diff --git a/pyproject.toml b/pyproject.toml
index c0103a1cd6db5f7f9e3018201077498e198c3cfb..f0328248e8503099ecd248f79dd9d2612c9a8ddf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,9 +14,6 @@ extension-pkg-allow-list='rapidjson'
max-line-length=80
[tool.pylint.deprecated_builtins]
-# We want to use proper logging, so we can control *ALL* output bei the Abseil
-# logger, hence: deprecate 'print'
-bad-functions = ["map", "filter", "print"]
# Run the spell check every once in a while, having it enabled always, is too
# annoying.
diff --git a/validation/.spelling b/validation/.spelling
index fecbba386b657adaafab938a7e299310259ce95f..5d4c8a6c473cac08229109dbc9ffa4d35912d146 100644
--- a/validation/.spelling
+++ b/validation/.spelling
@@ -1,4 +1,9 @@
CIF
+Dockerfile
+MSA
UTF
+gzipped
stdout
uncategorised
+usr
+whitespaces
diff --git a/validation/test-suite.py b/validation/test-suite.py
index 494e4ec8cc9629dc627a92799862cf197fa8c351..f673549a8b469b7a4b9b8bcff280e67f8f5823e6 100644
--- a/validation/test-suite.py
+++ b/validation/test-suite.py
@@ -22,7 +22,7 @@ DCKR_IMG_RPO = ( # Docker image "name"
"registry.scicore.unibas.ch/schwede/modelcif-converters/"
+ "mmcif-dict-suite"
)
-# collection of docker commads used
+# collection of docker commands used
DCKR_CMDS = {
"build": [DCKR, "build"],
"images": [DCKR, "images", "--format", "json"],
@@ -116,8 +116,8 @@ def _check_docker_installed():
def _get_modelcif_dic_version():
- """Get the latest versionstring of the ModelCIF dictionary from the
- official GitHub repo."""
+ """Get the latest version string of the ModelCIF dictionary from the
+ official GitHub repository."""
rspns = requests.get(
"https://api.github.com/repos/ihmwg/ModelCIF/contents/archive",
headers={"accept": "application/vnd.github+json"},
@@ -352,7 +352,8 @@ def _main():
if not opts.local:
# Make sure Docker is installed and necessary commands are available.
_do_step(_check_docker_installed, "checking Docker installation")
- # Get expected image tag (latest ModelCIF dic version from GitHub)
+ # Get expected image tag (latest ModelCIF dictionary version from
+ # GitHub).
dic_version = _do_step(
_get_modelcif_dic_version,
"fetching latest ModelCIF dictionary version",
@@ -405,6 +406,3 @@ def _main():
if __name__ == "__main__":
_main()
-
-# LocalWords: pylint argparse ArgumentParser subprocess sys DCKR args exc
-# LocalWords: stdout stderr FileNotFoundError CalledProcessError returncode
diff --git a/validation/validate-mmcif-file.py b/validation/validate-mmcif-file.py
index 8d05e56299b2f4d10b2e1830c4108e47faebe8cd..e117c44778782b94154b6fd281c122d1e4d9fb04 100755
--- a/validation/validate-mmcif-file.py
+++ b/validation/validate-mmcif-file.py
@@ -11,9 +11,9 @@ and thus, won't be merged into the model mmCIF file and won't be checked.
# pylint: enable=invalid-name
# ToDo: enable testing of gzipped files
-# ToDo: add "modelcif-pedantic" mode, fail on categories that are technically
+# ToDo: add `modelcif-pedantic` mode, fail on categories that are technically
# allowed but discouraged to be used, like _exptl
-# ToDo: Remove pip installs which are in requirements.txt from Dockerfile
+# ToDo: Remove pip installs which are in `requirements.txt` from Dockerfile
from io import TextIOWrapper
import argparse
@@ -41,7 +41,6 @@ import mmcif.io.PdbxExceptions
def _parse_command_line():
"""Get arguments."""
parser = argparse.ArgumentParser(description=__doc__)
-
parser.add_argument(
"model_cif",
type=str,
@@ -102,9 +101,7 @@ def _parse_command_line():
help="Write some messages to stdout instead of just having it as JSON. "
+ "Useful for debugging on the command line.",
)
-
opts = parser.parse_args()
-
# post process arguments
if opts.extend_validated_file is not None:
if opts.extend_validated_file == " same ":
@@ -158,7 +155,7 @@ def _parse_parser_file(filename):
def _parse_diag_file(filename):
"""Parse the diagnosis file of CifCheck."""
- # CifCheck places the diag file in the cwd.
+ # CifCheck places the diag file in the current working directory.
diagfile = filename + "-diag.log"
if not os.path.exists(diagfile):
return []
@@ -285,6 +282,50 @@ def _unzip_arc_cif(arc_zip, cif_file):
return assoc_data
+def _get_assoc_data_from_zip_arc(
+ dat_cat, archives, assoc_dir, assoc_files, cifcheck
+):
+ """Extract data to be appended to the main CIF file from associated
+ archives."""
