Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Allow extra volume bindings and custom wrapper config file #678

Merged
merged 4 commits into from
Sep 4, 2022
Merged

Allow extra volume bindings and custom wrapper config file #678

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
d3e09fc
Add `ODK_BINDS` option to `run.sh`.
gouttegd Aug 30, 2022
40c1e12
Add `ODK_DOCKER_OPTIONS` variable to the `run.sh` script.
gouttegd Aug 31, 2022
99de795
Source a `run.sh.conf` file if it exists.
gouttegd Aug 31, 2022
1329e2b
Update CHANGELOG.md.
gouttegd Aug 31, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@
- [It is now possible](https://github.com/INCATools/ontology-development-kit/pull/640) to execute the Docker image through [Singularity](https://apptainer.org).
- The `IMAGE` variable, which can used to specify an alternative ODK image, [has been renamed](https://github.com/INCATools/ontology-development-kit/pull/655) to `ODK_IMAGE`.
- A new variable `ODK_TAG` has been introduced, allowing to specify an alternative tag (default is `latest`). A tag may also be specified directly as part of the `ODK_IMAGE` variable (as in `ODK_IMAGE=odkfull:v1.3.1`).
- A new variable `ODK_BINDS` has been introduced, allowing to specify extra bindings between a directory on the host computer and a directory inside the Docker container.
- Variables used by the `run.sh` script can now be set in a `src/ontology/run.sh.conf` file, which will be sourced by the wrapper script.

# v1.3.1

Expand Down
2 changes: 2 additions & 0 deletions template/.gitignore.jinja2
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,8 @@ src/ontology/target/
src/ontology/tmp/*
!src/ontology/tmp/README.md

src/ontology/run.sh.conf

src/ontology/imports/*_terms_combined.txt

src/patterns/data/**/*.ofn
Expand Down
16 changes: 14 additions & 2 deletions template/src/ontology/run.sh.jinja2
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,10 @@
#
# See README-editors.md for more details.

if [ -f run.sh.conf ]; then
source run.sh.conf
fi

ODK_IMAGE=${ODK_IMAGE:-odkfull}
TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }')
if [ -n "$TAG_IN_IMAGE" ]; then
Expand All @@ -37,15 +41,23 @@ fi
VOLUME_BIND=$PWD/../../:/work
WORK_DIR=/work/src/ontology

if [ -n "$ODK_BINDS" ]; then
VOLUME_BIND="$VOLUME_BIND,$ODK_BINDS"
fi

if [ -n "$USE_SINGULARITY" ]; then
{% if project.use_external_date is sameas True %}export TODAY=$(date +%Y-%m-%d){% endif %}
singularity exec --cleanenv \
singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \
--env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \
--bind $VOLUME_BIND \
matentzn marked this conversation as resolved.
Show resolved Hide resolved
-W $WORK_DIR \
docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
else
docker run -v $VOLUME_BIND -w $WORK_DIR -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" {% if project.use_external_date is sameas True %}-e TODAY=`date +%Y-%m-%d` {% endif %}--rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')"
matentzn marked this conversation as resolved.
Show resolved Hide resolved
docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \
-e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \
{% if project.use_external_date is sameas True %}-e TODAY=`date +%Y-%m-%d` {% endif %} \
--rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
fi

case "$@" in
Expand Down