00_mongo.sh

#!/bin/sh
# Set up and start a mongodb instance in a kubernetes cluster
# USAGE: $0 [clean] [deletedata]
# *clean* runs cleanup procedures only, skips starting services again
# *deletedata* removes persistent storage data entirely
#
# todo: indefinitely growing journal on VM hosts
#  - perhaps: https://docs.mongodb.com/manual/reference/command/compact/

# get the script directory before creating any files
scriptdir="$(dirname "$(readlink -f "$0")")"
. "$scriptdir/services/deploytools"

# get given command line flags
clean="$(getScriptFlags clean "$@")"
deletedata="$(getScriptFlags deletedata "$@")"
noauth="$(getScriptFlags noauth "$@")"

loadSiteConfig
checkVars NFS_SERVER || exit 1

#chartname="bitnami/mongodb-sharded" # for NUMA support
chartname="bitnami/mongodb"

set -x
# ensure infrastucture namespace exists
NS_FILE="$(find "$scriptdir/namespaces" -iname '*.yaml')"
NS="$(sed -n -e '/^metadata/{:a;n;s/^\s\+name:\s*\(\w\+\)/\1/;p;Ta' -e'}' "$NS_FILE")"
if [ -z "$NS" ]; then
    echo "Could not determine desired namespace!"
    exit 1
fi
if ! (kubectl get ns -o jsonpath='{.items[*].metadata.name}' | grep -qi "\\<$NS\\>"); then
    echo "Could not find namespace, creating '$NS'."
    kubectl create -f "$NS_FILE"
fi
# list all namespaces for debugging
# kubectl get ns -o jsonpath='{.items[*].metadata.name}'; echo

pvcfg="$scriptdir/definitions/mongo_pv_nfs.yaml"
echo "-> Using NFS for persistent volumes."
echo "   Please make sure the configured NFS shares can be mounted:"
echo "   '$pvcfg'"
mpath="$(awk -F':' '/path:/{sub(/^ */,"",$2);print $2}' "$pvcfg" | sort -u)"
if ! [ -d "$mpath" ]; then
    mkdir -p "$mpath"
    chmod a+w "$mpath"
fi

get_podids() {
    kubectl get po -n $NS | grep -o '[a-zA-Z0-9-]*mongo[a-zA-Z0-9-]*'
}
# remove the pod
svc=local-mongodb
remove_pod() {
    local svc="$1"
    podids="$(get_podids)"
    pvnames="$(kubectl get pv -n $NS -o json | \
        jq -r "(.items[] | select(.spec.claimRef.name|contains(\"$svc\"))).metadata.name")"
    helm del $svc --namespace "$NS"
    # delete volume claims
    for pvc in $(kubectl get pvc -n dev -o json | jq -r "(.items[]|select(.metadata.labels.\"app.kubernetes.io/instance\"==\"$svc\")).metadata.name"); do
        kubectl delete pvc -n $NS $pvc
    done
    # reclaim PV
    for pvname in $pvnames; do
        kubectl patch pv "$pvname" -p '{"spec":{"claimRef":null}}'
        # delete old volume first
        echo "Waiting for mongodb persistentvolume being removed ... "
        while kubectl -n "$NS" get pv | grep -q $pvname; do
            # https://github.com/kubernetes/kubernetes/issues/77258#issuecomment-502209800
            kubectl patch pv "$pvname" -p '{"metadata":{"finalizers":null}}'
            timeout 6 kubectl delete pv "$pvname"
        done
        kubectl -n dev wait --for=delete "pvc/$svc"
        echo "done."
    done
    for podid in $podids; do
        kubectl -n dev wait --for=delete "pod/$podid"
    done
}
remove_pod $svc

if [ ! -z "$deletedata" ]; then
    echo "Delete the underlying data!"
    datapath="$(awk -F: '/path/ {sub("^\\s*","",$2); print $2}' "$pvcfg")"
    [ -d "$datapath" ] && rm -R "$datapath/data"
fi

[ -z "$clean" ] || exit # done here in cleanup mode

# create the persistent volume first
adjustServerAddr "$NFS_SERVER" "$pvcfg" | kubectl apply -f -
# reset root password in existing db:
# - restart service with auth disabled
#   ./00_mongo.sh noauth
# - change pwd of user root in db: db.changeUserPassword('root', <password>)
#   - log in by following shown notes after mongodb setup
# - recreate pod with auth enabled
#   ./00_mongo.sh
# - update k8s secret, set MONGODB_ROOT_PASSWORD env var before:
#   kubectl -ndev get secret local-mongodb -o json | jq ".data[\"mongodb-root-password\"]=\"$(echo "$MONGODB_ROOT_PASSWORD" | base64)\"" | kubectl apply -f -

# start mongodb in no-auth mode first
cmd="helm install $svc $chartname --namespace $NS
    --set auth.rootPassword=$SC_MONGO_ROOTPWD
    --set containerSecurityContext.runAsUser=2001
    --set containerSecurityContext.runAsGroup=2001
    --set podSecurityContext.fsGroup=2001
    --set resourcesPreset=xlarge"
# extra arguments for sharded variant
echo "$chartname" | grep -q shard && cmd="$cmd
    --set common.mongodbEnableNumactl=true --set shards=1
    --set auth.replicaSetKey=craNophBajinkei"
tmpcmd="$cmd"
# --set auth.enabled=false
echo "$tmpcmd"; eval $tmpcmd
for podid in $(get_podids); do
    kubectl -n dev wait --for=condition=ready --timeout=5m "pod/$podid"
done