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Author SHA1 Message Date
Tobias Kussel
74c913cd0c Add documentation for proxy (credential) special character escaping 2025-12-12 11:26:42 +01:00
20 changed files with 48 additions and 240 deletions

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@@ -73,7 +73,7 @@ We recommend to install Docker(-compose) from its official sources as described
A Bridgehead communicates to all central components via outgoing HTTPS connections.
Your site might require an outgoing proxy (i.e. HTTPS forward proxy) to connect to external servers; you should discuss this with your local systems administration. In that case, you will need to note down the URL of the proxy. If the proxy requires authentication, you will also need to make a note of its username and password. This information will be used later on during the installation process. TLS terminating proxies are also supported, see [here](#tls-terminating-proxies). Apart from the Bridgehead itself, you may also need to configure the proxy server in [git](https://gist.github.com/evantoli/f8c23a37eb3558ab8765) and [docker](https://docs.docker.com/network/proxy/).
Your site might require an outgoing proxy (i.e. HTTPS forward proxy) to connect to external servers; you should discuss this with your local systems administration. In that case, you will need to note down the URL of the proxy. If the proxy requires authentication, you will also need to make a note of its username and password. This information will be used later on during the installation process. Special characters in the proxy values, e.g. in the access credentials, must be [URL-encoded](https://en.wikipedia.org/wiki/Percent-encoding), e.g. by replacing `@` with `%40`, `/` with `%2F` and so on. TLS terminating proxies are also supported, see [here](#tls-terminating-proxies). Apart from the Bridgehead itself, you may also need to configure the proxy server in [git](https://gist.github.com/evantoli/f8c23a37eb3558ab8765) and [docker](https://docs.docker.com/network/proxy/).
The following URLs need to be accessible (prefix with `https://`):
* To fetch code and configuration from git repositories
@@ -536,6 +536,8 @@ and restart the docker daemon:
sudo systemctl restart docker
```
Please note that special characters in the proxy value, such as `#?!()[]{}`, must be double escaped using `%%`.
For more information, please consult the [official documentation](https://docs.docker.com/config/daemon/systemd/#httphttps-proxy).
### Monitoring

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@@ -1,6 +1,6 @@
#!/bin/bash
if [ -n "${DS_DIRECTORY_USER_NAME}" ] || [ -n "${DS_DIRECTORY_USER_TOKEN}" ]; then
if [ -n "${DS_DIRECTORY_USER_NAME}" ]; then
log INFO "Directory sync setup detected -- will start directory sync service."
OVERRIDE+=" -f ./$PROJECT/modules/directory-sync-compose.yml"
fi

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@@ -3,8 +3,6 @@ services:
lens:
container_name: lens_federated-search
image: samply/cce-explorer:main
environment:
PUBLIC_SPOT_URL: https://${HOST}/prod
labels:
- "traefik.http.services.lens.loadbalancer.server.port=3000"
- "traefik.enable=true"

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@@ -15,7 +15,7 @@ services:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_itcc.rule=Host(`${HOST}`) && PathPrefix(`/itcc-localdatamanagement`)"
- "traefik.http.routers.blaze_itcc.rule=PathPrefix(`/itcc-localdatamanagement`)"
- "traefik.http.middlewares.itcc_b_strip.stripprefix.prefixes=/itcc-localdatamanagement"
- "traefik.http.services.blaze_itcc.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_itcc.middlewares=itcc_b_strip,auth"
@@ -34,6 +34,7 @@ services:
EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
CQL_PROJECTS_ENABLED: "itcc"
volumes:
- /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on:

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@@ -1,6 +0,0 @@
#!/bin/bash
if [ -n "$ENABLE_OMICS" ];then
OVERRIDE+=" -f ./$PROJECT/modules/itcc-omics-ingest.yaml"
GENERATE_API_KEY="$(generate_simple_password 'omics')"
fi

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@@ -1,14 +0,0 @@
services:
omics-endpoint:
image: ghcr.io/samply/itcc-omics-ingest:main
environment:
- API_KEY=${GENERATE_API_KEY}
volumes:
- /var/cache/bridgehead/omics/data:/data/uploads
labels:
- "traefik.http.routers.omics.rule=Host(`${HOST}`) && PathPrefix(`/api/omics`)"
- "traefik.enable=true"
- "traefik.http.services.omics.loadbalancer.server.port=6080"
- "traefik.http.routers.omics.tls=true"
- "traefik.http.middlewares.omics-stripprefix.stripprefix.prefixes=/api"
- "traefik.http.routers.omics.middlewares=omics-stripprefix"

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@@ -1,47 +1,33 @@
version: "3.7"
services:
itcc-explorer:
container_name: lens_itcc_explorer
image: samply/itcc-explorer:main
environment:
HOST: "0.0.0.0"
BIND_ADDR: "0.0.0.0:3000"
PUBLIC_ENVIRONMENT: ${PUBLIC_ENVIRONMENT}
landing:
container_name: lens_federated-search
image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
labels:
- "traefik.enable=true"
- "traefik.http.routers.itcc.rule=Host(`${HOST}`) && PathPrefix(`/`)"
- "traefik.http.routers.itcc.entrypoints=websecure"
- "traefik.http.services.itcc.loadbalancer.server.port=3000"
- "traefik.http.routers.itcc.tls=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=80"
- "traefik.http.routers.landing.tls=true"
spot:
image: samply/rustyspot:latest
image: docker.verbis.dkfz.de/ccp-private/central-spot
environment:
BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
BEAM_PROXY_URL: http://beam-proxy:8081
BEAM_URL: http://beam-proxy:8081
BEAM_PROXY_ID: ${SITE_ID}
BEAM_BROKER_ID: ${BROKER_ID}
BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
CORS_ORIGIN: "https://${HOST}"
SITES: ${SITES}
TRANSFORM: LENS
PROJECT: "itcc"
BIND_ADDR: 0.0.0.0:8055
BEAM_APP_ID: "focus"
PROJECT_METADATA: "itcc"
depends_on:
- "beam-proxy"
labels:
- "traefik.enable=true"
- "traefik.http.services.spot.loadbalancer.server.port=8055"
- "traefik.http.services.spot.loadbalancer.server.port=8080"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
- "traefik.http.routers.spot.tls=true"
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"
beam-proxy:
environment:
APP_spot_KEY: ${FOCUS_BEAM_SECRET_SHORT}

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@@ -6,7 +6,6 @@ FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
PUBLIC_ENVIRONMENT=prod
for module in $PROJECT/modules/*.sh
do

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@@ -12,8 +12,7 @@ services:
BASE_URL: "http://bridgehead-kr-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"

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@@ -0,0 +1,6 @@
# Full Excel Export
curl --location --request POST 'https://${HOST}/ccp-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
--header 'x-api-key: ${EXPORT_API_KEY}'
# QB
curl --location --request POST 'https://${HOST}/ccp-reporter/generate?template-id=ccp'

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@@ -4,41 +4,32 @@ services:
deploy:
replicas: 1 #reactivate if lens is in use
container_name: lens_federated-search
image: docker.verbis.dkfz.de/ccp/kr-explorer:main
environment:
PUBLIC_SPOT_URL: https://${HOST}/prod
image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
labels:
- "traefik.http.services.lens.loadbalancer.server.port=3000"
- "traefik.enable=true"
- "traefik.http.routers.lens.rule=Host(`${HOST}`)"
- "traefik.http.routers.lens.tls=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=80"
- "traefik.http.routers.landing.tls=true"
spot:
image: samply/rustyspot:latest
image: docker.verbis.dkfz.de/ccp-private/central-spot
environment:
BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
BEAM_PROXY_URL: http://beam-proxy:8081
BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
CORS_ORIGIN: "https://${HOST}"
SITES: ${SITES}
TRANSFORM: LENS
PROJECT: kr
BIND_ADDR: 0.0.0.0:8055
BEAM_URL: http://beam-proxy:8081
BEAM_PROXY_ID: ${SITE_ID}
BEAM_BROKER_ID: ${BROKER_ID}
BEAM_APP_ID: "focus"
PROJECT_METADATA: "kr_supervisors"
depends_on:
- "beam-proxy"
labels:
- "traefik.enable=true"
- "traefik.http.services.spot.loadbalancer.server.port=8055"
- "traefik.http.services.spot.loadbalancer.server.port=8080"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
- "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod"
- "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
- "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
- "traefik.http.routers.spot.tls=true"
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"
beam-proxy:
environment:
APP_spot_KEY: ${FOCUS_BEAM_SECRET_SHORT}
- "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

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@@ -3,7 +3,7 @@ version: "3.7"
services:
obds2fhir-rest:
container_name: bridgehead-obds2fhir-rest
image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main
image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
environment:
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}

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@@ -3,7 +3,7 @@ BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=p.delpy@dkfz-heidelberg.de
SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL

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@@ -9,15 +9,6 @@ detectCompose() {
fi
}
# Encodes all characters not in unrestricted character set of RFC3986 Section 2.3
urlencode() {
for ((i=0;i<${#1};i++)); do
local c=${1:i:1}
[[ "$c" =~ [a-zA-Z0-9._~-] ]] && printf '%s' "$c" || printf '%%%02X' "'$c"
