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23 Commits

Author SHA1 Message Date
e5efd42861 fix: Disable landing page for now 2024-05-13 13:56:58 +00:00
f139965460 feat: Add root cert 2024-05-13 13:56:22 +00:00
0b42ff3e22 feat: leme setup 2024-05-13 11:47:00 +00:00
825f1a0b6c Added lemedart 2024-05-08 14:03:11 +02:00
714e46f082 Merge pull request #184 from samply/refactor/mainzelliste-return-ssl
Ensure Mainzelliste returns SSL in Responses
2024-04-29 08:33:00 +02:00
29c2b5ef69 refactor: Ensure Mainzelliste returns SSL in Responses
Before, the Mainzelliste would always use http instead of https then
referring to it self in responses
2024-04-26 11:29:38 +02:00
433edde75a Merge pull request #182 from samply/revert-177-maintenance/gbn
Revert "GBN maintenance mode"
2024-04-18 11:37:11 +02:00
fe3fc6204a Revert "GBN maintenance mode" 2024-04-18 11:01:04 +02:00
4b3b13b101 Merge pull request #177 from samply/maintenance/gbn
GBN maintenance mode
2024-04-17 20:47:35 +02:00
1afbf88a76 fix: use only bbmri broker 2024-04-16 09:23:42 +02:00
7d5f771181 Merge pull request #181 from samply/fix/secret-sync-args
fix: Generate public oidc client when there is no private client
2024-04-16 09:15:53 +02:00
f9a9baf13d fix: Generate public oidc client when there is no private client 2024-04-15 15:53:27 +02:00
d4259406a9 Merge pull request #180 from samply/fix/secret-sync
fix: Kill stale secret-sync instances
2024-04-15 13:18:38 +02:00
0745eab7b5 fix: Kill stale secret-sync instances 2024-04-15 13:14:46 +02:00
b404277083 Merge pull request #179 from samply/update/focus_0_4_4
update: dktk focus to 0.4.4
2024-04-15 11:02:31 +02:00
b767b3230f update: dktk focus to 0.4.4 2024-04-15 10:13:16 +02:00
dd653a7871 Merge pull request #178 from samply/PierreDelpy-patch-1
fix typo functions.sh
2024-04-15 09:09:47 +02:00
7418861e8c fix typo functions.sh 2024-04-15 09:08:56 +02:00
94b2c29bc7 GBN maintenance mode 2024-04-15 08:31:57 +02:00
ac3ff314ff Merge pull request #176 from samply/fix/bash-math
fix: Make math work on bash 4.2
2024-04-03 12:59:52 +02:00
2831fb9a22 fix: Make math work on bash 4.2 2024-04-02 14:36:23 +02:00
7934d912b8 Merge pull request #175 from samply/update/focus_0_4_2
Update focus to 0.4.2
2024-03-22 14:11:09 +01:00
70ad318b28 Update focus to 0.4.2 2024-03-22 13:59:42 +01:00
9 changed files with 123 additions and 18 deletions

View File

@ -29,6 +29,9 @@ case "$PROJECT" in
ccp) ccp)
#nothing extra to do #nothing extra to do
;; ;;
leme)
#nothing extra to do
;;
bbmri) bbmri)
#nothing extra to do #nothing extra to do
;; ;;
@ -96,6 +99,8 @@ case "$ACTION" in
;; ;;
stop) stop)
loadVars loadVars
# Kill stale secret-sync instances if present
docker kill $(docker ps -q --filter ancestor=docker.verbis.dkfz.de/cache/samply/secret-sync-local) 2>/dev/null || true
# HACK: This is temporarily to properly shut down false bridgehead instances (bridgehead-ccp instead ccp) # HACK: This is temporarily to properly shut down false bridgehead instances (bridgehead-ccp instead ccp)
$COMPOSE -p bridgehead-$PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down $COMPOSE -p bridgehead-$PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down
exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down

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@ -21,7 +21,7 @@ services:
- "traefik.http.routers.blaze_ccp.tls=true" - "traefik.http.routers.blaze_ccp.tls=true"
focus: focus:
image: docker.verbis.dkfz.de/cache/samply/focus:0.4.1 image: docker.verbis.dkfz.de/cache/samply/focus:0.4.4
container_name: bridgehead-focus container_name: bridgehead-focus
environment: environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT} API_KEY: ${FOCUS_BEAM_SECRET_SHORT}

View File

@ -29,6 +29,7 @@ services:
container_name: bridgehead-patientlist container_name: bridgehead-patientlist
environment: environment:
- TOMCAT_REVERSEPROXY_FQDN=${HOST} - TOMCAT_REVERSEPROXY_FQDN=${HOST}
- TOMCAT_REVERSEPROXY_SSL=true
- ML_SITE=${IDMANAGEMENT_FRIENDLY_ID} - ML_SITE=${IDMANAGEMENT_FRIENDLY_ID}
- ML_DB_PASS=${PATIENTLIST_POSTGRES_PASSWORD} - ML_DB_PASS=${PATIENTLIST_POSTGRES_PASSWORD}
- ML_API_KEY=${IDMANAGER_LOCAL_PATIENTLIST_APIKEY} - ML_API_KEY=${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}

