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Copyright (c) 2022, SIB - Swiss Institute of Bioinformatics and
Biozentrum - University of Basel
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
README.md
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......@@ -2,6 +2,7 @@
This is a collection of tools, code and examples used for converting user's modelling projects into [ModelCIF format](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/) for upload to [ModelArchive](https://www.modelarchive.org) (MA). The whole repository has grown over time from bulk uploads to MA, we assisted users with. Do not expect everything to work out of the box, old conversion projects may be outdated by now.
If you have questions and/ or need assistance in converting your models to ModelCIF, feel free to contact the [MA team](https://modelarchive.org/contact).
## ModelCIF resources
......
projects/docker/Dockerfile
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......@@ -64,7 +64,7 @@ ARG ADD_DEV
RUN set -e pipefail; \
if test xYES = x`echo ${ADD_DEV} | tr '[:lower:]' '[:upper:]'`; then \
apt-get update -y; \
apt-get install -y emacs; \
apt-get install -y emacs less; \
pip install pylint black; \
apt-get purge -y --auto-remove pip; \
fi
......
projects/docker/README.md
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......@@ -129,7 +129,7 @@ $ DOCKER_BUILDKIT=1 docker build -f docker/Dockerfile --build-arg MMCIF_USER_ID=
$
```
For working on a translation script, it is convenient to mount the complete Git repository when running the Docker container interactively. This makes sure `pyproject.toml` is available from the repository root to `black` and `pylint`:
For working on a translation script, it is convenient to mount the complete Git repository when running the Docker container interactively. This makes sure [`pyproject.toml`](pyproject.toml) is available from the repository root to `black` and `pylint`:
```terminal
$ touch .history
......
pyproject.toml
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......@@ -8,4 +8,7 @@ reports='no'
# A comma-separated list of package or module names from where C extensions may
# be loaded. Extensions are loading into the active Python interpreter and may
# run arbitrary code
extension-pkg-allow-list='rapidjson'
\ No newline at end of file
extension-pkg-allow-list='rapidjson
[tool.pylint.FORMAT]
max-line-length=80
validation/Dockerfile
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......@@ -7,7 +7,7 @@ ARG VERSION_PYTHON
ARG VERSION_BASE_IMAGE
ARG VERSION_CPP_DICT_PACK="v2.500"
ARG VERSION_PY_MMCIF="0.76"
ARG VERSION_PY_MMCIF="0.79"
## Set up environment
ENV MMCIF_DICTS_DIR="/usr/local/share/mmcif-dict-suite" \
......@@ -78,7 +78,7 @@ 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="1.4.2"
ARG USE_DICT_VERSION="1.4.3"
ENV USE_DICT_VERSION=${USE_DICT_VERSION}
LABEL org.modelarchive.dict_release="${USE_DICT_VERSION}"
WORKDIR ${SRC_DIR}
......@@ -97,7 +97,7 @@ RUN set -e pipefail; \
gunzip *.gz; \
#
## Fetch the merged ModelCIF dictionary
if test x${USE_DICT_VERSION} == xlatest; then \
if test x${USE_DICT_VERSION} = xlatest; then \
export _MA_DICT_URL="${_GIT_URL}/dist/mmcif_ma.dic"; \
fi; \
curl ${_MA_DICT_URL} -s -L -o mmcif_ma.dic; \
......@@ -134,7 +134,7 @@ RUN set -e pipefail; \
# switch to development version via build-arg
ARG ADD_DEV
RUN set -e pipefail; \
if test xYES == x`echo ${ADD_DEV} | tr '[:lower:]' '[:upper:]'`; then \
if test xYES = x`echo ${ADD_DEV} | tr '[:lower:]' '[:upper:]'`; then \
apk add bash emacs gcc build-base; \
/usr/local/bin/python -m pip install pylint black; \
apk del gcc build-base; \
......
validation/README.md
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[[_TOC_]]
# ModelCIF validation tool
This is a tool to check that the formatting of ModelCIF files complies with the ModelCIF format declaration (aka "dictionary"). Upon successful validation, a ModelCIF file can be extended with the dictionary version the file was compared to (option [`--extend-validated-file`](#add-validation-dictionary-to-ModelCIF-file)). For more basic mmCIF validation, the dictionary of the underlying PDBx/mmCIF format is also available.
