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Add output directory validation and graceful exit in main.py #91

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Add output directory validation and graceful exit in main.py #91

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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
__pycache__/
*.egg-info/
_version.py
.DS_Store

20 changes: 20 additions & 0 deletions stormworkflow/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
from importlib.resources import files
from argparse import ArgumentParser
from pathlib import Path
import sys

import yaml
from packaging.version import Version
Expand Down Expand Up @@ -134,6 +135,25 @@ def main():

wf = scripts.joinpath('workflow.sh')

# Check output directory is writeable and exists
output_dir = conf['RUN_OUT']
if not output_dir:
_logger.error(f"Output directory {output_dir} is not defined in configuration")

# convert to absolute path
output_dir = os.path.abspath(output_dir)
try:
os.makedirs(output_dir,exist_ok=True)
except Exception as e:
_logger.error(f"Can not create output directory {output_dir}: {e}")
sys.exit(1)
if not os.access(output_dir,os.W_OK):
_logger.error(f"Output directory {output_dir} is not writeable")
sys.exit(1)

# update configurations with absolute path
conf['RUN_OUT'] = output_dir

run_env = os.environ.copy()
run_env['L_SCRIPT_DIR'] = slurm.joinpath('.')
for k, v in conf.items():
Expand Down