bridgehead/lib/functions.sh

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#!/bin/bash -e
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detectCompose() {
if [[ "$(docker compose version 2>/dev/null)" == *"Docker Compose version"* ]]; then
COMPOSE="docker compose"
else
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COMPOSE="docker-compose"
# This is intended to fail on startup in the next prereq check.
fi
}
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setupProxy() {
### Note: As the current data protection concepts do not allow communication via HTTP,
### we are not setting a proxy for HTTP requests.
local http="no"
local https="no"
if [ $HTTPS_PROXY_URL ]; then
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local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
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 $hostport | sed -e 's,:.*,,g')"
HTTPS_PROXY_PORT="$(echo $hostport | sed -e 's,^.*:,:,g' -e 's,.*:\([0-9]*\).*,\1,g' -e 's,[^0-9],,g')"
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')"
local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$HTTPS_PROXY_PASSWORD@$fqdn)"
https="authenticated"
else
HTTPS_PROXY_FULL_URL=$HTTPS_PROXY_URL
https="unauthenticated"
fi
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fi
log INFO "Configuring proxy servers: $http http proxy (we're not supporting unencrypted comms), $https https proxy"
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export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
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}
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exitIfNotRoot() {
if [ "$EUID" -ne 0 ]; then
log "ERROR" "Please run as root"
fail_and_report 1 "Please run as root"
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fi
}
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checkOwner(){
COUNT=$(find $1 ! -user $2 |wc -l)
if [ $COUNT -gt 0 ]; then
log ERROR "$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."
return 1
fi
return 0
}
printUsage() {
echo "Usage: bridgehead start|stop|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
echo "PROJECTNAME should be one of ccp|bbmri"
}
checkRequirements() {
if ! lib/prerequisites.sh $@; then
log "ERROR" "Validating Prerequisites failed, please fix the error(s) above this line."
fail_and_report 1 "Validating prerequisites failed."
else
return 0
fi
}
fetchVarsFromVault() {
[ -e /etc/bridgehead/vault.conf ] && source /etc/bridgehead/vault.conf
if [ -z "$BW_MASTERPASS" ] || [ -z "$BW_CLIENTID" ] || [ -z "$BW_CLIENTSECRET" ]; then
log "ERROR" "Please supply correct credentials in /etc/bridgehead/vault.conf."
return 1
fi
set +e
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 $@)
RET=$?
if [ $RET -ne 0 ]; then
echo "Code: $RET"
echo $PASS
return $RET
fi
eval $(echo -e "$PASS" | sed 's/\r//g')
set -e
return 0
}
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fetchVarsFromVaultByFile() {
VARS_TO_FETCH=""
for line in $(cat $@); do
if [[ $line =~ .*=[\"]*\<VAULT\>[\"]*.* ]]; then
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VARS_TO_FETCH+="$(echo -n $line | sed 's/=.*//') "
fi
done
if [ -z "$VARS_TO_FETCH" ]; then
return 0
fi
log INFO "Fetching $(echo $VARS_TO_FETCH | wc -w) secrets from Vault ..."
fetchVarsFromVault $VARS_TO_FETCH
return 0
}
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assertVarsNotEmpty() {
MISSING_VARS=""
for VAR in $@; do
if [ -z "${!VAR}" ]; then
MISSING_VARS+="$VAR "
fi
done
if [ -n "$MISSING_VARS" ]; then
log "ERROR" "Mandatory variables not defined: $MISSING_VARS"
return 1
fi
return 0
}
fixPermissions() {
CHOWN=$(which chown)
sudo $CHOWN -R bridgehead /etc/bridgehead /srv/docker/bridgehead
}
source lib/monitoring.sh
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report_error() {
CODE=$1
shift
log ERROR "$@"
hc_send $CODE "$@"
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}
fail_and_report() {
report_error $@
exit $1
}
setHostname() {
if [ -z "$HOST" ]; then
export HOST=$(hostname -f | tr "[:upper:]" "[:lower:]")
log DEBUG "Using auto-detected hostname $HOST."
