From 90e42dd61c91789664c046141fbcbb720ca9901c Mon Sep 17 00:00:00 2001
From: B13nch3n <b13nch3n_01@theb-si.de>
Date: Tue, 23 May 2023 09:14:05 +0200
Subject: [PATCH] Make validation work with dictionary version 1.4.5 (info on
PDBx dic split up into its single components)
---
validation/Dockerfile | 6 ++--
validation/get-mmcif-dict-versions.py | 44 ++++-----------------------
2 files changed, 8 insertions(+), 42 deletions(-)
diff --git a/validation/Dockerfile b/validation/Dockerfile
index 0ccd36c..7e91748 100644
--- a/validation/Dockerfile
+++ b/validation/Dockerfile
@@ -80,7 +80,7 @@ COPY --chmod=755 validate-mmcif-file.py /usr/local/bin/validate-mmcif-file
## https://github.com/ihmwg/ModelCIF/blob/master/dist/mmcif_ma.dic.
## Dictionaries do not change that frequently therefore we skip the hassle of
## keeping them in an external volume.
-ARG USE_DICT_VERSION="1.4.4"
+ARG USE_DICT_VERSION="1.4.5"
ENV USE_DICT_VERSION=${USE_DICT_VERSION}
LABEL org.modelarchive.dict_release="${USE_DICT_VERSION}"
WORKDIR ${SRC_DIR}
@@ -118,9 +118,7 @@ RUN set -e pipefail; \
-dictSdbFile ${MMCIF_DICTS_DIR}/mmcif_pdbx_v50.dic.sdb; \
#
## Get versions of ModelCIF & PDBx/mmCIF dictionaries
- get-mmcif-dict-versions --parent-location ${_GIT_URL}/base/mmcif_pdbx_v50.dic \
- --child-location ${_MA_DICT_URL} \
- mmcif_ma.dic; \
+ get-mmcif-dict-versions --child-location ${_MA_DICT_URL} mmcif_ma.dic; \
mv mmcif_ma_version.json ${MMCIF_DICTS_DIR}/; \
#
## Make SDBs readable and keep possible error logs from building them
diff --git a/validation/get-mmcif-dict-versions.py b/validation/get-mmcif-dict-versions.py
index da1f1ea..7532e5b 100755
--- a/validation/get-mmcif-dict-versions.py
+++ b/validation/get-mmcif-dict-versions.py
@@ -25,15 +25,6 @@ def _parse_command_line():
metavar="<DICTIONARY FILE>",
help="The mmCIF dictionary file to read the versions from.",
)
- parser.add_argument(
- "--parent",
- "-p",
- type=str,
- metavar="<NAME OF PARENT DICT>",
- help="Name of to the 'parent' dictionary. This is the one the other "
- + "dictionary is appended to. This is usually the mmcif_pdbx_v50.dic.",
- default="mmcif_pdbx_v50.dic",
- )
parser.add_argument(
"--output",
"-o",
@@ -42,14 +33,6 @@ def _parse_command_line():
help="Path to store the JSON file with the version at.",
default="mmcif_ma_version.json",
)
- parser.add_argument(
- "--parent-location",
- "-u",
- type=str,
- metavar="<URL OF PARENT DICT FILE>",
- help="Download location of the parent dictionary file.",
- default=None,
- )
parser.add_argument(
"--child-location",
"-l",
@@ -90,7 +73,7 @@ def _get_data_item(itm, cat, file_name, cat_data):
return val[0]
-def _get_versions(dic_file, parent_name, io_adapter):
+def _get_versions(dic_file, io_adapter):
"""Fetch the 'category_group_list' object and assemble a version for the
dictionary."""
@@ -112,24 +95,11 @@ def _get_versions(dic_file, parent_name, io_adapter):
ttl = _get_data_item("title", "dictionary", dic_file, dic)
dic_version = {"title": ttl, "version": vrsn}
- cmp = _get_data_cat("pdbx_dictionary_component", dic_file, cntnr)
- dc_idx = cmp.getAttributeIndex("dictionary_component_id")
- vs_idx = cmp.getAttributeIndex("version")
- for row in cmp:
- if row[dc_idx] == parent_name:
- vrsn = row[vs_idx]
- prnt_version = {"title": parent_name, "version": vrsn}
- break
-
- return dic_version, prnt_version
+ return dic_version
-def _add_dict_location(parent, child, parent_loc, child_loc):
+def _add_dict_location(child, child_loc):
"""Add URLs to the dictionary versions if available."""
- if parent_loc is None:
- parent["location"] = "."
- else:
- parent["location"] = parent_loc
if child_loc is None:
child["location"] = "."
else:
@@ -141,13 +111,11 @@ def _main():
opts = _parse_command_line()
io_adapter = IoAdapterPy(False, sys.stdout)
- c_vrsn, p_vrsn = _get_versions(opts.dic_file, opts.parent, io_adapter)
+ c_vrsn = _get_versions(opts.dic_file, io_adapter)
- _add_dict_location(
- p_vrsn, c_vrsn, opts.parent_location, opts.child_location
- )
+ _add_dict_location(c_vrsn, opts.child_location)
with open(opts.output, "w", encoding="utf8") as jfh:
- json.dump({"versions": [p_vrsn, c_vrsn]}, jfh)
+ json.dump({"versions": [c_vrsn]}, jfh)
if __name__ == "__main__":
--
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