done
echo
}
setupProxy() {
### Note: As the current data protection concepts do not allow communication via HTTP,
### we are not setting a proxy for HTTP requests.
@@ -31,12 +22,9 @@ setupProxy() {
HTTPS_PROXY_HOST="$(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
local ESCAPED_PASSWORD="$(echo $HTTPS_PROXY_PASSWORD | od -An -v -t x1 | sed -e 's/[[:space:]]//g' -e 's/\([0-9a-f][0-9a-f]\)/%\1/g' | tr -d '\n')"
local CURL_ESCAPED_PW="$(urlencode $HTTPS_PROXY_PASSWORD)"
local proto="$(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:$ESCAPED_PASSWORD@$fqdn)"
CURL_HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$CURL_ESCAPED_PW@$fqdn)"
HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$HTTPS_PROXY_PASSWORD@$fqdn)"
https="authenticated"
else
HTTPS_PROXY_FULL_URL=$HTTPS_PROXY_URL
@@ -45,7 +33,7 @@ setupProxy() {
fi
log INFO "Configuring proxy servers: $http http proxy (we're not supporting unencrypted comms), $https https proxy"
export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL CURL_HTTPS_PROXY_FULL_URL
export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
}
exitIfNotRoot() {

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@@ -47,8 +47,8 @@ function hc_send(){
if [ -n "$2" ]; then
MSG="$2\n\nDocker stats:\n$UPTIME"
echo -e "$MSG" | https_proxy=$CURL_HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null -X POST --data-binary @- "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
echo -e "$MSG" | https_proxy=$HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null -X POST --data-binary @- "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
else
https_proxy=$CURL_HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
https_proxy=$HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
fi
}

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@@ -71,7 +71,7 @@ source ${PROJECT}/vars
if [ "${PROJECT}" != "minimal" ]; then
set +e
SERVERTIME="$(https_proxy=$CURL_HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
RET=$?
set -e
if [ $RET -ne 0 ]; then

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@@ -1,123 +0,0 @@
source ../functions.sh
test_setupProxy() {
# simple logger for tests
log() { :; }
local failures=0
local total=0
assert_eq() {
local label="$1" got="$2" expected="$3"
total=$((total + 1))
if [[ "$got" != "$expected" ]]; then
failures=$((failures + 1))
printf 'FAIL: %s\n got: %q\n expected: %q\n\n' "$label" "$got" "$expected"
else
printf 'ok: %s\n' "$label"
fi
}
run_case() {
local name="$1"
local url="$2"
local u="$3"
local p="$4"
local exp_host="$5"
local exp_port="$6"
local exp_full="$7"
HTTPS_PROXY_URL="$url"
HTTPS_PROXY_USERNAME="$u"
HTTPS_PROXY_PASSWORD="$p"
setupProxy >/dev/null 2>&1
assert_eq "$name host" "$HTTPS_PROXY_HOST" "$exp_host"
assert_eq "$name port" "$HTTPS_PROXY_PORT" "$exp_port"
assert_eq "$name full" "$HTTPS_PROXY_FULL_URL" "$exp_full"
}
echo "Running setupProxy tests..."
