def import_cwl(wf_path, name):
wf_target_name = "{}.{}".format(name, supported_workflow_exts["CWL"][0])
wf_target_path = get_path("wf", wf_target=wf_target_name)
assert not os.path.exists(wf_target_path), f"The workflow with name \"{wf_target_name}\" already exists."
try:
packed_cwl = pack_cwl(wf_path)
except Exception as e:
raise AssertionError(
"The provided CWL document is not valid, the error was: {}".format(str(e))
)
temp_dir = make_temp_dir()
wf_temp_path = os.path.join(temp_dir, "packed.cwl")
try:
with open(wf_temp_path, 'w') as cwl_file:
json.dump(packed_cwl, cwl_file)
except Exception as e:
raise AssertionError("Could not write CWL file.")
job_templ_path = os.path.join(temp_dir, "job_templ.xlsx")
generate_job_template_from_wf(
workflow_file=wf_temp_path,
wf_type="CWL",
output_file=job_templ_path,
show_please_fill=True
)
copyfile(wf_temp_path, wf_target_path)
job_templ_target_path = get_path("job_templ", wf_target=wf_target_name)
copyfile(job_templ_path, job_templ_target_path)
rmtree(temp_dir)
def import_wdl(wf_path, name, wf_imports_zip_path=None):
wf_target_name = "{}.{}".format(name, supported_workflow_exts["WDL"][0])
wf_target_path = get_path("wf", wf_target=wf_target_name)
assert not os.path.exists(
wf_target_path
), f"The workflow with name \"{wf_target_name}\" already exists."
if wf_imports_zip_path is not None:
# move wf and wf_import_zip to another dir for save unzipping
# this is needed as the WDL library cannot yet
temp_val_dir = make_temp_dir()
wf_val_path = os.path.join(temp_val_dir, "wf_to_validate.wdl")
copyfile(wf_path, wf_val_path)
wf_imports_zip_val_path = os.path.join(temp_val_dir, "imports.zip")
copyfile(wf_imports_zip_path, wf_imports_zip_val_path)
try:
with zipfile.ZipFile(wf_imports_zip_val_path, "r") as zip_ref:
zip_ref.extractall(temp_val_dir)
except Exception as e:
raise AssertionError(
"Could not extract the imports zip of the workflow, the error was: {}"
.format(str(e)))
else:
wf_val_path = wf_path
try:
set_event_loop(new_event_loop())
_ = load_and_validate_wdl(wf_val_path)
except Exception as e:
raise AssertionError(
"The provided WDL document is not valid, the error was: {}".format(
str(e)))
temp_dir = make_temp_dir()
job_templ_path = os.path.join(temp_dir, "job_templ.xlsx")
generate_job_template_from_wf(workflow_file=wf_val_path,
wf_type="WDL",
output_file=job_templ_path,
show_please_fill=True)
copyfile(wf_path, wf_target_path)
job_templ_target_path = get_path("job_templ", wf_target=wf_target_name)
copyfile(job_templ_path, job_templ_target_path)
if wf_imports_zip_path is not None:
rmtree(temp_val_dir)
wf_imports_zip_target_path = get_path("wf_imports_zip",
wf_target=wf_target_name)
copyfile(wf_imports_zip_path, wf_imports_zip_target_path)
rmtree(temp_dir)