62
leme/docker-compose.yml Normal file
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@ -0,0 +1,62 @@
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:latest
container_name: bridgehead-leme-blaze
environment:
BASE_URL: "http://bridgehead-leme-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
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_leme.rule=PathPrefix(`/leme-localdatamanagement`)"
- "traefik.http.middlewares.leme_b_strip.stripprefix.prefixes=/leme-localdatamanagement"
- "traefik.http.services.blaze_leme.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_leme.middlewares=leme_b_strip,auth"
- "traefik.http.routers.blaze_leme.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:0.4.4
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
BEAM_APP_ID_LONG: focus.${PROXY_ID}
PROXY_ID: ${PROXY_ID}
BLAZE_URL: "http://bridgehead-leme-blaze:8080/fhir/"
BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
depends_on:
- "beam-proxy"
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/leme/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

20
leme/root.crt.pem Normal file
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@ -0,0 +1,20 @@
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----

14
leme/vars Normal file
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@ -0,0 +1,14 @@
BROKER_ID=broker-test.health-innovation-lab.eu
BROKER_URL=http://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
FOCUS_RETRY_COUNT=32
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
# for module in $PROJECT/modules/*.sh
# do
# log DEBUG "sourcing $module"
# source $module
# done

View File

@ -164,15 +164,15 @@ setHostname() {
optimizeBlazeMemoryUsage() { optimizeBlazeMemoryUsage() {
if [ -z "$BLAZE_MEMORY_CAP" ]; then if [ -z "$BLAZE_MEMORY_CAP" ]; then
system_memory_in_mb=$(LC_ALL=C free -m | grep 'Mem:' | awk '{print $2}'); system_memory_in_mb=$(LC_ALL=C free -m | grep 'Mem:' | awk '{print $2}');
export BLAZE_MEMORY_CAP=$(("$system_memory_in_mb"/4)); export BLAZE_MEMORY_CAP=$(($system_memory_in_mb/4));
fi fi
if [ -z "$BLAZE_RESOURCE_CACHE_CAP" ]; then if [ -z "$BLAZE_RESOURCE_CACHE_CAP" ]; then
available_system_memory_chuncks=$((BLAZE_MEMORY_CAP / 1000)) available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
if [ $available_system_memory_chuncks -eq 0 ]; then if [ $available_system_memory_chunks -eq 0 ]; then
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." log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
export BLAZE_RESOURCE_CACHE_CAP=128000; export BLAZE_RESOURCE_CACHE_CAP=128000;
else else
export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chuncks * 312500)) export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
fi fi
fi fi
} }
@ -289,7 +289,7 @@ function sync_secrets() {
if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
secret_sync_args="OIDC:OIDC_CLIENT_SECRET:private;$OIDC_PRIVATE_REDIRECT_URLS" secret_sync_args="OIDC:OIDC_CLIENT_SECRET:private;$OIDC_PRIVATE_REDIRECT_URLS"
fi fi
if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then if [[ $OIDC_PUBLIC_REDIRECT_URLS != "" ]]; then
if [[ $secret_sync_args == "" ]]; then if [[ $secret_sync_args == "" ]]; then
secret_sync_args="OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS" secret_sync_args="OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
else else

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@ -49,6 +49,9 @@ case "$PROJECT" in
ccp) ccp)
site_configuration_repository_middle="git.verbis.dkfz.de/bridgehead-configurations/bridgehead-config-" site_configuration_repository_middle="git.verbis.dkfz.de/bridgehead-configurations/bridgehead-config-"
;; ;;
leme)
site_configuration_repository_middle="git.verbis.dkfz.de/bridgehead-configurations/bridgehead-config-"
;;
bbmri) bbmri)
site_configuration_repository_middle="git.verbis.dkfz.de/bbmri-bridgehead-configs/" site_configuration_repository_middle="git.verbis.dkfz.de/bbmri-bridgehead-configs/"
;; ;;

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@ -46,15 +46,15 @@ services:
# Wait 1s before marking this service healthy. Required for the oauth2-proxy to talk to the OIDC provider on startup which will fail if the forward proxy is not started yet. # Wait 1s before marking this service healthy. Required for the oauth2-proxy to talk to the OIDC provider on startup which will fail if the forward proxy is not started yet.
test: ["CMD", "sleep", "1"] test: ["CMD", "sleep", "1"]
landing: # landing:
container_name: bridgehead-landingpage # container_name: bridgehead-landingpage
image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:main # image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:main
labels: # labels:
- "traefik.enable=true" # - "traefik.enable=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)" # - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=80" # - "traefik.http.services.landing.loadbalancer.server.port=80"
- "traefik.http.routers.landing.tls=true" # - "traefik.http.routers.landing.tls=true"
environment: # environment:
HOST: ${HOST} # HOST: ${HOST}
PROJECT: ${PROJECT} # PROJECT: ${PROJECT}
SITE_NAME: ${SITE_NAME} # SITE_NAME: ${SITE_NAME}