/job specific)
# for a given xls config
messages = []
try:
data_req = request.get_json()
access_token = data_req["access_token"]
username = data_req["username"]
login_required(access_token=access_token, username=username)
access_token = data_req["access_token"]
job_name = data_req["job_name"]
run_names = sorted(data_req["run_names"])
exec_profile_name = data_req["exec_profile"]
max_parrallel_exec_user_def = int(
data_req["parallel_exec"]) if "parallel_exec" in data_req.keys(
) else None
started_runs, already_running_runs = exec_runs(
job_name,
run_names,
exec_profile_name,
username=username,
max_parrallel_exec_user_def=max_parrallel_exec_user_def,
access_token=access_token)
if len(started_runs) > 0:
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
"Successfully started execution for runs: " +
", ".join(started_runs)
})
if len(already_running_runs) > 0:
messages.append({
"time":
get_time_string(),
"type":
"warning",
"text":
"Following runs are already running or have already finished: "
+ ", ".join(already_running_runs) +
". To restart them, reset them first."
})
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": {}, "messages": messages})
def delete_account():
messages = []
data = {"success": False}
try:
login_required()
data_req = request.get_json()
username = data_req["username"]
current_user_id = current_user.get_id()
assert username == load_user(
current_user_id
).username, "The entered username does not match your account."
delete_user(current_user_id)
data = {"success": True}
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
"Successfully deleted your account. You will be logged out."
})
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 change_password():
messages = []
data = {"success": False}
try:
validate_local_login_enabled()
data_req = request.get_json()
access_token = data_req["access_token"]
username = data_req["username"]
old_password = data_req["old_password"]
new_password = data_req["new_password"]
new_rep_password = data_req["new_rep_password"]
login_required(access_token=access_token, username=username)
db_connector.user_manager.change_password(username, old_password,
new_password,
new_rep_password)
data = {"success": True}
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
"Successfully changed password. You will be logged out."
})
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_trs_uri():
messages = []
data = []
try:
data_req = request.get_json()
access_token = data_req["access_token"]
login_required(access_token=access_token)
trs_uri = data_req["trs_uri"]
import_name = data_req["import_name"]
import_worflow_by_trs(uri=trs_uri,
name=import_name,
access_token=access_token)
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 register():
messages = []
data = {"success": False}
try:
validate_local_login_enabled()
data_req = request.get_json()
username = data_req["username"]
email = data_req["email"]
password = data_req["password"]
rep_password = data_req["rep_password"]
db_connector.user_manager.create(username=username,
email=email,
password=password,
rep_password=rep_password,
level="user",
status="approval_needed")
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
"Successfully send. An administrator will need to approve your account."
})
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 change_password():
messages = []
data = {"success": False}
try:
login_required()
data_req = request.get_json()
old_password = data_req["old_password"]
new_password = data_req["new_password"]
new_rep_password = data_req["new_rep_password"]
change_password_(current_user.get_id(), old_password, new_password,
new_rep_password)
data = {"success": True}
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
"Successfully changed password. You will be logged out."
})
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 terminate_runs():
messages = []
data = {}
try:
data_req = request.get_json()
access_token = data_req["access_token"]
login_required(access_token=access_token)
job_name = data_req["job_name"]
run_names = sorted(data_req["run_names"])
mode = data_req["mode"] # one of terminate, reset, delete
succeeded, could_not_be_terminated, could_not_be_cleaned = terminate_runs_by_name(
job_name, run_names, mode)
if len(succeeded) > 0:
messages.append({
"time":
get_time_string(),
"type":
"success",
"text":
"Successfully terminated/reset/deleted runs: " +
", ".join(succeeded)
})
if len(could_not_be_terminated) > 0:
messages.append({
"time":
get_time_string(),
"type":
"warning",
"text":
"Following runs could not be terminated: " +
", ".join(could_not_be_terminated)
})
if len(could_not_be_cleaned) > 0:
messages.append({
"time":
get_time_string(),
"type":
"warning",
"text":
"Following runs could not be cleaned: " +
", ".join(could_not_be_cleaned)
})
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 delete_job():
messages = []
data = {}
try:
data_req = request.get_json()
access_token = data_req["access_token"]
login_required(access_token=access_token)
job_name = data_req["job_name"]
results = delete_job_by_name(job_name)
if results["status"] == "success":
pass
elif results["status"] == "failed run termination":
if len(results["could_not_be_terminated"]) > 0:
messages.append({
"time":
get_time_string(),
"type":
"error",
"text":
"Following runs could not be terminated: " +
", ".join(results["could_not_be_terminated"])
})
if len(results["could_not_be_cleaned"]) > 0:
messages.append({
"time":
get_time_string(),
"type":
"error",
"text":
"Following runs could not be cleaned: " +
", ".join(results["could_not_be_cleaned"])
})
else:
messages.append({
"time":
get_time_string(),
"type":
"error",
"text":
"Could not delete job dir for \"" + job_name + "\"."
