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make.sh
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make.sh
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#!/usr/bin/env bash
# If you are on macOS, please make sure that /usr/bin/env bash is NOT the
# default /bin/bash! On macOS bash is effectively deprecated and this script
# will not work!
# TL:DR
quick_n_VeryDirtyStart="
docker swarm leave --force && docker swarm init --advertise-addr 127.0.0.1 && \
./unmake.sh && sudo rm -fr CHRIS_REMOTE_FS && rm -fr CHRIS_REMOTE_FS && \
./make.sh -U -I -i
"
#
# NAME
#
# make.sh
#
# SYNPOSIS
#
# make.sh [-h] [-i] [-s] [-U] [-I] \
# [-O <swarm|kubernetes>] \
# [-P <hostIp>] \
# [-S <storeBase>] \
# [local|fnndsc[:dev]]
#
# DESC
#
# 'make.sh' is the main entry point for instantiating a complete backend dev
# environment.
#
# Using appropriate flags, this script can skip various introductory or infor-
# mational steps, deploy ancillary pfcon/pman services on Docker Swarm or
# Kubernetes, toggle unit/integration testing ON/OFF and/or detach the
# interactive terminal from the main chris_dev service.
#
# TYPICAL CASES:
#
# ┌─────────────────────────────────────┐
# │ Most of the time, you will do this: │
# ├─────────────────────────────────────┴─────────────────────────────────────┐
# │ Skip unit and integration tests and start backend in daemon mode on a │
# │ SWARM clsuter (the "dev" way when you want to test new plugins etc): │
# └───────────────────────────────────────────────────────────────────────────┘
#
# THIS IS ONLY THE CASE FOR A SWARM CLUSTER-- which is a typical dev case:
# To totally tear down the cluster and start fresh:
#
# docker swarm leave --force && \
# docker swarm init --advertise-addr 127.0.0.1 && \
# ./unmake.sh && sudo rm -fr CHRIS_REMOTE_FS && rm -fr CHRIS_REMOTE_FS && \
# ./make.sh -U -I -i
#
# Run full CUBE instantiation with tests (the "real-do-only-once" way
# to be sure the system actually works on your env) on Swarm:
#
# ./unmake.sh ; sudo rm -fr CHRIS_REMOTE_FS; rm -fr CHRIS_REMOTE_FS; ./make.sh
#
# Skip unit and integration tests and skip the intro
# (the "quick-n-dirty" way -- when you are deep in dev mode and
# restarting the system for the 50th time on a Monday morning):
#
# ./unmake.sh
# sudo rm -fr CHRIS_REMOTE_FS; rm -fr CHRIS_REMOTE_FS; ./make.sh -U -I -i -s
#
# NOTE: What's up with the "sudo rm..." followed by "rm ..."?
#
# This is a rather unintuitive work around if ChRIS is being
# instantiated on a NFS mounted volume (with the `rootsquash`
# set). Files down directory trees created by running ChRIS
# dockerized services might have mixed ownership and trying
# to delete these files as `root` on the host running the
# service might not remove files owned by a different user.
#
# Hence this rather counter-intuitive construct where sometimes
# being `root` is not sufficient in deleting leftover files or
# directories.
