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deploy.sh
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deploy.sh
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#!/bin/bash
#
# NAME
#
# deploy.sh
#
# SYNPOSIS
#
# deploy.sh [-h]
# [-O <swarm|kubernetes>] \
# [-N <namespace>] \
# [-T <host|nfs>] \
# [-P <nfsServerIp>] \
# [-S <storeBase>] \
# [-D <storageBase>] \
# [up|down]
#
# DESC
#
# 'deploy.sh' script will depending on the argument deploy the ChRIS set
# of services in production or tear down the system.
#
# TYPICAL CASES:
#
# Deploy ChRIS services into a single-machine Swarm cluster:
#
# deploy.sh up
#
#
# Deploy ChRIS services into a single-machine Kubernetes cluster:
#
# deploy.sh -O kubernetes up
#
#
# Deploy ChRIS services into a multi-machine Kubernetes cluster:
#
# deploy.sh -O kubernetes -T nfs -P <nfsServerIp> -S <storeBase> -D <storageBase> up
#
# ARGS
#
#
# -h
#
# Optional print usage help.
#
# -i
#
# Optional initialize ChRIS with the chris user account and copy plugins. Useful
# to initialize ChRIS the first time the deployment is made.
#
# -O <swarm|kubernetes>
#
# Explicitly set the orchestrator. Default is swarm.
#
# -N <namespace>
#
# Explicitly set the kubernetes namespace to <namespace>. Default is chris.
# Not used for swarm.
#
# -T <host|nfs>
#
# Explicitly set the storage type for the STOREBASE dir and DBs. Default is host.
# Note: The nfs storage type is not implemented for swarm orchestrator yet.
#
# -P <nfsServerIp>
#
# Set the IP address of the NFS server. Required when storage type is set to 'nfs'.
# Not used for 'host' storage type.
#
# -S <storeBase>
#
# Explicitly set the STOREBASE dir to <storeBase>. This is the remote ChRIS
# filesystem where pfcon and plugins share data (usually externally mounted NFS).
# Must be specified or the shell environment variable STOREBASE must be set when
# using nfs storage type.
#
# -D <storageBase>
#
# Explicitly set the ChRIS persistent storage directory to <storageBase>. This
# is a directory containing a few subdirectories used to persist ChRIS services'
# databases. The subdirectories are 'chrisDB', 'storeDB', 'queueDB' and 'swiftDB'.
# Must be specified or the shell environment variable STORAGEBASE must be set when
# using nfs storage type. The directory tree must already exist on the NFS server.
#
# [up|down] (optional, default = 'up')
#
# Denotes whether to fire up or tear down the production set of services.
#
#
source ./decorate.sh
source ./cparse.sh
declare -i STEP=0
declare -i b_initializeChris=0
ORCHESTRATOR=swarm
NAMESPACE=chris
STORAGE_TYPE=host
HERE=$(pwd)
print_usage () {
echo "Usage: ./deploy.sh [-h] [-i] [-O <swarm|kubernetes>] [-N <namespace>] [-T <host|nfs>]
[-P <nfsServerIp>] [-S <storeBase>] [-D <storageBase>] [up|down]"
exit 1
}
while getopts ":hiO:N:T:P:S:D:" opt; do
case $opt in
h) print_usage
;;
i) b_initializeChris=1
;;
O) ORCHESTRATOR=$OPTARG
if ! [[ "$ORCHESTRATOR" =~ ^(swarm|kubernetes)$ ]]; then
echo "Invalid value for option -- O"
print_usage
fi
;;
N) NAMESPACE=$OPTARG
;;
T) STORAGE_TYPE=$OPTARG
if ! [[ "$STORAGE_TYPE" =~ ^(host|nfs)$ ]]; then
echo "Invalid value for option -- T"
print_usage
fi
;;
P) NFS_SERVER=$OPTARG
;;
S) STOREBASE=$OPTARG
;;
D) STORAGEBASE=$OPTARG
;;
\?) echo "Invalid option -- $OPTARG"
print_usage
;;
:) echo "Option requires an argument -- $OPTARG"
print_usage
;;
esac
done
shift $(($OPTIND - 1))
if [[ $STORAGE_TYPE == nfs ]]; then
if [[ $ORCHESTRATOR == swarm ]]; then
echo -e "Sorry, nfs storage type is not supported for swarm orchestrator yet" | ./boxes.sh
exit 1
fi
if [ -z ${NFS_SERVER+x} ]; then
echo "-P <NFS_SERVER> (the NFS server ip address) must be specified or the shell
environment variable NFS_SERVER must be set when using nfs storage type"
print_usage
fi
if [ -z ${STOREBASE+x} ]; then
echo "-S <storeBase> must be specified or the shell environment variable STOREBASE
must be set when using nfs storage type"
print_usage
fi
if [ -z ${STORAGEBASE+x} ]; then
echo "-D <storageBase> must be specified or the shell environment variable
STORAGEBASE must be set when using nfs storage type"
print_usage
fi
fi
COMMAND=up
if (( $# == 1 )) ; then
COMMAND=$1
if ! [[ "$COMMAND" =~ ^(up|down)$ ]]; then
echo "Invalid value $COMMAND"
print_usage
fi
fi
title -d 1 "Setting global exports..."