fi
}
# Takes 1) The Backup Directory Path 2) The name of the Service to be backuped
# Creates 3 Backups: 1) For the past seven days 2) For the current month and 3) for each calendar week
createEncryptedPostgresBackup(){
docker exec "$2" bash -c 'pg_dump -U $POSTGRES_USER $POSTGRES_DB --format=p --no-owner --no-privileges' | \
# TODO: Encrypt using /etc/bridgehead/pki/${SITE_ID}.priv.pem | \
tee "$1/$2/$(date +Last-%A).sql" | \
tee "$1/$2/$(date +%Y-%m).sql" > \
"$1/$2/$(date +%Y-KW%V).sql"
}
# from: https://gist.github.com/sj26/88e1c6584397bb7c13bd11108a579746
# ex. use: retry 5 /bin/false
function retry {
local retries=$1
shift
local count=0
until "$@"; do
exit=$?
wait=$((2 ** $count))
count=$(($count + 1))
if [ $count -lt $retries ]; then
echo "Retry $count/$retries exited with code $exit, retrying in $wait seconds..."
sleep $wait
else
echo "Retry $count/$retries exited with code $exit, giving up."
return $exit
fi
done
return 0
}
function bk_is_running {
detectCompose
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RUNNING="$($COMPOSE -p $PROJECT -f minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE ps -q)"
NUMBEROFRUNNING=$(echo "$RUNNING" | wc -l)
if [ $NUMBEROFRUNNING -ge 2 ]; then
return 0
else
return 1
fi
}
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function do_enroll_inner {
PARAMS=""
MANUAL_PROXY_ID="${1:-$PROXY_ID}"
if [ -z "$MANUAL_PROXY_ID" ]; then
log ERROR "No Proxy ID set"
exit 1
else
log INFO "Enrolling Beam Proxy Id $MANUAL_PROXY_ID"
fi
SUPPORT_EMAIL="${2:-$SUPPORT_EMAIL}"
if [ -n "$SUPPORT_EMAIL" ]; then
PARAMS+="--admin-email $SUPPORT_EMAIL"
fi
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
}
function do_enroll {
do_enroll_inner $@
}
add_basic_auth_user() {
USER="${1}"
PASSWORD="${2}"
NAME="${3}"
PROJECT="${4}"
FILE="/etc/bridgehead/${PROJECT}.local.conf"
ENCRY_CREDENTIALS="$(docker run --rm docker.verbis.dkfz.de/cache/httpd:alpine htpasswd -nb $USER $PASSWORD | tr -d '\n' | tr -d '\r')"
if [ -f $FILE ] && grep -R -q "$NAME=" $FILE # if a specific basic auth user already exists:
then
sed -i "/$NAME/ s|='|='$ENCRY_CREDENTIALS,|" $FILE
else
echo -e "\n## Basic Authentication Credentials for:\n$NAME='$ENCRY_CREDENTIALS'" >> $FILE;
fi
log DEBUG "Saving clear text credentials in $FILE. If wanted, delete them manually."
sed -i "/^$NAME/ s|$|\n# User: $USER\n# Password: $PASSWORD|" $FILE
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}
function clone_repo_if_nonexistent() {
local repo_url="$1" # First argument: Repository URL
local target_dir="$2" # Second argument: Target directory
local branch_name="$3" # Third argument: Branch name
echo Repo directory: $target_dir
# Check if the target directory exists
if [ ! -d "$target_dir" ]; then
echo "Directory '$target_dir' does not exist. Cloning the repository..."
# Clone the repository
git clone "$repo_url" "$target_dir"
fi
# Change to the cloned directory
cd "$target_dir"
# Checkout the specified branch
git checkout "$branch_name"
echo "Checked out branch '$branch_name'."
cd -
}
function clone_transfair_if_nonexistent() {
local base_dir="$1"
clone_repo_if_nonexistent https://github.com/samply/transFAIR.git $base_dir/transfair ehds2
}
function clone_focus_if_nonexistent() {
local base_dir="$1"
clone_repo_if_nonexistent https://github.com/samply/focus.git $base_dir/focus ehds2
}
function build_transfair() {
local base_dir="$1"
# We only take the touble to build transfair if:
#
# 1. There is data available (any CSV files) and
# 2. There is no data lock file (which means that no ETL has yet been run).
if ls ../ecdc/data/*.[cC][sS][vV] 1> /dev/null 2>&1 && [ ! -f ../ecdc/data/lock ]; then
cd $base_dir/transfair
git pull
docker build --progress=plain -t samply/transfair --no-cache .
cd -
fi
}
function build_focus() {
local base_dir="$1"
cd $base_dir/focus
git pull
docker build --progress=plain -f DockerfileWithBuild -t samply/focus --no-cache .
cd -
}