##
# ARGS
#
#
# -h
#
# Optional print usage help.
#
# -O <swarm|kubernetes>
#
# Explicitly set the orchestrator. Default is swarm.
#
# -P <hostIp>
#
# Explicitly set the IP address of the machine running this script. This
# parameter is required when the -O flag is set to kubernetes. Not used
# for swarm.
#
# -U
#
# Skip the UNIT tests.
#
# -I
#
# Skip the INTEGRATION tests.
#
# -S <storeBase>
#
# Explicitly set the STOREBASE dir to <storeBase>. This is the remote
# ChRIS filesystem where pfcon and plugins share data.
#
# -i
#
# Optional do not automatically attach interactive terminal to chris_dev
# container.
#
# -s
#
# Optional skip intro steps. This skips the check on latest versions
# of containers and the interval version number printing. Makes for
# slightly faster startup.
#
# [local|fnndsc[:dev]] (optional, default = 'fnndsc')
#
# If specified, denotes the container "family" to use.
#
# If a colon suffix exists, then this is interpreted to further
# specify the TAG, i.e :dev in the example above.
#
# The 'fnndsc' family are the containers as hosted on docker hub.
# Using 'fnndsc' will always attempt to pull the latest container first.
#
# The 'local' family are containers that are assumed built on the local
# machine and assumed to exist. The 'local' containers are used when
# the 'pfcon/pman' services are being locally developed/debugged.
#
#
source ./decorate.sh
source ./cparse.sh
declare -i STEP=0
declare -i b_norestartinteractive_chris_dev=0
declare -i b_skipIntro=0
declare -i b_skipUnitTests=0
declare -i b_skipIntegrationTests=0
ORCHESTRATOR=swarm
HERE=$(pwd)
CREPO=fnndsc
if [[ -f .env ]] ; then
source .env
fi
catw() {
FILE=$1
COLOR=$2
if (( !${#COLOR} )) ; then
COLOR=White
fi
if [[ -f $FILE ]] ; then
cat dc.out |\
sed 's/[[:alnum:]]+:/\n&/g' |\
sed -E 's/(.{80})/\1\n/g' | ./boxes.sh $COLOR
fi
}
dc_check () {
STATUS=$1
DCECHO=$2
thisStatusCheckOK=0
if [[ $STATUS != "0" ]] ; then
if (( ${#DCECHO} )) ; then
echo -en "\033[2A\033[2K"
catw dc.out LightRed
else
echo -en "\033[3A\033[2K"
fi
else
thisStatusCheckOK=1
if (( ${#DCECHO} )) ; then
echo -en "\033[2A\033[2K"
catw dc.out White
else
echo -en "\033[3A\033[2K"
fi
fi
}
dc_check_code () {
STATUS=$1
CODE=$2
DCECHO=$3
if (( $CODE > 1 )) ; then
if [[ ${#DCECHO} ]] ; then
echo -en "\033[2A\033[2K"
catw dc.out LightRed
else
echo -en "\033[3A\033[2K"
fi
else
if [[ ${#DCECHO} ]] ; then
echo -en "\033[2A\033[2K"
catw dc.out White
else
echo -en "\033[3A\033[2K"
fi
fi
}
print_usage () {
echo "Usage: ./make.sh [-h] [-i] [-s] [-U] [-I] [-O <swarm|kubernetes>] [-P <hostIp>] [-S <storeBase>] [local|fnndsc[:dev]]"
exit 1
}
while getopts ":hisUIO:P:S:" opt; do
case $opt in
h) print_usage
;;
i) b_norestartinteractive_chris_dev=1
;;
s) b_skipIntro=1
;;
U) b_skipUnitTests=1
;;
I) b_skipIntegrationTests=1
;;
O) ORCHESTRATOR=$OPTARG
if ! [[ "$ORCHESTRATOR" =~ ^(swarm|kubernetes)$ ]]; then
echo "Invalid value for option -- O"
print_usage
fi
;;
P) HOSTIP=$OPTARG
;;
