From 0a3c7dc4397ef50079b5fafd5d04cb72b40f4421 Mon Sep 17 00:00:00 2001
From: B13nch3n <b13nch3n_01@theb-si.de>
Date: Mon, 27 Jun 2022 14:47:29 +0200
Subject: [PATCH] Change error handling
---
.gitignore | 1 +
validation/validate-mmcif-file.py | 22 +++++-----------------
2 files changed, 6 insertions(+), 17 deletions(-)
create mode 100644 .gitignore
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..60ce4b6
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+\.DS_Store
diff --git a/validation/validate-mmcif-file.py b/validation/validate-mmcif-file.py
index 3eaa64e..dff916f 100755
--- a/validation/validate-mmcif-file.py
+++ b/validation/validate-mmcif-file.py
@@ -423,16 +423,16 @@ class _CifCheck:
universal_newlines=True,
cwd=cifcheck_wd,
)
+
error_lst = []
# get error messages on the command line
- filename = os.path.basename(filepath)
- if cps.returncode != 0:
- error_lst = _parse_cifcheck_stderr(cps.stderr)
- error_lst.extend(_parse_parser_file(filename))
+ error_lst.extend(_parse_cifcheck_stderr(cps.stderr))
+ error_lst.extend(_parse_parser_file(filepath))
+ if len(error_lst) > 0:
raise _CifCheckFailedError(cifcheck_cmd, error_lst)
# get messages from diagnosis file
- error_lst.extend(_parse_diag_file(os.path.join(cifcheck_wd, filename)))
+ error_lst.extend(_parse_diag_file(filepath))
return error_lst
@@ -625,12 +625,6 @@ def _main():
cifcheck.make_json_output()
sys.exit(1)
- # do a first check of the model cif alone to make sure its actual cif
- success = cifcheck.run(opts.model_cif)
- if not success:
- cifcheck.make_json_output()
- sys.exit(1)
-
# check for associated files referenced by the model cif file
assoc_files, model_cif_data, entry_id_map = _get_associated_files(
opts.model_cif
@@ -641,12 +635,6 @@ def _main():
# make sure associated files exist and merge all of them into the model
for assoc, entry_id in assoc_files:
assoc_path = os.path.join(opts.associates_dir, assoc)
- # CifCheck the file to make sure its actually cif, diagnosis messages do
- # not matter at this point as an incomplete file is tested.
- success = cifcheck.run(assoc_path)
- if not success:
- cifcheck.make_json_output()
- sys.exit(1)
# merge the model.cif and the associated file
msgs = _merge_cif_data(
model_cif_data, assoc_path, entry_id, entry_id_map
--
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