if [[ $STORAGE_TYPE == host ]]; then
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 [[ $ORCHESTRATOR == kubernetes ]]; then
if [ -z ${STORAGEBASE+x} ]; then
if [[ ! -d CHRIS_STORAGE_FS ]] ; then
mkdir -p CHRIS_STORAGE_FS/chrisDB
mkdir CHRIS_STORAGE_FS/storeDB
mkdir CHRIS_STORAGE_FS/queueDB
mkdir CHRIS_STORAGE_FS/swiftDB
fi
STORAGEBASE=$HERE/CHRIS_STORAGE_FS
else
if [[ ! -d $STORAGEBASE ]] ; then
mkdir -p $STORAGEBASE/chrisDB
mkdir $STORAGEBASE/storeDB
mkdir $STORAGEBASE/queueDB
mkdir $STORAGEBASE/swiftDB
fi
fi
fi
fi
echo -e "ORCHESTRATOR=$ORCHESTRATOR" | ./boxes.sh
echo -e "exporting STORAGE_TYPE=$STORAGE_TYPE" | ./boxes.sh
export STORAGE_TYPE=$STORAGE_TYPE
if [[ $STORAGE_TYPE == nfs ]]; then
echo -e "exporting NFS_SERVER=$NFS_SERVER" | ./boxes.sh
export NFS_SERVER=$NFS_SERVER
fi
echo -e "exporting STOREBASE=$STOREBASE" | ./boxes.sh
export STOREBASE=$STOREBASE
if [[ $ORCHESTRATOR == kubernetes ]]; then
echo -e "exporting NAMESPACE=$NAMESPACE" | ./boxes.sh
export NAMESPACE=$NAMESPACE
echo -e "exporting STORAGEBASE=$STORAGEBASE" | ./boxes.sh
export STORAGEBASE=$STORAGEBASE
fi
windowBottom
if [[ "$COMMAND" == 'up' ]]; then
title -d 1 "Starting ChRIS production deployment on $ORCHESTRATOR"
if [[ $ORCHESTRATOR == swarm ]]; then
echo "docker stack deploy -c swarm/prod/docker-compose.yml chris_stack" | ./boxes.sh ${LightCyan}
docker stack deploy -c swarm/prod/docker-compose.yml chris_stack
elif [[ $ORCHESTRATOR == kubernetes ]]; then
echo "kubectl create namespace $NAMESPACE" | ./boxes.sh ${LightCyan}
namespace=$(kubectl get namespaces $NAMESPACE --no-headers -o custom-columns=:metadata.name 2> /dev/null)
if [ -z "$namespace" ]; then
kubectl create namespace $NAMESPACE
else
echo "$NAMESPACE namespace already exists, skipping creation"
fi
if [[ $STORAGE_TYPE == host ]]; then
echo "kubectl kustomize kubernetes/prod/overlays/host | envsubst | kubectl apply -f -" | ./boxes.sh ${LightCyan}
kubectl kustomize kubernetes/prod/overlays/host | envsubst | kubectl apply -f -
else
echo "kubectl kustomize kubernetes/prod/overlays/nfs | envsubst | kubectl apply -f -" | ./boxes.sh ${LightCyan}
kubectl kustomize kubernetes/prod/overlays/nfs | envsubst | kubectl apply -f -
fi
fi
windowBottom
if (( b_initializeChris )); then
title -d 1 "Waiting for ChRIS containers to start running on $ORCHESTRATOR"
echo "This might take a few minutes... please be patient." | ./boxes.sh ${Yellow}
for i in {1..50}; do
sleep 5
if [[ $ORCHESTRATOR == swarm ]]; then
chris=$(docker ps -f name=chris.1. -q)
elif [[ $ORCHESTRATOR == kubernetes ]]; then
chris=$(kubectl get pods -n $NAMESPACE --selector="app=chris,env=production" --field-selector=status.phase=Running --output=jsonpath='{.items[*].metadata.name}')
fi
if [ -n "$chris" ]; then
echo "" | ./boxes.sh
echo "Success: chris container is running on $ORCHESTRATOR" | ./boxes.sh ${Green}
echo "" | ./boxes.sh
break
fi
done
if [ -z "$chris" ]; then
echo "" | ./boxes.sh
echo "Error: couldn't start chris container on $ORCHESTRATOR" | ./boxes.sh ${Red}
echo "" | ./boxes.sh
exit 1
fi
windowBottom
title -d 1 "Waiting until CUBE is ready to accept connections..."