S) STOREBASE=$OPTARG
;;
\?) echo "Invalid option -- $OPTARG"
print_usage
;;
:) echo "Option requires an argument -- $OPTARG"
print_usage
;;
esac
done
shift $(($OPTIND - 1))
if [[ $ORCHESTRATOR == kubernetes ]]; then
if [ -z ${HOSTIP+x} ]; then
echo "-P <hostIp> (this machine's ip address) must be specified or the shell
environment variable HOSTIP must be set when using kubernetes orchestrator"
print_usage
fi
fi
if (( $# == 1 )) ; then
REPO=$1
export CREPO=$(echo $REPO | awk -F \: '{print $1}')
export TAG=$(echo $REPO | awk -F \: '{print $2}')
if (( ${#TAG} )) ; then
TAG=":$TAG"
fi
fi
declare -a A_CONTAINER=(
"fnndsc/chris:dev^CHRISREPO"
"fnndsc/chris_store^STOREREPO"
"fnndsc/pfcon${TAG}^PFCONREPO"
"fnndsc/pman${TAG}^PMANREPO"
"fnndsc/docker-swift-onlyone^SWIFTREPO"
)
rm -f dc.out ; title -d 1 "Setting global exports"
boxcenter "-= ORCHESTRATOR =-"
boxcenter "$ORCHESTRATOR" LightCyan
boxcenter ""
if [[ $ORCHESTRATOR == kubernetes ]]; then
echo -e "HOSTIP=$HOSTIP" | ./boxes.sh
echo -e "exporting REMOTENETWORK=false " | ./boxes.sh
export REMOTENETWORK=false
echo -e "exporting PFCONDNS=pfcon.remote " | ./boxes.sh
export PFCONDNS=pfcon.remote
boxcenter "exporting PFCONIP=$HOSTIP "
export PFCONIP=$HOSTIP
fi
if [ -z ${STOREBASE+x} ]; then
if [[ ! -d CHRIS_REMOTE_FS ]] ; then
mkdir CHRIS_REMOTE_FS
fi
STOREBASE=$HERE/CHRIS_REMOTE_FS
else
if [[ ! -d $STOREBASE ]] ; then
mkdir -p $STOREBASE
fi
fi
if (( ${#STOREBASE} > 80 )) ; then
STOREBASEdisp="...${STOREBASE: -77}"
else
STOREBASEdisp=$STOREBASE
fi
boxcenter "-= STOREBASE =-"
echo "${STOREBASEdisp}" | ./boxes.sh LightCyan
export STOREBASE=$STOREBASE
windowBottom
rm -f dc.out ; title -d 1 "Pulling non-'local/' core containers where needed" \
"and creating appropriate .env for docker-compose"
printf "${LightCyan}%13s${Green}%-67s${Yellow}\n" \
"$ docker pull" " library/postgres" | ./boxes.sh
windowBottom
docker pull postgres:13 >& dc.out
dc_check $? "PRINT"
echo "" | ./boxes.sh
printf "${LightCyan}%13s${Green}%-67s${Yellow}\n" \
"$ docker pull" " library/rabbitmq" | ./boxes.sh
windowBottom
docker pull rabbitmq:3 >& dc.out
dc_check $? "PRINT"
if (( ! b_skipIntro )) ; then
echo "# Variables declared here are available to" > .env
echo "# docker-compose on execution" >>.env
for CORE in ${A_CONTAINER[@]} ; do
cparse $CORE "REPO" "CONTAINER" "MMN" "ENV"
echo "${ENV}=${REPO}" >>.env
if [[ $REPO != "local" ]] ; then
echo "" | ./boxes.sh
CMD="docker pull ${REPO}/$CONTAINER"
printf "${LightCyan}%13s${Green}%-67s${Yellow}\n" \
"$ docker pull" " ${REPO}/$CONTAINER" | ./boxes.sh
windowBottom
$CMD >& dc.out
# sleep 1
dc_check $? "PRINT"
fi
done
echo "TAG=" >>.env
fi
windowBottom
if (( ! b_skipIntro )) ; then
rm -f dc.out ; title -d 1 "Ancillary services version info:"
boxcenter ""
for CORE in ${A_CONTAINER[@]} ; do
cparse $CORE "REPO" "CONTAINER" "MMN" "ENV"
if [[ $CONTAINER != "chris:dev" && \
$CONTAINER != "chris_store" && \
$CONTAINER != "docker-swift-onlyone" ]] ; then