echo
# 1) Basic https host:port
run_case "basic https" \
"https://proxy.example.org:8443" "" "" \
"proxy.example.org" "8443" \
"https://proxy.example.org:8443"
# 2) https without port -> default 443
run_case "https no port" \
"https://proxy.example.org" "" "" \
"proxy.example.org" "443" \
"https://proxy.example.org"
# 3) no scheme, host:port -> defaults scheme=https
run_case "no scheme hostport" \
"proxy.example.org:3128" "" "" \
"proxy.example.org" "3128" \
"https://proxy.example.org:3128"
# 4) URL with path/query/fragment
run_case "ignores path" \
"https://proxy.example.org:8443/some/path?x=1#y" "" "" \
"proxy.example.org" "8443" \
"https://proxy.example.org:8443"
# 5) explicit env creds inserted
run_case "env creds override" \
"https://proxy.example.org:8443" "alice" "secret" \
"proxy.example.org" "8443" \
"https://alice:secret@proxy.example.org:8443"
# 6) embedded creds used if env creds absent
run_case "embedded creds" \
"https://bob:pw@proxy.example.org:8443" "" "" \
"proxy.example.org" "8443" \
"https://bob:pw@proxy.example.org:8443"
# 7) env creds override embedded creds
run_case "env overrides embedded" \
"https://bob:pw@proxy.example.org:8443" "alice" "secret" \
"proxy.example.org" "8443" \
"https://alice:secret@proxy.example.org:8443"
# 8) IPv6 literal with port
run_case "ipv6 with port" \
"https://[2001:db8::1]:8080" "" "" \
"2001:db8::1" "8080" \
"https://[2001:db8::1]:8080"
# 9) IPv6 literal without port -> default 443
run_case "ipv6 no port" \
"https://[2001:db8::1]" "" "" \
"2001:db8::1" "443" \
"https://[2001:db8::1]"
# 10) http scheme rejected -> outputs empty
HTTPS_PROXY_URL="http://proxy.example.org:8080"
HTTPS_PROXY_USERNAME=""
HTTPS_PROXY_PASSWORD=""
setupProxy >/dev/null 2>&1
assert_eq "http rejected host" "${HTTPS_PROXY_HOST:-}" ""
assert_eq "http rejected port" "${HTTPS_PROXY_PORT:-}" ""
assert_eq "http rejected full" "${HTTPS_PROXY_FULL_URL:-}" ""
# 11) empty URL -> outputs empty but no failure
HTTPS_PROXY_URL=""
setupProxy >/dev/null 2>&1
assert_eq "empty url host" "${HTTPS_PROXY_HOST:-}" ""
assert_eq "empty url port" "${HTTPS_PROXY_PORT:-}" ""
assert_eq "empty url full" "${HTTPS_PROXY_FULL_URL:-}" ""
echo
echo "Tests complete: $((total - failures))/$total passed."
if (( failures > 0 )); then
echo "Some tests failed."
return 1
fi
return 0
}
test_setupProxy

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@@ -32,7 +32,7 @@ services:
forward_proxy:
container_name: bridgehead-forward-proxy
image: samply/bridgehead-forward-proxy:pr-16
image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
environment:
HTTPS_PROXY: ${HTTPS_PROXY_URL}
HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USERNAME}

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@@ -1,13 +0,0 @@
services:
osiris2fhir:
container_name: bridgehead-osiris2fhir
image: docker.verbis.dkfz.de/ccp/osiris2fhir:${SITE_ID}
environment:
SALT: ${LOCAL_SALT}
labels:
- "traefik.enable=true"
- "traefik.http.routers.osiris2fhir.rule=PathPrefix(`/osiris2fhir`)"
- "traefik.http.middlewares.osiris2fhir_strip.stripprefix.prefixes=/osiris2fhir"
- "traefik.http.services.osiris2fhir.loadbalancer.server.port=8080"
- "traefik.http.routers.osiris2fhir.tls=true"
- "traefik.http.routers.osiris2fhir.middlewares=osiris2fhir_strip,auth"

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@@ -1,6 +0,0 @@
#!/bin/bash
if [ -n "$ENABLE_OSIRIS2FHIR" ]; then
log INFO "oBDS2FHIR-REST setup detected -- will start osiris2fhir module."
OVERRIDE+=" -f ./pscc/modules/osiris2fhir-compose.yml"
LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
fi