From 5646680c436f8a0837596a76726bc5233f75e236 Mon Sep 17 00:00:00 2001
From: B13nch3n <b13nch3n_01@theb-si.de>
Date: Mon, 30 May 2022 11:01:35 +0200
Subject: [PATCH] Adapt to new way of providing the ModelCIF dict
---
validation/Dockerfile | 52 ++++++++++++++++++++-----------------------
1 file changed, 24 insertions(+), 28 deletions(-)
diff --git a/validation/Dockerfile b/validation/Dockerfile
index 1393478..2af9344 100644
--- a/validation/Dockerfile
+++ b/validation/Dockerfile
@@ -1,5 +1,5 @@
-ARG VERSION_PYTHON="3.6.15"
-ARG VERSION_BASE_IMAGE="python:${VERSION_PYTHON}-alpine3.15"
+ARG VERSION_PYTHON="3.7"
+ARG VERSION_BASE_IMAGE="python:${VERSION_PYTHON}-alpine3.16"
FROM ${VERSION_BASE_IMAGE}
# We need to declare ARGs again which were declared before the build stage
# (FROM directive), otherwise they won't be available in this stage.
@@ -62,39 +62,32 @@ RUN set -e pipefail; \
extra-cmake-modules tcsh; \
apk add libstdc++
-## Add a dedicated user for mmCIF file validation
-## MMCIF_USER_ID can be used to avoid file permission issues in development.
-ARG MMCIF_USER_ID=501
-RUN adduser -S -u ${MMCIF_USER_ID} mmcif-vldtr
-## Copy tools (already in use during dictionary SDB creation)
+## Copy tools/ entrypoint script
COPY --chmod=755 get-mmcif-dict-versions.py \
/usr/local/bin/get-mmcif-dict-versions
+COPY --chmod=755 entrypoint.sh /
+COPY --chmod=755 validate-mmcif-file.py /usr/local/bin/validate-mmcif-file
-## Create dictionaries for validating mmCIF files. To rebuild dictionaries,
-## rebuild the container with build argument DICT_FETCH_DATE="<DATA>.n" so
-## only the RUN Command for building the dictionary is triggered. The ".n"
-## should be an increasing number to enable simple multiple builds in one
-## day, in case something goes wrong.
+## Create dictionaries for validating mmCIF files.
+## The version to be created is controlled by build argument USE_DICT_VERSION.
+## Use a versions vailable at
+## https://github.com/ihmwg/ModelCIF/tree/master/archive or the special word
+## "latest", that will use
+## https://github.com/ihmwg/ModelCIF/blob/master/dist/mmcif_ma.dic.
## Dictionaries do not change that frequently therefore we skip the hassle of
## keeping them in an external volume.
-ARG DICT_FETCH_DATE="2022-05-16.1"
-# ToDo: use commit instead of USE_DICT_RELEASE
-ARG USE_DICT_RELEASE="master"
-ENV DICT_FETCH_DATE=${DICT_FETCH_DATE}
-ENV USE_DICT_RELEASE=${USE_DICT_RELEASE}
-LABEL org.modelarchive.dict-fetch-date="${DICT_FETCH_DATE}"
-LABEL org.modelarchive.dict_release="${USE_DICT_RELEASE}"
+ARG USE_DICT_VERSION="1.4.1"
+ENV USE_DICT_VERSION=${USE_DICT_VERSION}
+LABEL org.modelarchive.dict_release="${USE_DICT_VERSION}"
WORKDIR ${SRC_DIR}
RUN set -e pipefail; \
apk add curl; \
export _DICT_DIR="${SRC_DIR}/mmcif_dicts"; \
export _DICT_URL="https://mmcif.wwpdb.org/dictionaries/ascii"; \
- export _PATHSPEC="557bda7"; \
- export _REPO_URL="https://raw.githubusercontent.com/ihmwg/ModelCIF/${_PATHSPEC}"; \
- export _MA_DICT_URL="${_REPO_URL}/dist/mmcif_ma.dic"; \
- export _DICT_REPO="ModelCIF.git"; \
+ export _GIT_URL="https://raw.github.com/ihmwg/ModelCIF/master"; \
+ export _MA_DICT_URL="${_GIT_URL}/archive/mmcif_ma-v${USE_DICT_VERSION}.dic"; \
mkdir ${_DICT_DIR}; \
mkdir ${MMCIF_DICTS_DIR}; \
cd ${_DICT_DIR}; \
@@ -104,8 +97,9 @@ RUN set -e pipefail; \
gunzip *.gz; \
#
## Fetch the merged ModelCIF dictionary
- #
- ## Fetch the Git repo with the dictionaries
+ if test x${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; \
#
## Build the ModelCIF SDB
@@ -137,15 +131,17 @@ RUN set -e pipefail; \
apk del curl
-COPY --chmod=755 entrypoint.sh /
-COPY --chmod=755 validate-mmcif-file.py /usr/local/bin/validate-mmcif-file
-
# for development
#RUN set -e pipefail; \
# apk add bash emacs gcc build-base; \
# /usr/local/bin/python -m pip install pylint black; \
# apk del gcc build-base
+## Add a dedicated user for mmCIF file validation
+## MMCIF_USER_ID can be used to avoid file permission issues in development.
+ARG MMCIF_USER_ID=501
+RUN adduser -S -u ${MMCIF_USER_ID} mmcif-vldtr
+
USER mmcif-vldtr
ENTRYPOINT ["/entrypoint.sh"]
--
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