CMD="docker run --rm ${REPO}/$CONTAINER --version"
if [[ $CONTAINER == "pfcon" || \
$CONTAINER == "pman" ]] ; then
CMD="docker inspect -f '{{ (index .Config.Labels \"org.opencontainers.image.version\") }}' $REPO/$CONTAINER"
fi
echo "$ $CMD" | ./boxes.sh LightCyan
windowBottom
sh -c "$CMD" >& dc.out
dc_check_code $? 1 "PRINT"
fi
done
fi
boxcenter ""
windowBottom
rm -f dc.out ; title -d 1 "Changing permissions to 755 on" "$HERE"
cd $HERE
echo "$ chmod -R 755 $HERE" | ./boxes.sh LightCyan
windowBottom
chmod -R 755 $HERE &> dc.out
dc_check $? "PRINT"
windowBottom
rm -f dc.out ; title -d 1 "Checking that STOREBASE directory tree is empty" "${STOREBASE}"
chmod -R 777 $STOREBASE
b_FSOK=1
type -all tree >/dev/null 2>/dev/null
if (( ! $? )) ; then
tree $STOREBASE | ./boxes.sh
report=$(tree $STOREBASE | tail -n 1)
if [[ "$report" != "0 directories, 0 files" ]] ; then
b_FSOK=0
fi
else
report=$(find $STOREBASE 2>/dev/null)
lines=$(echo "$report" | wc -l)
if (( lines != 1 )) ; then
b_FSOK=0
fi
fi
if (( ! b_FSOK )) ; then
boxcenter "The STOREBASE directory must be empty!" LightRed
boxcenter ""
boxcenter "Please manually clean it and re-run." Yellow
boxcenter "This script will now exit with code '1'." Yellow
windowBottom
exit 1
fi
printf "${LightCyan}%40s${LightGreen}%40s\n" \
"Tree state" "[ OK ]" | ./boxes.sh
windowBottom
if [[ $ORCHESTRATOR == swarm ]]; then
rm -f dc.out ; title -d 1 "Creating overlay network: remote"
echo "$ docker network create -d overlay --attachable remote" | ./boxes.sh LightCyan
windowBottom
docker network create -d overlay --attachable remote >& dc.out
dc_check $? "PRINT"
windowBottom
fi
rm -f dc.out ; title -d 1 "Starting remote pfcon containerized environment on" \
"-= $ORCHESTRATOR =-"
if [[ $ORCHESTRATOR == swarm ]]; then
echo "$ docker stack deploy -c swarm/docker-compose_remote.yml pfcon_stack"\
| ./boxes.sh LightCyan
windowBottom
docker stack deploy -c swarm/docker-compose_remote.yml pfcon_stack >& dc.out
elif [[ $ORCHESTRATOR == kubernetes ]]; then
echo "$ envsubst < kubernetes/pfcon_dev.yaml | kubectl apply -f -" \
| ./boxes.sh LightCyan
windowBottom
envsubst < kubernetes/remote.yaml | kubectl apply -f - >& dc.out
fi
dc_check $? "PRINT"
windowBottom
rm -f dc.out ; title -d 1 "Waiting for remote pfcon containers to start running on"\
"-= $ORCHESTRATOR =-"
echo "Starting pfcon... please be patient." | ./boxes.sh Yellow
windowBottom
for i in {1..10}; do
sleep 5
if [[ $ORCHESTRATOR == swarm ]]; then
pfcon=$(docker ps -f name=pfcon_stack_pfcon.1 -q)
elif [[ $ORCHESTRATOR == kubernetes ]]; then
pfcon=$(kubectl get pods --selector="app=pfcon,env=production" \
--field-selector=status.phase=Running -- \
output=jsonpath='{.items[*].metadata.name}')
fi
if [ -n "$pfcon" ]; then
echo -en "\033[3A\033[2K"
boxcenter ""
boxcenter "Success: pfcon container is running on $ORCHESTRATOR" LightGreen
boxcenter ""
break
fi
done
if [ -z "$pfcon" ]; then
echo -en "\033[3A\033[2K"