if [[ $ORCHESTRATOR == swarm ]]; then
docker exec $chris sh -c 'while ! curl -sSf http://localhost:8000/api/v1/users/ 2> /dev/null; do sleep 5; done;'
elif [[ $ORCHESTRATOR == kubernetes ]]; then
kubectl exec $chris -c chris -n $NAMESPACE -- sh -c 'while ! curl -sSf http://localhost:8000/api/v1/users/ 2> /dev/null; do sleep 5; done;'
fi
windowBottom
title -d 1 "Creating superuser chris in ChRIS store"
if [[ $ORCHESTRATOR == swarm ]]; then
docker exec -it $chris_store sh -c 'python manage.py createsuperuser --username chris --email [email protected]'
elif [[ $ORCHESTRATOR == kubernetes ]]; then
chris_store=$(kubectl get pods -n $NAMESPACE --selector="app=chris-store,env=production" --output=jsonpath='{.items[*].metadata.name}')
kubectl exec -it $chris_store -n $NAMESPACE -- sh -c 'python manage.py createsuperuser --username chris --email [email protected]'
fi
windowBottom
title -d 1 "Creating superuser chris in CUBE"
if [[ $ORCHESTRATOR == swarm ]]; then
docker exec -it $chris sh -c 'python manage.py createsuperuser --username chris --email [email protected]'
elif [[ $ORCHESTRATOR == kubernetes ]]; then
kubectl exec -it $chris -c chris -n $NAMESPACE -- sh -c 'python manage.py createsuperuser --username chris --email [email protected]'
fi
windowBottom
title -d 1 "Uploading the plugin fnndsc/pl-dircopy"
if [[ $ORCHESTRATOR == swarm ]]; then
docker exec $chris_store python plugins/services/manager.py add pl-dircopy chris https://github.com/FNNDSC/pl-dircopy fnndsc/pl-dircopy --descriptorstring "$(docker run --rm fnndsc/pl-dircopy dircopy --json 2> /dev/null)"
elif [[ $ORCHESTRATOR == kubernetes ]]; then
kubectl exec $chris_store -n $NAMESPACE -- python plugins/services/manager.py add pl-dircopy chris https://github.com/FNNDSC/pl-dircopy fnndsc/pl-dircopy --descriptorstring "$(docker run --rm fnndsc/pl-dircopy dircopy --json 2> /dev/null)"
fi
windowBottom
title -d 1 "Uploading the plugin fnndsc/pl-topologicalcopy"
if [[ $ORCHESTRATOR == swarm ]]; then
docker exec $chris_store python plugins/services/manager.py add pl-topologicalcopy chris https://github.com/FNNDSC/pl-topologicalcopy fnndsc/pl-topologicalcopy --descriptorstring "$(docker run --rm fnndsc/pl-topologicalcopy topologicalcopy --json 2> /dev/null)"
elif [[ $ORCHESTRATOR == kubernetes ]]; then
kubectl exec $chris_store -n $NAMESPACE -- python plugins/services/manager.py add pl-topologicalcopy chris https://github.com/FNNDSC/pl-topologicalcopy fnndsc/pl-topologicalcopy --descriptorstring "$(docker run --rm fnndsc/pl-topologicalcopy topologicalcopy --json 2> /dev/null)"
fi
windowBottom
title -d 1 "Adding host compute environment"
if [[ $ORCHESTRATOR == swarm ]]; then
docker exec $chris python plugins/services/manager.py add host "http://pfcon.remote:5005/api/v1/" --description "Remote compute"
elif [[ $ORCHESTRATOR == kubernetes ]]; then
kubectl exec $chris -c chris -n $NAMESPACE -- python plugins/services/manager.py add host "http://pfcon.${NAMESPACE}:5005/api/v1/" --description "Remote compute"
fi
windowBottom
title -d 1 "Registering pl-dircopy from store to CUBE"
if [[ $ORCHESTRATOR == swarm ]]; then
docker exec $chris python plugins/services/manager.py register host --pluginname pl-dircopy
elif [[ $ORCHESTRATOR == kubernetes ]]; then
kubectl exec $chris -c chris -n $NAMESPACE -- python plugins/services/manager.py register host --pluginname pl-dircopy
fi
windowBottom
title -d 1 "Registering pl-topologicalcopy from store to CUBE"
if [[ $ORCHESTRATOR == swarm ]]; then
docker exec $chris python plugins/services/manager.py register host --pluginname pl-topologicalcopy
elif [[ $ORCHESTRATOR == kubernetes ]]; then
kubectl exec $chris -c chris -n $NAMESPACE -- python plugins/services/manager.py register host --pluginname pl-topologicalcopy
fi
windowBottom
fi
fi
if [[ "$COMMAND" == 'down' ]]; then
title -d 1 "Destroying ChRIS production deployment on $ORCHESTRATOR"
if [[ $ORCHESTRATOR == swarm ]]; then
echo "docker stack rm chris_stack" | ./boxes.sh ${LightCyan}
docker stack rm chris_stack
elif [[ $ORCHESTRATOR == kubernetes ]]; then
if [[ $STORAGE_TYPE == host ]]; then
echo "kubectl kustomize kubernetes/prod/overlays/host | envsubst | kubectl delete -f -" | ./boxes.sh ${LightCyan}
kubectl kustomize kubernetes/prod/overlays/host | envsubst | kubectl delete -f -
else
echo "kubectl kustomize kubernetes/prod/overlays/nfs | envsubst | kubectl delete -f -" | ./boxes.sh ${LightCyan}
kubectl kustomize kubernetes/prod/overlays/nfs | envsubst | kubectl delete -f -
fi
fi
windowBottom
fi