unf
/
containers
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

wip

This commit is contained in:
bpinsard 2024-02-08 13:40:01 -05:00
parent 3005669eba
commit fe95059f1c
4 changed files with 17 additions and 12 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
docker/dicom_indexer/Dockerfile
View File

@ -1,5 +1,5 @@
FROM python:3.12-alpine FROM python:3.12-alpine
RUN apk add --no-cache ca-certificates tzdata \ RUN apk add --no-cache ca-certificates tzdata 7zip jq\
git openssh-client git-annex curl bzip2 bash glab\ git openssh-client git-annex curl bzip2 bash glab\
&& cp /usr/share/zoneinfo/UTC /etc/localtime \ && cp /usr/share/zoneinfo/UTC /etc/localtime \
&& apk del tzdata \ && apk del tzdata \
@ -12,6 +12,6 @@ RUN pip install --break-system-packages --no-cache-dir datalad ssh_agent_setup p
ADD indexer /indexer ADD indexer /indexer
COPY entrypoint.sh /entrypoint.sh COPY entrypoint.sh /entrypoint.sh
RUN chmod +x /entrypoint.sh RUN chmod +x /entrypoint.sh
CMD /entrypoint.sh ENTRYPOINT ["bash", "/entrypoint.sh"]
WORKDIR /work WORKDIR /work

23
docker/dicom_indexer/entrypoint.sh
View File

@ -1,21 +1,24 @@
#!/bin/bash #!/bin/bash
CONTAINER_ID=$(basename $(cat /proc/1/cpuset)) CONTAINER_ID=$(basename $(cat /proc/1/cpuset))
GITLAB_TOKEN_SECRET=/var/run/secrets/dicom_bot_gitlab_token GITLAB_TOKEN_SECRET=$(cat /var/run/secrets/dicom_bot_gitlab_token 2>/dev/null)
GITLAB_TOKEN=${GITLAB_TOKEN_SECRET:=$GITLAB_TOKEN}
# only export keys when deploying as a service on swarm # only export keys when deploying as a service on swarm
# TODO: should try using gitlab runner mechanism if not # TODO: should try using gitlab runner mechanism if not
if [ -e $GITLAB_TOKEN_SECRET ] ; then if [ -n "${GITLAB_TOKEN}" ] ; then
# generate container specific ssh-key # generate container specific ssh-key
ssh-keygen -f /root/.ssh/id_rsa -N '' ssh-keygen -f /root/.ssh/id_rsa -N ''
# register it for dicom_bot user # register it for dicom_bot user
curl -X POST -F "private_token=$(cat $GITLAB_TOKEN_SECRET)" \ echo 'registering the ssh key'
ssh_key_json=$(curl -X POST -F "private_token=${GITLAB_TOKEN}" \
-F "title="$(cat /etc/hostname)${CONTAINER_ID:0:12} -F "key=$(cat ~/.ssh/id_rsa.pub)" \ -F "title="$(cat /etc/hostname)${CONTAINER_ID:0:12} -F "key=$(cat ~/.ssh/id_rsa.pub)" \
"${GITLAB_API_URL}/user/keys" "${GITLAB_API_URL}/user/keys")
fi fi
git config --global init.defaultBranch main git config --global init.defaultBranch main
mkdir -p ~/.ssh/known_hosts
install -m 600 /dev/stdin ~/.ssh/known_hosts <<< "$SSH_KNOWN_HOSTS"
# example # example
# /usr/bin/storescp \ # /usr/bin/storescp \
@ -26,12 +29,12 @@ git config --global init.defaultBranch main
# --exec-on-eostudy "python3 $DICOM_ROOT/exec_on_study_received.py #p " 2100 >> $DICOM_DATA_ROOT/storescp.log # --exec-on-eostudy "python3 $DICOM_ROOT/exec_on_study_received.py #p " 2100 >> $DICOM_DATA_ROOT/storescp.log
# run whatever command was passed (storescp or python index_dicoms directly) # run whatever command was passed (storescp or python index_dicoms directly)
echo $@ $@
bash -c "$@"
if [ -e $GITLAB_TOKEN_SECRET ] ; then if [ -n "${GITLAB_TOKEN}" ] ; then
# unregister the temporary ssh key # unregister the temporary ssh key
curl -X DELETE -F "private_token=$(cat $GITLAB_TOKEN_SECRET)" \ ssh_key_id=$(jq .id <<< $ssh_key_json)
curl -X DELETE -F "private_token=${GITLAB_TOKEN}" \
-F "title="$(cat /etc/hostname)${CONTAINER_ID:0:12} -F "title="$(cat /etc/hostname)${CONTAINER_ID:0:12}
"${GITLAB_API_URL}/user/keys" "${GITLAB_API_URL}/users/keys/${ssh_key_id}"
fi fi

1
docker/dicom_indexer/indexer/repo_templates/bids/.gitlab-ci.yml
View File

@ -1,5 +1,6 @@
include: include:
- local: /.ci-env.yml - local: /.ci-env.yml
- project: "$NI_DATAOPS_GITLAB_ROOT/ci-pipelines" - project: "$NI_DATAOPS_GITLAB_ROOT/ci-pipelines"
ref: refactor
file: file:
- 'ci-pipelines/bids/bids_repo.yml' - 'ci-pipelines/bids/bids_repo.yml'

1
docker/dicom_indexer/indexer/repo_templates/dicom_study/.gitlab-ci.yml
View File

@ -2,5 +2,6 @@
include: include:
- local: /.ci-env.yml - local: /.ci-env.yml
- project: "$NI_DATAOPS_GITLAB_ROOT/ci-pipelines" - project: "$NI_DATAOPS_GITLAB_ROOT/ci-pipelines"
ref: refactor
file: file:
- 'ci-pipelines/sources/dicoms_study.yml' - 'ci-pipelines/sources/dicoms_study.yml'