})
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_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_file():
messages = []
data = {}
try:
# load metadata:
metadata = json_loads(request.form.get("meta"))
dir_path = metadata["dir_path"]
job_name = metadata["job_name"] if "job_name" in metadata.keys(
) else None
access_token = metadata["access_token"]
login_required(access_token=access_token)
assert 'file' in request.files, 'No file received.'
import_file = request.files['file']
assert import_file.filename != '', "No file specified."
filename = secure_filename(import_file.filename)
# check if dir path allowed:
allowed_dirs = get_allowed_base_dirs(job_name=job_name,
allow_input=False,
allow_upload=True,
allow_download=False)
assert dir_path != "", "Path does not exist or you have no permission to enter it."
dir_path = normalize_path(dir_path)
assert os.path.exists(dir_path) and \
os.path.isdir(dir_path) and \
check_if_path_in_dirs(dir_path, allowed_dirs) is not None, \
"Path does not exist or you have no permission to enter it."
import_filepath = os.path.join(dir_path, filename)
import_file.save(import_filepath)
data["file_path"] = import_filepath
messages.append({
"time": get_time_string(),
"type": "success",
"text": "Successfully uploaded file."
})
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 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 get_job_list():
messages = []
jobs = []
try:
login_required()
job_ids = get_job_ids()
# for each dir:
# - check if form sheet present
# - if yes:
# - read in form sheet metadata
# - get list of runs
for job_id in job_ids:
job_dir = get_path("job_dir", job_id=job_id)
try:
job_param_sheet = get_path("job_param_sheet", job_id=job_id)
except AssertionError as e:
continue
job_param_sheet_metadata = get_job_templ_info(
"metadata", job_templ_path=job_param_sheet)
if "workflow_name" not in job_param_sheet_metadata.keys(
) or job_param_sheet_metadata["workflow_name"] == "":
messages.append({
"time":
get_time_string(),
"type":
"warning",
"text":
"No workflow name was specified in the job_param_sheet of job \""
+ job_id + "\". Ignoring."
})
continue
wf_target = job_param_sheet_metadata["workflow_name"]
jobs.append({
"job_id": job_id,
"job_abs_path": job_dir,
"wf_target": wf_target
})
except AssertionError as e:
messages.append(handle_known_error(e, return_front_end_message=True))
messages.append(
handle_unknown_error(
e,
alt_err_message=
"An unkown error occured reading the execution directory",
return_front_end_message=True))
# get exec profiles names:
exec_profile_names = list(app.config["EXEC_PROFILES"].keys())
exec_profile_params = {}
for exec_profile_name in exec_profile_names:
exec_profile_params[exec_profile_name] = {
"max_retries":
app.config["EXEC_PROFILES"][exec_profile_name]["max_retries"],
"max_parallel_exec":
app.config["EXEC_PROFILES"][exec_profile_name]
["max_parallel_exec"],
"allow_user_decrease_max_parallel_exec":
app.config["EXEC_PROFILES"][exec_profile_name]
["allow_user_decrease_max_parallel_exec"],
}
return jsonify({
"data": {
"exec_profiles": exec_profile_names,
"exec_profile_params": exec_profile_params,
"jobs": jobs
},
"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})
