mirror of https://github.com/samply/bridgehead.git
374 lines
12 KiB
Bash
374 lines
12 KiB
Bash
#!/bin/bash -e
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detectCompose() {
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if [[ "$(docker compose version 2>/dev/null)" == *"Docker Compose version"* ]]; then
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COMPOSE="docker compose"
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else
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COMPOSE="docker-compose"
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# This is intended to fail on startup in the next prereq check.
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fi
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}
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setupProxy() {
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### Note: As the current data protection concepts do not allow communication via HTTP,
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### we are not setting a proxy for HTTP requests.
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local http="no"
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local https="no"
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if [ $HTTPS_PROXY_URL ]; then
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local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
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local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
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local hostport=$(echo $HTTPS_PROXY_URL | sed -e "s,$proto,,g" | cut -d/ -f1)
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HTTPS_PROXY_HOST="$(echo $hostport | sed -e 's,:.*,,g')"
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HTTPS_PROXY_PORT="$(echo $hostport | sed -e 's,^.*:,:,g' -e 's,.*:\([0-9]*\).*,\1,g' -e 's,[^0-9],,g')"
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if [[ ! -z "$HTTPS_PROXY_USERNAME" && ! -z "$HTTPS_PROXY_PASSWORD" ]]; then
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local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
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local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
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HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$HTTPS_PROXY_PASSWORD@$fqdn)"
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https="authenticated"
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else
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HTTPS_PROXY_FULL_URL=$HTTPS_PROXY_URL
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https="unauthenticated"
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fi
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fi
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log INFO "Configuring proxy servers: $http http proxy (we're not supporting unencrypted comms), $https https proxy"
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export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
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}
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exitIfNotRoot() {
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if [ "$EUID" -ne 0 ]; then
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log "ERROR" "Please run as root"
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fail_and_report 1 "Please run as root"
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fi
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}
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checkOwner(){
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COUNT=$(find $1 ! -user $2 |wc -l)
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if [ $COUNT -gt 0 ]; then
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log ERROR "$COUNT files in $1 are not owned by user $2. Run find $1 ! -user $2 to see them, chown -R $2 $1 to correct this issue."
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return 1
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fi
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return 0
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}
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printUsage() {
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echo "Usage: bridgehead start|stop|logs|docker-logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
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echo "PROJECTNAME should be one of ccp|bbmri"
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}
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checkRequirements() {
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if ! lib/prerequisites.sh $@; then
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log "ERROR" "Validating Prerequisites failed, please fix the error(s) above this line."
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fail_and_report 1 "Validating prerequisites failed."
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else
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return 0
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fi
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}
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fetchVarsFromVault() {
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[ -e /etc/bridgehead/vault.conf ] && source /etc/bridgehead/vault.conf
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if [ -z "$BW_MASTERPASS" ] || [ -z "$BW_CLIENTID" ] || [ -z "$BW_CLIENTSECRET" ]; then
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log "ERROR" "Please supply correct credentials in /etc/bridgehead/vault.conf."
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return 1
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fi
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set +e
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PASS=$(BW_MASTERPASS="$BW_MASTERPASS" BW_CLIENTID="$BW_CLIENTID" BW_CLIENTSECRET="$BW_CLIENTSECRET" docker run --rm -e BW_MASTERPASS -e BW_CLIENTID -e BW_CLIENTSECRET -e http_proxy docker.verbis.dkfz.de/cache/samply/bridgehead-vaultfetcher:latest $@)
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RET=$?
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if [ $RET -ne 0 ]; then
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echo "Code: $RET"
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echo $PASS
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return $RET
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fi
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eval $(echo -e "$PASS" | sed 's/\r//g')
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set -e
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return 0
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}
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fetchVarsFromVaultByFile() {
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VARS_TO_FETCH=""
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for line in $(cat $@); do
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if [[ $line =~ .*=[\"]*\<VAULT\>[\"]*.* ]]; then
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VARS_TO_FETCH+="$(echo -n $line | sed 's/=.*//') "
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fi
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done
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if [ -z "$VARS_TO_FETCH" ]; then
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return 0
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fi
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log INFO "Fetching $(echo $VARS_TO_FETCH | wc -w) secrets from Vault ..."