This is a tool to check that the formatting of [ModelCIF](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/) files complies with the ModelCIF format declaration (aka "dictionary"). Upon successful validation, a ModelCIF file can be extended with the dictionary version the file was compared to (option [`--extend-validated-file`](#add-dictionary-information-used-for-validation-to-modelcif-file)). For more basic [mmCIF](https://mmcif.wwpdb.org) validation, the dictionary of the underlying [PDBx/mmCIF](https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) format is also available.
The easiest way to run validation is from Docker container.
The easiest way to run validation is from [Docker](https://www.docker.com) container.
The tool itself is a wrapper around the [`CifCheck`](https://github.com/rcsb/cpp-dict-pack) tool by [RCSB](https://www.rcsb.org/).
If you have questions about ModelCIF validation, feel free to contact the [MA team](https://modelarchive.org/contact).
[[_TOC_]]
## How to run the validation tool
This is just a description of the validation tool itself. When running it from inside a container, the command needs to be prefixed with the instructions to start the container. Find information for running the validation container in "[How to run the container](#how-to-run-the-container)".
This is just a description of the [validation tool](./validate-mmcif-file.py) itself. When running it from inside a container, the command needs to be prefixed with the instructions to start the container. Find information for running the validation Docker container in "[How to run the Docker container](#how-to-run-the-docker-container)".
Upon completion, if there hasn't been any error running the command, the validation tool returns a concise report in JSON format. That output is meant to be input to a website or any kind of nicely formatted report. Output can also be stored as a file. If the tested ModelCIF file is fully compliant with the ModelCIF format, the JSON output has
Upon completion, if there hasn't been any error running the command, the validation tool returns a concise report in [JSON](https://www.json.org/json-en.html) format. That output is meant to be input to a website or any kind of nicely formatted report. Output can also be stored as a JSON formatted file. If the tested ModelCIF file is fully compliant with the ModelCIF format, the JSON output has
- `status` "completed"
- no messages in the `cifcheck-errors` list
- no messages in the `diagnosis` list
- `versions` of the dictionaries the file was tested against
Format violations will be listed in `diagnosis`.
`cifcheck-errors` gathers errors from the `CifCheck` command. This has nothing to do with wrong formatting - messages in this list mean that `CifCheck` has "crashed". This should not happen, possible issues with `CifCheck` should be caught by the validation tool. Feel free to report them to the [MA team](https://modelarchive.org/contact).
The most basic way to invoke the validation tool is just with a ModelCIF file (example shows the command plus possible output):
```bash
$ validate-mmcif-file model.cif
{"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.358","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.0","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/dist/mmcif_ma.dic"}]}
{"cifcheck-errors":[],"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.361","location":"https://raw.github.com/ihmwg/ModelCIF/master/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.3","location":"https://raw.github.com/ihmwg/ModelCIF/master/archive/mmcif_ma-v1.4.3.dic"}]}
$
```
### Add dictionary information used for validation to ModelCIF file
Since both dictionaries, ModelCIF and PDBx/mmCIF, represent actively developed file formats, different versions exist. While extending them, quite some thinking goes into making only non-breaking changes. The idea is that a ModelCIF file formatted following dictionary 1.3, is still valid with version 1.4. But the version number also tells you which feature to expect from a ModelCIF file, so it seems like a good idea to keep the version inside the file.
Since both dictionaries, ModelCIF and PDBx/mmCIF, represent actively developed file formats, different versions exist. While extending them, quite some thinking goes into making only non-breaking changes. The idea is that a ModelCIF file formatted following dictionary version 1.3, is still valid with dictionary version 1.4. But the version number also tells you which features to expect in a ModelCIF file, so it seems like a good idea to keep the version inside the file.
The validation tool can add the version upon positive validation, enabled by the `--extend-validated-file` (`-e`).
The validation tool can add the version upon positive validation, enabled by `--extend-validated-file` (`-e`).
