mirror of https://github.com/samply/bridgehead.git
Merge branch 'main' into feature/datashield
This commit is contained in:
patrickskowronekdkfz
GitHub
commit
4fac079aec
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@ -8,8 +8,9 @@ services:
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container_name: bridgehead-bbmri-blaze
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environment:
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BASE_URL: "http://bridgehead-bbmri-blaze:8080"
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JAVA_TOOL_OPTIONS: "-Xmx4g"
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LOG_LEVEL: "debug"
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JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
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DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
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DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
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ENFORCE_REFERENTIAL_INTEGRITY: "false"
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volumes:
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- "blaze-data:/app/data"
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@ -51,6 +51,7 @@ loadVars() {
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fi
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fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
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setHostname
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optimizeBlazeMemoryUsage
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[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
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set +a
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@ -6,7 +6,9 @@ services:
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container_name: bridgehead-ccp-blaze
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environment:
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BASE_URL: "http://bridgehead-ccp-blaze:8080"
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JAVA_TOOL_OPTIONS: "-Xmx4g"
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JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
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DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
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DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
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ENFORCE_REFERENTIAL_INTEGRITY: "false"
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volumes:
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- "blaze-data:/app/data"
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@ -19,7 +21,7 @@ services:
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- "traefik.http.routers.blaze_ccp.tls=true"
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focus:
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image: docker.verbis.dkfz.de/cache/samply/focus:0.4.0
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image: docker.verbis.dkfz.de/cache/samply/focus:0.4.1
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container_name: bridgehead-focus
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environment:
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API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
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@ -6,6 +6,7 @@ services:
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container_name: bridgehead-dnpm-backend
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environment:
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- ZPM_SITE=${ZPM_SITE}
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- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
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volumes:
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- /etc/bridgehead/dnpm:/bwhc_config:ro
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- ${DNPM_DATA_DIR}:/bwhc_data
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@ -14,14 +14,15 @@ if [ -n "${ENABLE_DNPM_NODE}" ]; then
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log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
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exit 1
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fi
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if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
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echo "Override of landing page url already in place"
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else
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echo "Adding override of landing page url"
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if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
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echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
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else
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echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
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fi
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fi
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DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
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if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
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echo "Override of landing page url already in place"
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else
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echo "Adding override of landing page url"
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if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
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echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
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else
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echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
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fi
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fi
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fi
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@ -155,6 +155,28 @@ setHostname() {
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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_chuncks=$((BLAZE_MEMORY_CAP / 1000))
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if [ $available_system_memory_chuncks -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_chuncks * 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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@ -67,29 +67,30 @@ log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
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source /etc/bridgehead/${PROJECT}.conf
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source ${PROJECT}/vars
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set +e
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SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
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RET=$?
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set -e
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if [ $RET -ne 0 ]; then
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log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
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log WARN "Unable to check clock skew due to previous error."
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else
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log INFO "Checking clock skew ..."
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if [ "${PROJECT}" != "minimal" ]; then
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set +e
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SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
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RET=$?
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set -e
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if [ $RET -ne 0 ]; then
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log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
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log WARN "Unable to check clock skew due to previous error."
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else
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log INFO "Checking clock skew ..."
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SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
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MYTIME=$(date +%s)
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SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
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SKEW=$(echo $SKEW | awk -F- '{print $NF}')
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SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
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if [ $SKEW -ge 300 ]; then
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report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
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exit 1
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elif [ $SKEW -ge 60 ]; then
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log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
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fi
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SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
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MYTIME=$(date +%s)
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SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
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SKEW=$(echo $SKEW | awk -F- '{print $NF}')
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SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
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if [ $SKEW -ge 300 ]; then
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report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
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exit 1
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elif [ $SKEW -ge 60 ]; then
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log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
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fi
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fi
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fi
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checkPrivKey() {
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if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
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log INFO "Success - private key found."
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@ -100,7 +101,7 @@ checkPrivKey() {
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return 0
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}
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if [[ "$@" =~ "noprivkey" ]]; then
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if [[ "$@" =~ "noprivkey" || "${PROJECT}" != "minimal" ]]; then
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log INFO "Skipping check for private key for now."
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else
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checkPrivKey || exit 1
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@ -6,6 +6,7 @@ services:
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container_name: bridgehead-dnpm-backend
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environment:
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- ZPM_SITE=${ZPM_SITE}
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- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
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volumes:
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- /etc/bridgehead/dnpm:/bwhc_config:ro
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- ${DNPM_DATA_DIR}:/bwhc_data
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@ -14,14 +14,15 @@ if [ -n "${ENABLE_DNPM_NODE}" ]; then
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log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
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exit 1
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fi
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if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
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echo "Override of landing page url already in place"
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else
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echo "Adding override of landing page url"
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if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
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echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
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else
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echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
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fi
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fi
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DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
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if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
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echo "Override of landing page url already in place"
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else
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echo "Adding override of landing page url"
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if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
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echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
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else
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echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
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fi
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fi
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fi
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