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fetchVarsFromVault $VARS_TO_FETCH
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return 0
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}
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assertVarsNotEmpty() {
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MISSING_VARS=""
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for VAR in $@; do
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if [ -z "${!VAR}" ]; then
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MISSING_VARS+="$VAR "
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fi
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done
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if [ -n "$MISSING_VARS" ]; then
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log "ERROR" "Mandatory variables not defined: $MISSING_VARS"
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return 1
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fi
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return 0
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}
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fixPermissions() {
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CHOWN=$(which chown)
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sudo $CHOWN -R bridgehead /etc/bridgehead /srv/docker/bridgehead
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}
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source lib/monitoring.sh
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report_error() {
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CODE=$1
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shift
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log ERROR "$@"
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hc_send $CODE "$@"
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}
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fail_and_report() {
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report_error $@
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exit $1
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}
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setHostname() {
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if [ -z "$HOST" ]; then
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export HOST=$(hostname -f | tr "[:upper:]" "[:lower:]")
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log DEBUG "Using auto-detected hostname $HOST."
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fi
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}
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# This function optimizes the usage of memory through blaze, according to the official performance tuning guide:
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# https://github.com/samply/blaze/blob/master/docs/tuning-guide.md
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# Short summary of the adjustments made:
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# - set blaze memory cap to a quarter of the system memory
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# - set db block cache size to a quarter of the system memory
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# - limit resource count allowed in blaze to 1,25M per 4GB available system memory
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optimizeBlazeMemoryUsage() {
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if [ -z "$BLAZE_MEMORY_CAP" ]; then
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system_memory_in_mb=$(LC_ALL=C free -m | grep 'Mem:' | awk '{print $2}');
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export BLAZE_MEMORY_CAP=$(($system_memory_in_mb/4));
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fi
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if [ -z "$BLAZE_RESOURCE_CACHE_CAP" ]; then
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available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
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if [ $available_system_memory_chunks -eq 0 ]; then
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log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
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export BLAZE_RESOURCE_CACHE_CAP=128000;
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else
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export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
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fi
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fi
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}
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# Takes 1) The Backup Directory Path 2) The name of the Service to be backuped
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# Creates 3 Backups: 1) For the past seven days 2) For the current month and 3) for each calendar week
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createEncryptedPostgresBackup(){
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docker exec "$2" bash -c 'pg_dump -U $POSTGRES_USER $POSTGRES_DB --format=p --no-owner --no-privileges' | \
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# TODO: Encrypt using /etc/bridgehead/pki/${SITE_ID}.priv.pem | \
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tee "$1/$2/$(date +Last-%A).sql" | \
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tee "$1/$2/$(date +%Y-%m).sql" > \
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"$1/$2/$(date +%Y-KW%V).sql"
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}
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# from: https://gist.github.com/sj26/88e1c6584397bb7c13bd11108a579746
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# ex. use: retry 5 /bin/false
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function retry {
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local retries=$1
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shift
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local count=0
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until "$@"; do
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exit=$?
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wait=$((2 ** $count))
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count=$(($count + 1))
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if [ $count -lt $retries ]; then
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echo "Retry $count/$retries exited with code $exit, retrying in $wait seconds..."
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sleep $wait
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else
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echo "Retry $count/$retries exited with code $exit, giving up."
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return $exit
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fi
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done
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return 0
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}
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function bk_is_running {
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detectCompose
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RUNNING="$($COMPOSE -p $PROJECT -f minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE ps -q)"
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NUMBEROFRUNNING=$(echo "$RUNNING" | wc -l)
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if [ $NUMBEROFRUNNING -ge 2 ]; then
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return 0
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else
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return 1
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fi
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}
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function do_enroll_inner {
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PARAMS=""
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MANUAL_PROXY_ID="${1:-$PROXY_ID}"
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if [ -z "$MANUAL_PROXY_ID" ]; then
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log ERROR "No Proxy ID set"
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exit 1
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else
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log INFO "Enrolling Beam Proxy Id $MANUAL_PROXY_ID"
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fi
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SUPPORT_EMAIL="${2:-$SUPPORT_EMAIL}"
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if [ -n "$SUPPORT_EMAIL" ]; then
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PARAMS+="--admin-email $SUPPORT_EMAIL"
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fi
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docker run --rm -v /etc/bridgehead/pki:/etc/bridgehead/pki docker.verbis.dkfz.de/cache/samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $PARAMS
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chmod 600 $PRIVATEKEYFILENAME
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}
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function do_enroll {
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do_enroll_inner $@
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}
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add_basic_auth_user() {
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USER="${1}"
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PASSWORD="${2}"
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NAME="${3}"
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PROJECT="${4}"
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FILE="/etc/bridgehead/${PROJECT}.local.conf"
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ENCRY_CREDENTIALS="$(docker run --rm docker.verbis.dkfz.de/cache/httpd:alpine htpasswd -nb $USER $PASSWORD | tr -d '\n' | tr -d '\r')"
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if [ -f $FILE ] && grep -R -q "$NAME=" $FILE # if a specific basic auth user already exists:
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then
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sed -i "/$NAME/ s|='|='$ENCRY_CREDENTIALS,|" $FILE
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else
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echo -e "\n## Basic Authentication Credentials for:\n$NAME='$ENCRY_CREDENTIALS'" >> $FILE;
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fi
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log DEBUG "Saving clear text credentials in $FILE. If wanted, delete them manually."