boxcenter
boxcenter "Error: couldn't start pfcon container on $ORCHESTRATOR" Red
boxcenter "This script will now terminate with exit code '2'." Red
boxcenter
windowBottom
exit 2
fi
windowBottom
rm -f dc.out ; title -d 1 "Starting CUBE containerized development environment using " \
"./docker-compose_dev.yml"
echo "This might take a few minutes... please be patient." | ./boxes.sh Yellow
echo "$ docker-compose -f docker-compose_dev.yml up -d" | ./boxes.sh LightCyan
windowBottom
docker-compose -f docker-compose_dev.yml up -d >& dc.out
dc_check $? "PRINT"
windowBottom
rm -f dc.out ; title -d 1 "Waiting until ChRIS database server is ready to accept connections"
echo "This might take a few minutes... please be patient." | ./boxes.sh Yellow
windowBottom
docker-compose -f docker-compose_dev.yml \
exec chris_dev_db sh -c \
'while ! psql -U chris -d chris_dev -c "select 1" > dc.out 2> /dev/null; do sleep 5; done;'
dc_check $? "PRINT"
echo "" | ./boxes.sh
boxcenter "ChRIS database is ready to accept connections" LightGreen
echo "" | ./boxes.sh
windowBottom
rm -f dc.out ; title -d 1 "Waiting until CUBE is ready to accept connections"
echo "This might take a few minutes... please be patient." | ./boxes.sh Yellow
windowBottom
docker-compose -f docker-compose_dev.yml \
exec chris_dev sh -c \
'while ! curl -sSf http://localhost:8000/api/v1/users/ >/dev/null 2>/dev/null ; do sleep 5; done;' \
> dc.out 2>&1
dc_check $? "PRINT"
echo "" | ./boxes.sh
boxcenter "CUBE API is ready to accept connections" LightGreen
echo "" | ./boxes.sh
windowBottom
rm -f dc.out ; title -d 1 "Waiting until remote pfcon is ready to accept connections"
echo "This might take a few minutes... please be patient." | ./boxes.sh Yellow
windowBottom
docker-compose -f docker-compose_dev.yml \
exec chris_dev sh -c \
'while ! curl -sSf http://pfcon.remote:30005/api/v1/health/ 2> /dev/null; do
sleep 5; done;' \
> dc.out
dc_check $? "PRINT"
echo "" | ./boxes.sh
echo "" | ./boxes.sh
boxcenter "Remote pfcon is ready to accept connections" LightGreen
echo "" | ./boxes.sh
windowBottom
if (( ! b_skipUnitTests )) ; then
rm -f dc.out ; title -d 1 "Running CUBE Unit tests"
echo "This might take a few minutes... please be patient." | ./boxes.sh Yellow
windowBottom
docker-compose -f docker-compose_dev.yml \
exec chris_dev python manage.py \
test --exclude-tag integration
status=$?
rm -f dc.out ; title -d 1 "CUBE Unit tests' results"
if (( $status == 0 )) ; then
printf "%40s${LightGreen}%40s${NC}\n" \
"CUBE Unit tests" "[ success ]" | ./boxes.sh
else
printf "%40s${Red}%40s${NC}\n" \
"CUBE Unit tests" "[ failure ]" | ./boxes.sh
fi
windowBottom
fi
if (( ! b_skipIntegrationTests )) ; then
rm -f dc.out ; title -d 1 "Running CUBE Integration tests"
echo "This might take a while... please be patient." | ./boxes.sh Yellow
windowBottom
docker-compose -f docker-compose_dev.yml \
exec chris_dev python manage.py \
test --tag integration
status=$?
