mirror of
https://github.com/samply/bridgehead.git
synced 2025-07-04 03:00:20 +02:00
153f654397
The check for the presence of data in the TransFAIR updating function only worked for single CSV files. Tis commit corrects that. Now also do a git pull on the various repos, to keep things up to date.
304 lines
8.0 KiB
Bash
304 lines
8.0 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|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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# 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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function clone_repo_if_nonexistent() {
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local repo_url="$1" # First argument: Repository URL
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local target_dir="$2" # Second argument: Target directory
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local branch_name="$3" # Third argument: Branch name
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echo Repo directory: $target_dir
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# Check if the target directory exists
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if [ ! -d "$target_dir" ]; then
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echo "Directory '$target_dir' does not exist. Cloning the repository..."
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# Clone the repository
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git clone "$repo_url" "$target_dir"
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fi
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# Change to the cloned directory
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cd "$target_dir"
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# Checkout the specified branch
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git checkout "$branch_name"
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echo "Checked out branch '$branch_name'."
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cd -
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}
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function clone_transfair_if_nonexistent() {
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local base_dir="$1"
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clone_repo_if_nonexistent https://github.com/samply/transFAIR.git $base_dir/transfair ehds2
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}
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function clone_focus_if_nonexistent() {
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local base_dir="$1"
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clone_repo_if_nonexistent https://github.com/samply/focus.git $base_dir/focus ehds2
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}
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function build_transfair() {
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local base_dir="$1"
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# We only take the touble to build transfair if:
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#
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# 1. There is data available (any CSV files) and
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# 2. There is no data lock file (which means that no ETL has yet been run).
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if ls ../ecdc/data/*.[cC][sS][vV] 1> /dev/null 2>&1 && [ ! -f ../ecdc/data/lock ]; then
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cd $base_dir/transfair
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git pull
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docker build --progress=plain -t samply/transfair --no-cache .
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cd -
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fi
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}
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function build_focus() {
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local base_dir="$1"
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cd $base_dir/focus
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git pull
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docker build --progress=plain -f DockerfileWithBuild -t samply/focus --no-cache .
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cd -
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}
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