Update traefik dashboard routing rules

Traefik uses the `/api` path for the internal api. For the dashboard to function, it needs to be routed, too.

bbmri/modules/directory-sync.sh

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

cce/modules/osiris2fhir-setup.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+if [ -n "$ENABLE_OSIRIS2FHIR" ]; then
+  log INFO "OSIRIS2FHIR-REST setup detected -- will start osiris2fhir module."
+  OVERRIDE+=" -f ./pscc/modules/osiris2fhir-compose.yml"
+  LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+fi

itcc/docker-compose.yml

@@ -32,7 +32,7 @@ services:
       BEAM_PROXY_URL: http://beam-proxy:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
       EPSILON: 0.28
-      QUERIES_TO_CACHE: "/queries_to_cache.conf"
+      QUERIES_TO_CACHE: '/queries_to_cache.conf'
       ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
     volumes:
       - /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
@@ -41,13 +41,12 @@ services:
       - "blaze"
 
   beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop-sockets
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}
       PROXY_ID: ${PROXY_ID}
       APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
-      APP_omics-endpoint_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
@@ -60,6 +59,7 @@ services:
       - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
       - /srv/docker/bridgehead/itcc/root.crt.pem:/conf/root.crt.pem:ro
 
+
 volumes:
   blaze-data:
 

itcc/modules/itcc-omics-ingest.sh

@@ -3,5 +3,4 @@
 if [ -n "$ENABLE_OMICS" ];then
   OVERRIDE+=" -f ./$PROJECT/modules/itcc-omics-ingest.yaml"
   GENERATE_API_KEY="$(generate_simple_password 'omics')"
-  PATIENTLIST_POSTGRES_PASSWORD=="$(generate_simple_password 'mainzelliste')"
 fi

itcc/modules/itcc-omics-ingest.yaml

@@ -1,20 +1,8 @@
 services:
   omics-endpoint:
-    image: ghcr.io/samply/itcc-omics-ingest:fix-task
+    image: ghcr.io/samply/itcc-omics-ingest:main
     environment:
-      API_KEY: ${GENERATE_API_KEY}
+      - API_KEY=${GENERATE_API_KEY}
-      RUST_LOG: debug
-      BEAM_ID: "omics-endpoint.${PROXY_ID}"
-      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_URL: http://beam-proxy:8081
-      ML_URL: http://mainzelliste:8080
-      BLAZE_URL: http://bridgehead-itcc-blaze:8080/fhir/
-      DWH_SOCKET_ID: "${DWH_SOCKET_ID}"
-      DWH_TASK_ID: "${DWH_TASK_ID}"
-      ENABLE_SOCKETS: true
-      PARTNER_ID: itcc-inform
-      ML_API_KEY: ${GENERATE_API_KEY}
-
     volumes:
       - /var/cache/bridgehead/omics/data:/data/uploads
     labels:
@@ -24,58 +12,3 @@ services:
       - "traefik.http.routers.omics.tls=true"
       - "traefik.http.middlewares.omics-stripprefix.stripprefix.prefixes=/api"
       - "traefik.http.routers.omics.middlewares=omics-stripprefix"
-
-  db:
-    image: postgres:15
-    container_name: db
-    restart: unless-stopped
-    environment:
-      POSTGRES_DB: mainzelliste
-      POSTGRES_USER: ${ML_DB_USER}
-      POSTGRES_PASSWORD: ${PATIENTLIST_POSTGRES_PASSWORD}
-    ports:
-      - "5432:5432"
-    volumes:
-      - db_data:/var/lib/postgresql/data
-    healthcheck:
-      test: ["CMD-SHELL", "pg_isready -U ${ML_DB_USER} -d mainzelliste"]
-      interval: 5s
-      timeout: 5s
-      retries: 10
-      start_period: 10s
-
-  mainzelliste:
-    image: medicalinformatics/mainzelliste:latest
-    container_name: mainzelliste
-    restart: unless-stopped
-    depends_on:
-      db:
-        condition: service_healthy
-    ports:
-      - 7887:8080
-
-    environment:
-      ML_API_KEY: ${GENERATE_API_KEY}
-      ML_DB_HOST: db
-      ML_DB_PORT: "5432"
-      ML_DB_NAME: mainzelliste
-      ML_DB_USER: ${ML_DB_USER}
-      ML_DB_PASS: ${PATIENTLIST_POSTGRES_PASSWORD}
-      ML_DB_DRIVER: org.postgresql.Driver
-      ML_DB_TYPE: postgresql
-      ML_LOG_LEVEL: INFO
-      ML_ALLOWEDREMOTEADDRESSES: "127.0.0.1,::1,172.16.0.0/12"
-
-    secrets:
-      - mainzelliste.docker.conf
-      - source: symmetric_key
-        target: /etc/resources/keys/symmetric_key.der
-
-volumes:
-  db_data:
-secrets:
-  mainzelliste.docker.conf:
-    file: /etc/bridgehead/mainzelliste/mainzelliste.docker.conf
-
-  symmetric_key:
-    file: /etc/bridgehead/mainzelliste/keyset_siv.json

itcc/vars

@@ -7,9 +7,6 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 PUBLIC_ENVIRONMENT=prod
-DWH_SOCKET_ID=socket.itcc-datalake.${BROKER_ID}
-DWH_TASK_ID=task.itcc-datalake.${BROKER_ID}
-ML_DB_USER=mainzelliste
 
 for module in $PROJECT/modules/*.sh
 do

kr/docker-compose.yml

@@ -12,7 +12,8 @@ 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
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-data:/app/data"

kr/modules/export-and-qb.curl-templates

@@ -1,6 +0,0 @@
-# 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'

kr/modules/lens-compose.yml

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

kr/modules/obds2fhir-rest-compose.yml

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

kr/vars

@@ -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=${FOCUS_RETRY_COUNT:-64}
-SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
+SUPPORT_EMAIL=p.delpy@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 

minimal/docker-compose.yml

@@ -16,7 +16,7 @@ services:
       - --entrypoints.web.http.redirections.entrypoint.scheme=https
     labels:
       - "traefik.enable=true"
-      - "traefik.http.routers.dashboard.rule=PathPrefix(`/dashboard/`)"
+      - "traefik.http.routers.dashboard.rule=PathPrefix(`/dashboard/`)||PathPrefix(`/api`)"
       - "traefik.http.routers.dashboard.entrypoints=websecure"
       - "traefik.http.routers.dashboard.service=api@internal"
       - "traefik.http.routers.dashboard.tls=true"

pscc/modules/osiris2fhir-compose.yml

@@ -0,0 +1,15 @@
+services:
+  osiris2fhir:
+    container_name: bridgehead-osiris2fhir
+    image: docker.verbis.dkfz.de/ccp/osiris2fhir
+    environment:
+      FHIR_PROFILE: ${PROJECT:-pscc}
+      LOG_LEVEL: ${LOG_LEVEL:-INFO}
+      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"

pscc/modules/osiris2fhir-setup.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+if [ -n "$ENABLE_OSIRIS2FHIR" ]; then
+  log INFO "OSIRIS2FHIR-REST setup detected -- will start osiris2fhir module."
+  OVERRIDE+=" -f ./pscc/modules/osiris2fhir-compose.yml"
+  LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+fi