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sed -i "/^$NAME/ s|$|\n# User: $USER\n# Password: $PASSWORD|" $FILE
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}
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OIDC_PUBLIC_REDIRECT_URLS=${OIDC_PUBLIC_REDIRECT_URLS:-""}
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OIDC_PRIVATE_REDIRECT_URLS=${OIDC_PRIVATE_REDIRECT_URLS:-""}
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# Add a redirect url to the public oidc client of the bridgehead
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function add_public_oidc_redirect_url() {
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if [[ $OIDC_PUBLIC_REDIRECT_URLS == "" ]]; then
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OIDC_PUBLIC_REDIRECT_URLS+="$(generate_redirect_urls $1)"
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else
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OIDC_PUBLIC_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
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fi
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}
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# Add a redirect url to the private oidc client of the bridgehead
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function add_private_oidc_redirect_url() {
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if [[ $OIDC_PRIVATE_REDIRECT_URLS == "" ]]; then
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OIDC_PRIVATE_REDIRECT_URLS+="$(generate_redirect_urls $1)"
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else
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OIDC_PRIVATE_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
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fi
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}
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function sync_secrets() {
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local delimiter=$'\x1E'
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local secret_sync_args=""
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if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
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secret_sync_args="OIDC:OIDC_CLIENT_SECRET:private;$OIDC_PRIVATE_REDIRECT_URLS"
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fi
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if [[ $OIDC_PUBLIC_REDIRECT_URLS != "" ]]; then
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if [[ $secret_sync_args == "" ]]; then
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secret_sync_args="OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
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else
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secret_sync_args+="${delimiter}OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
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fi
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fi
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if [[ $secret_sync_args == "" ]]; then
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return
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fi
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mkdir -p /var/cache/bridgehead/secrets/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/secrets/'. Please run sudo './bridgehead install $PROJECT' again."
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touch /var/cache/bridgehead/secrets/oidc
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docker run --rm \
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-v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
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-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
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-v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
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-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
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-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
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-e NO_PROXY=localhost,127.0.0.1 \
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-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
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-e PROXY_ID=$PROXY_ID \
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-e BROKER_URL=$BROKER_URL \
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-e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
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-e SECRET_DEFINITIONS=$secret_sync_args \
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docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
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set -a # Export variables as environment variables
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source /var/cache/bridgehead/secrets/*
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set +a # Export variables in the regular way
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}
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capitalize_first_letter() {
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input="$1"
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capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"
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echo "$capitalized"
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}
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# Generate a string of ',' separated string of redirect urls relative to $HOST.
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# $1 will be appended to the url
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# If the host looks like dev-jan.inet.dkfz-heidelberg.de it will generate urls with dev-jan and the original $HOST as url Authorities
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function generate_redirect_urls(){
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local redirect_urls="https://${HOST}$1"
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local host_without_proxy="$(echo "$HOST" | cut -d '.' -f1)"
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# Only append second url if its different and the host is not an ip address
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if [[ "$HOST" != "$host_without_proxy" && ! "$HOST" =~ ^[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
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redirect_urls+=",https://$host_without_proxy$1"
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fi
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echo "$redirect_urls"
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}
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# This password contains at least one special char, a random number and a random upper and lower case letter
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generate_password(){
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local seed_text="$1"
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local seed_num=$(awk 'BEGIN{FS=""} NR==1{print $10}' /etc/bridgehead/pki/${SITE_ID}.priv.pem | od -An -tuC)
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local nums="1234567890"
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local n=$(echo "$seed_num" | awk '{print $1 % 10}')
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local random_digit=${nums:$n:1}
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local n=$(echo "$seed_num" | awk '{print $1 % 26}')
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local upper="ABCDEFGHIJKLMNOPQRSTUVWXYZ"
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local lower="abcdefghijklmnopqrstuvwxyz"
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local random_upper=${upper:$n:1}
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local random_lower=${lower:$n:1}
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local n=$(echo "$seed_num" | awk '{print $1 % 8}')
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local special='@#$%^&+='
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local random_special=${special:$n:1}
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local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
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local main_password=$(echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/\//A/g')
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echo "${main_password}${random_digit}${random_upper}${random_lower}${random_special}"
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}
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# This password only contains alphanumeric characters
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generate_simple_password(){
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local seed_text="$1"
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local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
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echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
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}
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docker_jq() {
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docker run --rm -i docker.verbis.dkfz.de/cache/jqlang/jq:latest "$@"
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}
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