+ idxs = _get_indeces(
+ dat_cat,
+ ["archive_file_id", "file_content", "file_format", "file_path"],
+ )
+ last_arc_id = ""
+ arc_zip = None
+ for row in dat_cat:
+ # Get a ZipFile object of the archive to read CIF files and check
+ # the presence of non-CIF files.
+ arc_id = row[idxs["archive_file_id"]]
+ arc_file = archives[arc_id][0]
+ if arc_id != last_arc_id:
+ last_arc_id = arc_id
+ if arc_zip is not None:
+ arc_zip.close()
+ arc_zip, arc_namelist = _get_arc_zipfile_handle(
+ arc_file, assoc_dir
+ )
+ if row[idxs["file_format"]] == "cif":
+ if row[idxs["file_content"]] == "local pairwise QA scores":
+ cif_file = row[idxs["file_path"]]
+ data = _unzip_arc_cif(arc_zip, cif_file)
+ assoc_files.append((data, archives[arc_id][1]))
+ elif row[idxs["file_content"]] != "other":
+ raise RuntimeError(
+ "Unknown associated CIF file content "
+ + f"found: {row[idxs['file_content']]}"
+ )
+ else:
+ if row[idxs["file_path"]] not in arc_namelist:
+ cifcheck.add_general_error(
+ f"ma_entry_associated_files.file_url '{arc_file}' is "
+ + "missing "
+ + "ma_associated_archive_file_details.file_path "
+ + f"'{row[idxs['file_path']]}'"
+ )
+ arc_zip.close()
+
+
def _get_associated_files(model_cif_file, assoc_dir, cifcheck):
"""Get the list of associated files from a model CIF file."""
# This is an intermediate step, so we do not need to check/ report anything
@@ -328,52 +369,14 @@ def _get_associated_files(model_cif_file, assoc_dir, cifcheck):
dat_cat = pdbx_cntnr.getObj("ma_associated_archive_file_details")
if dat_cat is None:
continue
- idxs = _get_indeces(
- dat_cat,
- ["archive_file_id", "file_content", "file_format", "file_path"],
- )
# get associated files/ data that can be added to the CIF content
- last_arc_id = ""
- arc_zip = None
- for row in dat_cat:
- # Get a ZipFile object of the archive to read CIF files and check
- # the presence of non-CIF files.
- arc_id = row[idxs["archive_file_id"]]
- arc_file = archives[arc_id][0]
- if arc_id != last_arc_id:
- last_arc_id = arc_id
- if arc_zip is not None:
- arc_zip.close()
- arc_zip, arc_namelist = _get_arc_zipfile_handle(
- arc_file, assoc_dir
- )
- if row[idxs["file_format"]] == "cif":
- if row[idxs["file_content"]] == "local pairwise QA scores":
- cif_file = row[idxs["file_path"]]
- data = _unzip_arc_cif(arc_zip, cif_file)
- assoc_files.append((data, archives[arc_id][1]))
- elif row[idxs["file_content"]] != "other":
- raise RuntimeError(
- "Unknown associated CIF file content "
- + f"found: {row[idxs['file_content']]}"
- )
- else:
- if row[idxs["file_path"]] not in arc_namelist:
- cifcheck.add_general_error(
- f"ma_entry_associated_files.file_url '{arc_file}' is "
- + "missing "
- + "ma_associated_archive_file_details.file_path "
- + f"'{row[idxs['file_path']]}'"
- )
- arc_zip.close()
+ _get_assoc_data_from_zip_arc(
+ dat_cat, archives, assoc_dir, assoc_files, cifcheck
+ )
return assoc_files, mdl_cif, entry_id_map
-# ToDo: def _get_assoc_data():
-# """Extract data to be appended to the main CIF file from associated archives."""
-
-
def _cmp_cif_rows(a_row, b_row, a_idxs, b_idxs, attrs):
"""Compare two CIF rows by given attributes"""
for i in attrs:
@@ -385,7 +388,7 @@ def _cmp_cif_rows(a_row, b_row, a_idxs, b_idxs, attrs):
def _add_row(row, src_idxs, dest_idxs, dest, attrs_l):
"""Add a data row to an existing data block with the right item order."""
- # create a new row fitting dest's order
+ # create a new row fitting `dest`'s order
new_row = list("?" * attrs_l)
for i, j in src_idxs.items():
new_row[dest_idxs[i]] = row[j]
@@ -394,7 +397,7 @@ def _add_row(row, src_idxs, dest_idxs, dest, attrs_l):
def _add_or_extend_rows(src, dest, common, not_in_dest):
"""Mix/ add rows from `src` into `dest`."""
