add command/entrypoin

docker/dicom_indexer/Dockerfile

@@ -1,6 +1,6 @@
-FROM alpine:3.19
+FROM python:3.12-alpine
 RUN apk add --no-cache ca-certificates tzdata \
-    python3 py3-pip 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 \
     && apk del tzdata \
     && rm -rf /tmp/* /var/cache/apk/*
@@ -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
-ENTRYPOINT /entrypoint.sh
+CMD /entrypoint.sh
 
 WORKDIR /work

docker/dicom_indexer/entrypoint.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+CONTAINER_ID=$(basename $(cat /proc/1/cpuset))
+GITLAB_TOKEN_SECRET=/var/run/secrets/dicom_bot_gitlab_token
+
+# only export keys when deploying as a service on swarm
+# TODO: should try using gitlab runner mechanism if not
+if [ -e $GITLAB_TOKEN_SECRET ] ; then
+	# generate container specific ssh-key
+	ssh-keygen -f  /root/.ssh/id_rsa -N ''
+	# register it for dicom_bot user
+	curl -X POST -F "private_token=$(cat $GITLAB_TOKEN_SECRET)" \
+	  -F "title="$(cat /etc/hostname)${CONTAINER_ID:0:12} -F "key=$(cat ~/.ssh/id_rsa.pub)" \
+	  "${GITLAB_API_URL}/user/keys"
+	fi
+
+git config --global init.defaultBranch main
+
+
+# example
+# /usr/bin/storescp \
+#  -aet DICOM_SERVER_SEQUOIA\
+#  -pm\
+#  -od $DICOM_TMP_DIR -su ''\
+#  --eostudy-timeout ${STORESCP_STUDY_TIMEOUT:=60} \
+#  --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 $GITLAB_TOKEN_SECRET ] ; then
+	# unregister the temporary ssh key
+	curl -X DELETE -F "private_token=$(cat $GITLAB_TOKEN_SECRET)" \
+	  -F "title="$(cat /etc/hostname)${CONTAINER_ID:0:12}
+	  "${GITLAB_API_URL}/user/keys"
+fi