Change error handling

.gitignore

+\.DS_Store

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