`-e` can take an alternative file name to write the validated ModelCIF file to, e.g. if one wants to keep the original ModelCIF file unaltered:
```bash
$ validate-mmcif-file -e validated_model.cif model.cif
{"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.358","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.0","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/dist/mmcif_ma.dic"}]}
{"cifcheck-errors":[],"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.361","location":"https://raw.github.com/ihmwg/ModelCIF/master/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.3","location":"https://raw.github.com/ihmwg/ModelCIF/master/archive/mmcif_ma-v1.4.3.dic"}]}
$
```
The last command will generate a new file `validated_model.cf` upon positive validation (`diagnosis` points to an empty list), with the `versions` added to the `_audit_conform` list inside the file.
The last command will generate a new file `validated_model.cf` upon positive validation (`diagnosis` points to an empty list), with the `versions` added to the [`_audit_conform`](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Categories/audit_conform.html) list inside the file.
To add the validation dictionaries to `_audit_conform` in the original ModelCIF file, just invoke `-e` without an alternative file name... well almost. By the way Python handles this kind of command line arguments, `-e` consumes everything after it, that does not start with a `-`, as a file name. So `validate-mmcif-file -e model.cif` would mean that `-e` assumes `model.cif` as its file name but then the command fails because it is missing the ModelCIF file to be validated. The solution is either putting `-e` at the beginning of the arguments list or after the ModelCIF file name at the very end, if there are no other command line arguments:
```bash
$ validate-mmcif-file model.cif -e
{"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.358","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.0","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/dist/mmcif_ma.dic"}]}
{"cifcheck-errors":[],"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.361","location":"https://raw.github.com/ihmwg/ModelCIF/master/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.3","location":"https://raw.github.com/ihmwg/ModelCIF/master/archive/mmcif_ma-v1.4.3.dic"}]}
$
```
### Base directory for associated files
For a ModelCIF file using the `_ma_entry_associated_files` category, the validation tool tries to merge associated data into the ModelCIF file, if `_ma_entry_associated_files.file_format` is `cif`. That way the outsourced data is validated, too.
For a ModelCIF file using the [`_ma_entry_associated_files`](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Categories/ma_entry_associated_files.html) category, the validation tool tries to merge associated data into the ModelCIF file, if [`_ma_entry_associated_files.file_format`](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Items/_ma_entry_associated_files.file_format.html) is `cif` and [`_ma_entry_associated_files.file_content`](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Items/_ma_entry_associated_files.file_content.html) is `local pairwise QA scores`. That way the outsourced data is validated, too.
Command line argument `--associates-dir` (`-a`) is used to declare the base directory associated files are stored in. Inside the directory, the path must follow what is defined in `_ma_entry_associated_files.file_url`. If the URL is just the file name, the file must be stored right in the associates directory. The following example works for `_ma_entry_associated_files.file_url model_pae.cif`
Command line argument `--associates-dir` (`-a`) is used to declare the base directory associated files are stored in. Inside the directory, the path must follow what is defined in [`_ma_entry_associated_files.file_url`](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Items/_ma_entry_associated_files.file_url.html). If the URL is just the file name, the file must be stored right in the associates directory. The following example works for `_ma_entry_associated_files.file_url model_pae.cif` (`grep` and `ls` are just used to illustrate the data situation)
```bash
$ grep _ma_entry_associated_files.file_url model.cif
......@@ -63,7 +70,7 @@ _ma_entry_associated_files.file_url model_pae.cif
$ ls extra
model_pae.cif
$ validate-mmcif-file -a extra model.cif
{"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.358","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.0","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/dist/mmcif_ma.dic"}]}
{"cifcheck-errors":[],"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.361","location":"https://raw.github.com/ihmwg/ModelCIF/master/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.3","location":"https://raw.github.com/ihmwg/ModelCIF/master/archive/mmcif_ma-v1.4.3.dic"}]}
$
```
......@@ -77,49 +84,82 @@ pae
$ ls extra/pae
model_pae.cif
$ validate-mmcif-file -a extra model.cif
{"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.358","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.0","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/dist/mmcif_ma.dic"}]}
{"cifcheck-errors":[],"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.361","location":"https://raw.github.com/ihmwg/ModelCIF/master/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.3","location":"https://raw.github.com/ihmwg/ModelCIF/master/archive/mmcif_ma-v1.4.3.dic"}]}
$
```
### Misc. arguments
**`--help`** (**`-h`**) Print a help/ usage page for the validation tool.
**`--dict-sdb <SDB FILE>`** (**`-d`**) Format dictionary in (binary) SDB format used for validating a ModelCIF file. The container comes with a SDB for ModelCIF and one for the original PDBx/mmCIF format.
