wip

docker/dicom_indexer/Dockerfile

@@ -1,5 +1,5 @@
 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\
     && cp /usr/share/zoneinfo/UTC /etc/localtime \
     && apk del tzdata \
@@ -12,6 +12,6 @@ RUN pip install --break-system-packages --no-cache-dir datalad ssh_agent_setup p
 ADD indexer /indexer
 COPY entrypoint.sh /entrypoint.sh
 RUN chmod +x /entrypoint.sh
-CMD /entrypoint.sh
+ENTRYPOINT ["bash", "/entrypoint.sh"]
 
 WORKDIR /work

docker/dicom_indexer/entrypoint.sh

@@ -1,21 +1,24 @@
 #!/bin/bash
 
 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
 # 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
 	ssh-keygen -f  /root/.ssh/id_rsa -N ''
 	# 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)" \
-	  "${GITLAB_API_URL}/user/keys"
+	  "${GITLAB_API_URL}/user/keys")
 	fi
 
 git config --global init.defaultBranch main
-
+mkdir -p ~/.ssh/known_hosts
+install -m 600 /dev/stdin ~/.ssh/known_hosts <<< "$SSH_KNOWN_HOSTS"
 
 # example
 # /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
 
 # 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
-	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}
-	  "${GITLAB_API_URL}/user/keys"
+	  "${GITLAB_API_URL}/users/keys/${ssh_key_id}"
 fi

docker/dicom_indexer/indexer/repo_templates/bids/.gitlab-ci.yml

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

docker/dicom_indexer/indexer/repo_templates/dicom_study/.gitlab-ci.yml

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