rm -f dc.out ; title -d 1 "CUBE Integration tests' results"
if (( $status == 0 )) ; then
printf "%40s${LightGreen}%40s${NC}\n" \
"CUBE Integration tests" "[ success ]" | ./boxes.sh
else
printf "%40s${Red}%40s${NC}\n" \
"CUBE Integration tests" "[ failure ]" | ./boxes.sh
fi
windowBottom
fi
# Setup users and plugins
docker-compose -f docker-compose_dev.yml run --rm chrisomatic
STEP=$(expr $STEP + 4 )
rm -f dc.out ; title -d 1 "Automatically creating two unlocked pipelines in the ChRIS STORE" \
"(unmutable and available to all users)"
S3_PLUGIN_VER=$(docker run --rm fnndsc/pl-s3retrieve s3retrieve --version)
SIMPLEDS_PLUGIN_VER=$(docker run --rm fnndsc/pl-simpledsapp simpledsapp --version)
PIPELINE_NAME="s3retrieve_v${S3_PLUGIN_VER}-simpledsapp_v${SIMPLEDS_PLUGIN_VER}"
printf "%20s${LightBlue}%60s${NC}\n" \
"Creating pipeline..." "[ $PIPELINE_NAME ]" | ./boxes.sh
STR1='[{"plugin_name": "pl-s3retrieve", "plugin_version": "'
STR2='", "plugin_parameter_defaults": [{"name": "bucket", "default": "somebucket"}, {"name": "awssecretkey", "default": "somekey"},
{"name": "awskeyid", "default": "somekeyid"}], "previous_index": null}, {"plugin_name": "pl-simpledsapp", "plugin_version": "'
STR3='", "previous_index": 0}]'
PLUGIN_TREE=${STR1}${S3_PLUGIN_VER}${STR2}${SIMPLEDS_PLUGIN_VER}${STR3}
windowBottom
docker-compose -f docker-compose_dev.yml \
exec chris_store python pipelines/services/manager.py \
add "${PIPELINE_NAME}" cubeadmin "${PLUGIN_TREE}" --unlock &> dc.out
dc_check $? "PRINT"
PIPELINE_NAME="simpledsapp_v${SIMPLEDS_PLUGIN_VER}-simpledsapp_v${SIMPLEDS_PLUGIN_VER}-simpledsapp_v${SIMPLEDS_PLUGIN_VER}"
printf "%20s${LightBlue}%60s${NC}\n" \
"Creating pipeline..." "[ $PIPELINE_NAME ]" | ./boxes.sh
STR4='[{"plugin_name": "pl-simpledsapp", "plugin_version": "'
STR5='", "previous_index": null},{"plugin_name": "pl-simpledsapp", "plugin_version": "'
STR6='", "previous_index": 0},{"plugin_name": "pl-simpledsapp", "plugin_version": "'
STR7='", "previous_index": 0}]'
PLUGIN_TREE=${STR4}${SIMPLEDS_PLUGIN_VER}${STR5}${SIMPLEDS_PLUGIN_VER}${STR6}${SIMPLEDS_PLUGIN_VER}${STR7}
windowBottom
docker-compose -f docker-compose_dev.yml \
exec chris_store python pipelines/services/manager.py \
add "${PIPELINE_NAME}" cubeadmin "${PLUGIN_TREE}" --unlock &> dc.out
dc_check $? "PRINT"
windowBottom
rm -f dc.out ; title -d 1 "Automatically creating a locked pipeline in CUBE" \
"(mutable by the owner and not available to other users)"
PIPELINE_NAME="s3retrieve_v${S3_PLUGIN_VER}-simpledsapp_v${SIMPLEDS_PLUGIN_VER}_1"
printf "%20s${LightBlue}%60s${NC}\n" \
"Creating pipeline..." "[ $PIPELINE_NAME ]" | ./boxes.sh
PLUGIN_TREE=${STR1}${S3_PLUGIN_VER}${STR2}${SIMPLEDS_PLUGIN_VER}${STR3}
windowBottom
docker-compose -f docker-compose_dev.yml \
exec chris_dev \
python pipelines/services/manager.py add "${PIPELINE_NAME}" \
cube "${PLUGIN_TREE}" >& dc.out
dc_check $? "PRINT"
windowBottom
rm -f dc.out ; title -d 1 "Automatically creating an unlocked pipeline in CUBE" \
