From 7c006c4a835a75ef51c45f93e401cc837e874817 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 10 Aug 2023 14:31:11 +0200
Subject: [PATCH] Add 'errors' to report
---
validation/validate-mmcif-file.py | 31 ++++++++++++++++++++++++-------
1 file changed, 24 insertions(+), 7 deletions(-)
diff --git a/validation/validate-mmcif-file.py b/validation/validate-mmcif-file.py
index 91b17f2..e3e4d0a 100755
--- a/validation/validate-mmcif-file.py
+++ b/validation/validate-mmcif-file.py
@@ -709,13 +709,6 @@ class _CifCheck:
Be aware, that cuts away the majority of the messages. But solving those
issues first, may already repair a mmCIF file."""
- not_implemented = ["errors"]
- for category in not_implemented:
- if len(self.check_results[category]) > 0:
- raise NotImplementedError(
- f"Results for category '{category}' not yet supported in "
- + "report."
- )
print("Report")
print("======")
print(f"Status of check: {self.check_results['status']}")
@@ -814,6 +807,30 @@ class _CifCheck:
for line in sorted(rprt["parchild_mm"]):
print(f" {line}")
+ # condense 'other' errors
+ rprt = {
+ "missing_files": {},
+ }
+ for line in self.check_results["errors"]:
+ match = re.match(r"ma_entry_associated_files.file_url '(?P<arc>.*)' is missing ma_associated_archive_file_details.file_path '(?P<fle>.*)'", line)
+ if match is not None:
+ try:
+ rprt["missing_files"][match.group('arc')].append(match.group('fle'))
+ except KeyError:
+ rprt["missing_files"][match.group('arc')] = [match.group('fle')]
+ continue
+ # Unmatched lines need to be added to above evaluation
+ raise RuntimeError(f'Unmatched error line found:\n"""{line}"""')
+
+ # print above evaluation in the report
+ print("Other issues:")
+ if len(rprt["missing_files"]) > 0:
+ print(" Missing (archive) )files:")
+ for arc, fles in rprt["missing_files"].items():
+ print(f" {arc}:")
+ for line in fles:
+ print(f" {line}")
+
# print erros/ messages caught
print("Errors by running CifCheck:")
for line in self.check_results["cifcheck-errors"]:
--
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