**`--dict-sdb <SDB FILE>`** (**`-d`**) Format dictionary in (binary) SDB format used for validating a ModelCIF file. The Docker container comes with a SDB for ModelCIF (`/usr/local/share/mmcif-dict-suite/mmcif_ma.sdb`) and one for the original PDBx/mmCIF (`/usr/local/share/mmcif-dict-suite/mmcif_pdbx_v50.dic.sdb`) format.
**`--out-file <JSON FILE>`** (**`-o`**) Instead of printing the output to `stdout`, store it in a JSON file.
**`--out-file <JSON FILE>`** (**`-o`**) Instead of printing the output to `stdout`, store it in a JSON formatted file.
**`--verbose`** (**`-v`**) Write information from intermediate steps to `stdout`. This includes the raw output of `CifCheck`.
**`--verbose`** (**`-v`**) Be more talkative.
## How to run the container
## How to run the Docker container
The call to the validation tool (almost) stays the same, it just needs instructions to start the Docker container as a prefix:
Calling the validation tool (almost) stays the same, it just needs instructions to start the Docker container as a prefix:
```bash
$ docker run --rm -v /home/user/models:/data registry.scicore.unibas.ch/schwede/mabakerimport/mmcif-dict-suite:dev validate-mmcif-file /data/model.cif
{"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.358","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.0","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/dist/mmcif_ma.dic"}]}
$ docker run --rm -v /home/user/models:/data registry.scicore.unibas.ch/schwede/modelcif-converters/mmcif-dict-suite:latest validate-mmcif-file /data/model.cif
{"cifcheck-errors":[],"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.361","location":"https://raw.github.com/ihmwg/ModelCIF/master/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.3","location":"https://raw.github.com/ihmwg/ModelCIF/master/archive/mmcif_ma-v1.4.3.dic"}]}
$
```
`docker run` is the call to execute a certain command inside a container. `--rm` makes sure that the container is removed from the system once the job completed.
- [`docker run`](https://docs.docker.com/engine/reference/commandline/run/) starts a new Docker container from image `registry.scicore.unibas.ch/schwede/modelcif-converters/mmcif-dict-suite:latest` and executes the `validate-mmcif-file` command inside the container.
- `--rm` makes sure that the container is removed from the system once the job completed.
- `-v` mounts directory `/home/user/models` from the local host computer to `/data` inside the Docker container, otherwise the `validate-mmcif-file` command has no access to local files. The bind mount makes the ModelCIF file `/home/user/models/model.cif` available as `/data/model.cif` to commands executed by `docker run`. Keep in mind, `validate-mmcif-file -e` and `validate-mmcif-file -a` also need to refer to `/data` (or any other local directory mounted in the Docker container).
## How to get the Docker container
Before running the Docker container, you need a local copy of its image. There are three ways to get it:
- `docker run` will pull it automatically upon first call
- [`docker pull`](https://docs.docker.com/engine/reference/commandline/pull/) the Docker image yourself before running it
- [`docker build`](https://docs.docker.com/engine/reference/commandline/build/) the Docker image from scratch
### How to pull a copy of the Docker container from our registry
With `docker pull`, the ready-made Docker image can be fetched from our [Docker registry](https://git.scicore.unibas.ch/schwede/modelcif-converters/container_registry/). Two kinds of Docker images are available, differentiated by tags. The `latest` tag refers to the Docker image with the most recent ModelCIF dictionary. This should be the default choice. For specific use cases, e.g. debugging, we also provide Docker images for older versions of the ModelCIF dictionary, those are tagged with the version number of the dictionary. The `latest` image is pulled like this:
```terminal
$ docker pull registry.scicore.unibas.ch/schwede/modelcif-converters/mmcif-dict-suite:latest
```
Since the container has its own internal file system separated, `-v` is utilised to mount a directory from the host into the container.