"(unmutable and available to all users)"
PIPELINE_NAME="simpledsapp_v${SIMPLEDS_PLUGIN_VER}-simpledsapp_v${SIMPLEDS_PLUGIN_VER}-simpledsapp_v${SIMPLEDS_PLUGIN_VER}"
printf "%20s${LightBlue}%60s${NC}\n" \
"Creating pipeline..." "[ $PIPELINE_NAME ]" | ./boxes.sh
PLUGIN_TREE=${STR4}${SIMPLEDS_PLUGIN_VER}${STR5}${SIMPLEDS_PLUGIN_VER}${STR6}${SIMPLEDS_PLUGIN_VER}${STR7}
windowBottom
docker-compose -f docker-compose_dev.yml \
exec chris_dev \
python pipelines/services/manager.py add "${PIPELINE_NAME}" \
cube "${PLUGIN_TREE}" --unlock >& dc.out
dc_check $? "PRINT"
windowBottom
# rm -f dc.out ; title -d 1 "Automatically creating an unlocked pipeline in CUBE" \
# "(unmutable and available to all users)"
# PIPELINE_NAME="DICOM_anonymization_and_tag_extractor"
# printf "%20s${LightBlue}%60s${NC}\n" \
# "Creating pipeline..." "[ $PIPELINE_NAME ]" | ./boxes.sh
# PLUGIN_TREE="[\n {\n \"plugin_name\": \"pl-simpledsapp\",\n \"plugin_version\": \"2.0.2\",\n \"previous_index\": null\n },\n {\n \"plugin_name\": \"pl-pfdicom_tagextract\",\n \"plugin_version\": \"3.1.2\",\n \"previous_index\": 0,\n \"plugin_parameter_defaults\": [\n {\n \"name\": \"extension\",\n \"default\": \".dcm\"\n },\n {\n \"name\": \"imageFile\",\n \"default\": \"m:%_nospc|-_ProtocolName.jpg\"\n },\n {\n \"name\": \"imageScale\",\n \"default\": \"3:none\"\n },\n {\n \"name\": \"outputFileStem\",\n \"default\": \"PHI-tags\"\n }\n ]\n },\n {\n \"plugin_name\": \"pl-pfdicom_tagsub\",\n \"plugin_version\": \"3.2.3\",\n \"previous_index\": 0,\n \"plugin_parameter_defaults\": [\n {\n \"name\": \"extension\",\n \"default\": \".dcm\"\n },\n {\n \"name\": \"tagInfo\",\n \"default\": \"PatientName,%_name|patientID_PatientName ++ PatientID,%_md5|7_PatientID ++ AccessionNumber,%_md5|8_AccessionNumber ++ PatientBirthDate,%_strmsk|******01_PatientBirthDate ++ re:.*hysician,%_md5|4_#tag ++ re:.*stitution,#tag ++ re:.*ddress,#tag\"\n },\n {\n \"name\": \"splitKeyValue\",\n \"default\": \",\"\n },\n {\n \"name\": \"splitToken\",\n \"default\": \"++\"\n }\n ]\n },\n {\n \"plugin_name\": \"pl-pfdicom_tagextract\",\n \"plugin_version\": \"3.1.2\",\n \"previous_index\": 2,\n \"plugin_parameter_defaults\": [\n {\n \"name\": \"extension\",\n \"default\": \".dcm\"\n },\n {\n \"name\": \"imageFile\"]"
# windowBottom
# docker-compose -f docker-compose_dev.yml \
# exec chris_dev \
# python pipelines/services/manager.py add "${PIPELINE_NAME}" \
# cube "${PLUGIN_TREE}" --unlock >& dc.out
# dc_check $? "PRINT"
# windowBottom
rm -f dc.out ; title -d 1 "Restarting CUBE's Django development server"
printf "${LightCyan}%40s${LightGreen}%40s\n" \
"Restarting" "chris_dev" | ./boxes.sh
windowBottom
docker-compose -f docker-compose_dev.yml restart chris_dev >& dc.out
dc_check $?
windowBottom
if (( ! b_norestartinteractive_chris_dev )) ; then
rm -f dc.out ; title -d 1 "Attaching interactive terminal (ctrl-a to detach)"
chris_dev=$(docker ps -f name=chris_dev -f ancestor=fnndsc/chris:dev -q)
docker attach --detach-keys ctrl-a $chris_dev
fi