Mercurial > repos > bimib > cobraxy
changeset 454:3654c08668f1 draft default tip
Uploaded
| author | francesco_lapi |
|---|---|
| date | Thu, 11 Sep 2025 21:02:09 +0000 |
| parents | 51f794fff930 |
| children | |
| files | COBRAxy/fromCSVtoCOBRA_beta.py |
| diffstat | 1 files changed, 2 insertions(+), 8 deletions(-) [+] |
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--- a/COBRAxy/fromCSVtoCOBRA_beta.py Thu Sep 11 20:58:37 2025 +0000 +++ b/COBRAxy/fromCSVtoCOBRA_beta.py Thu Sep 11 21:02:09 2025 +0000 @@ -61,8 +61,6 @@ # Basic sanity checks if not os.path.exists(ARGS.input): logging.error('Input file not found: %s', ARGS.input) - print(f"ERROR: Input file not found: {ARGS.input}", file=sys.stderr) - sys.exit(2) out_dir = os.path.dirname(os.path.abspath(ARGS.output)) if out_dir and not os.path.isdir(out_dir): @@ -71,8 +69,6 @@ logging.info('Created missing output directory: %s', out_dir) except Exception as e: logging.exception('Cannot create output directory: %s', out_dir) - print(f"ERROR: Cannot create output directory: {out_dir}", file=sys.stderr) - sys.exit(3) # Build the model from the CSV (NOTE: use ARGS.input here) model = modelUtils.build_cobra_model_from_csv(ARGS.input) @@ -88,16 +84,14 @@ cobra.io.save_yaml_model(model, ARGS.output) else: logging.error('Unknown format requested: %s', ARGS.format) - print(f"ERROR: Unknown format: {ARGS.format}", file=sys.stderr) - sys.exit(4) + print(f"ERROR: Unknown format: {ARGS.format}") + logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format) except Exception: # Log full traceback to the out_log so Galaxy users/admins can see what happened logging.exception('Unhandled exception in fromCSVtoCOBRA') - traceback.print_exc(file=sys.stderr) - sys.exit(1) if __name__ == '__main__':