### How to build the Docker container from scratch
- explain what command does
- explain volumes/ external mounts
- explain for -e
- explain for -a
Here is the command we use to generate the Docker image. It works when executed from within the [`validation/`](./validation) subdirectory of the [Git repository](https://git.scicore.unibas.ch/schwede/modelcif-converters):
## How to pull a copy of the container from our registry
```terminal
docker build -t registry.scicore.unibas.ch/schwede/modelcif-converters/mmcif-dict-suite:latest .
```
- since we use it ourselves and are involved in the development, we usually notice when a new dictionary comes out
When developing you own tools using the Docker image, there is one [build argument](https://docs.docker.com/engine/reference/commandline/build/#set-build-time-variables---build-arg) that adds an [editor](https://www.gnu.org/software/emacs/), [Black](https://black.readthedocs.io/en/stable/), [Pylint](https://pylint.org) and [bash](https://tiswww.case.edu/php/chet/bash/bashtop.html) to ease working in interactive sessions inside the Docker container:
## How to build the container from scratch
```terminal
docker build --build-arg ADD_DEV=yes -t registry.scicore.unibas.ch/schwede/modelcif-converters/mmcif-dict-suite:dev .
```
The [`pyproject.toml`](pyproject.toml) we use can be found in the Git repository root.
# Files in this directory
|Path |Content |
|-----------|----------------------------------------------------------------|
|[Dockerfile](./Dockerfile)|Build instructions for the Docker image|
|[README.md](./README.md)|This README|
|[entrypoint.sh](./entrypoint.sh)|Script executed on Docker container start|
|[get-mmcif-dict-versions.py](./get-mmcif-dict-versions.py)|Extract versions of mmCIF dictionaries, used for building the Docker image. Copied into the image as `get-mmcif-dict-versions.py`.|
|[validate-mmcif-file.py](./validate-mmcif-file.py)|Validation tool, copied into the image as `validate-mmcif-file`.|
<!-- LocalWords: PDBx ModelCIF TOC JSON CifCheck RCSB mmcif cif pdbx dic dir
LocalWords: url pae sdb SDB stdout
LocalWords: url pae sdb SDB stdout modelcif cifcheck arg Pylint DEV md
LocalWords: pyproject toml README entrypoint py
-->
validation/validate-mmcif-file.py
+ 14
− 6
View file @ ecaeef6a
......@@ -263,15 +263,22 @@ def _get_associated_files(model_cif_file, assoc_dir):
if dat_cat is None:
continue
idxs = _get_indeces(
dat_cat, ["archive_file_id", "file_format", "file_path"]
dat_cat,
["archive_file_id", "file_content", "file_format", "file_path"],
)
for row in dat_cat:
if row[idxs["file_format"]] == "cif":
arc_id = row[idxs["archive_file_id"]]
arc_file = archives[arc_id][0]
cif_file = row[idxs["file_path"]]
data = _unzip_arc_cif(arc_file, cif_file, assoc_dir)
assoc_files.append((data, archives[arc_id][1]))
if row[idxs["file_content"]] == "local pairwise QA scores":
arc_id = row[idxs["archive_file_id"]]
arc_file = archives[arc_id][0]
cif_file = row[idxs["file_path"]]
data = _unzip_arc_cif(arc_file, cif_file, assoc_dir)
assoc_files.append((data, archives[arc_id][1]))
elif row[idxs["file_content"]] not in ["other"]:
raise RuntimeError(
"Unknown associated CIF file content "
+ f"found: {row[idxs['file_content']]}"
)
return assoc_files, mdl_cif, entry_id_map
......@@ -469,6 +476,7 @@ class _CifCheck:
"""Run CifCheck for a given file and catch the output.
Returns False if the CifCheck execution itself failed."""
self.check_results["cifcheck-errors"] = []
try:
format_errors = self._execute(cif_file)
except _CifCheckFailedError as exc:
......
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