- # extend dest with new attributes
+ # extend `dest` with new attributes
for attr in not_in_dest:
dest.appendAttribute(attr)
s_idx = src.getAttributeIndexDict()
@@ -414,7 +417,7 @@ def _add_or_extend_rows(src, dest, common, not_in_dest):
break
if not match:
_add_row(src_row, s_idx, d_idx, dest, attrs_l)
- # extend dest rows that never matched with "?" as default value
+ # extend `dest` rows that never matched with "?" as default value
for i in d_rows:
dest_row = dest[i]
for attr in not_in_dest:
@@ -436,7 +439,7 @@ def _merge_cif_datacontainer(
not_in_p, in_both, _ = db_ctgry.cmpAttributeNames(p_ctgry)
_add_or_extend_rows(db_ctgry, p_ctgry, in_both, not_in_p)
else:
- # data category does not exist in parent, append it to datablock
+ # data category does not exist in parent, append it to data block
parent_datablock.append(db_ctgry)
@@ -452,14 +455,14 @@ def _merge_cif_data(model_cif_data, assoc_cif, row_entry_id, entry_id_map):
"""Merge contents of an associated file into CIF data."""
error_msgs = {"cifcheck-errors": []}
- # per datablock, check to which datablock it belongs in the parent cif
+ # per data block, check to which data block it belongs in the parent CIF
for assoc_cntnr in assoc_cif:
# check/ get 'entry_link'
assoc_entry_link = assoc_cntnr.getObj("entry_link")
if assoc_entry_link is None:
error_msgs["cifcheck-errors"].append(
'ERROR - category "entry_link" is mandatory, but it is not '
- + f'present in datablock "{assoc_cntnr.getName()}"'
+ + f'present in data block "{assoc_cntnr.getName()}"'
)
continue
# make sure entry_id exists for entry_link
@@ -470,8 +473,8 @@ def _merge_cif_data(model_cif_data, assoc_cif, row_entry_id, entry_id_map):
+ '"entry_id" is not in category "entry_link"'
)
continue
- # For each entry_id, look up the corresponding datablock in
- # model_cif_data and merge with that datablock.
+ # For each entry_id, look up the corresponding data block in
+ # model_cif_data and merge with that data block.
for row in assoc_entry_link:
entry_id = row[entry_id_idx]
if entry_id != row_entry_id:
@@ -564,10 +567,10 @@ class _CifCheck:
def _execute(self, filepath):
"""Execute the CifCheck tool on a model mmCIF file."""
# If permission errors occur with the source directory of the CIF file,
- # consider copying the file to a Python tempfile generated path. That
- # deals with missing $TMP, $TEMP, etc.... variables.
- # At the moment, cwd is switched to the source directory since CifCheck
- # copies the file, otherwise.
+ # consider copying the file to a Python `tempfile` generated path. That
+ # deals with missing `$TMP`, `$TEMP`, etc.... variables.
+ # At the moment, current working directory is switched to the source
+ # directory since CifCheck copies the file, otherwise.
cifcheck_filepath = os.path.basename(filepath)
cifcheck_cmd = [
"CifCheck",
@@ -671,7 +674,7 @@ class _CifCheck:
for x in self.version["versions"]
],
)
- # We want nicely formatted cif files, so place audit_conform
+ # We want nicely formatted CIF files, so place audit_conform
# after entry.
objs = pdbx_cntnr.getObjCatalog()
names = list(objs.keys())
@@ -802,7 +805,8 @@ class _CifCheck:
line,
)
if match is not None:
- # prepare a string to be removed from Mismatching parent/ child relationships
+ # prepare a string to be removed from Mismatching parent/ child
+ # relationships
chld = match.group("chld").split(".")[0][1:]
prnt = match.group("prnt").split(".")[0][1:]
try:
@@ -872,7 +876,7 @@ class _CifCheck:
self._condense_diagnosis_data()
self._condense_other_errors()
- # print erros/ messages caught
+ # print errors/ messages caught
if len(self.check_results["cifcheck-errors"]) > 0:
print("Errors by running CifCheck:")
for line in self.check_results["cifcheck-errors"]:
@@ -933,7 +937,7 @@ def _main():
cifcheck.make_json_output()
sys.exit(1)
- # check for associated files referenced by the model cif file
+ # check for associated files referenced by the model CIF file
assoc_files, model_cif_data, entry_id_map = _get_associated_files(
opts.model_cif,
opts.associates_dir,
@@ -944,15 +948,15 @@ def _main():
o_model_cif_data = copy.deepcopy(model_cif_data)
# make sure associated files exist and merge all of them into the model
for assoc, entry_id in assoc_files:
- # merge the model.cif and the associated file
+ # merge the model CIF and the associated file
msgs = _merge_cif_data(model_cif_data, assoc, entry_id, entry_id_map)
cifcheck.add_to_results(msgs)
validate_file = opts.model_cif
if assoc_files:
- # write merged data to disk, create tmp file, clean up when done
+ # write merged data to disk, create temporary file, clean up when done
cfh, cfn = tempfile.mkstemp(suffix=".cif", text=True)
- # register for deletion here and in cwd
+ # register for deletion here and in current working directory
atexit.register(_try_os_remove, cfn)
os.close(cfh)
_write_mmcif(cfn, model_cif_data)
@@ -992,5 +996,3 @@ def _main():
if __name__ == "__main__":
_main()
-
-# LocalWords: cif MSA FASTA pylint stdout CifCheck param src str dest cwd