refactor and clean up

itcc/docker-compose.yml

@@ -34,7 +34,6 @@ 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:

itcc/modules/itcc-omics-ingest.sh

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

itcc/modules/itcc-omics-ingest.yaml

@@ -0,0 +1,14 @@
+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"

itcc/modules/lens-compose.yml

@@ -1,33 +1,49 @@
 version: "3.7"
 services:
   landing:
-    container_name: lens_federated-search
+    container_name: lens_itcc_explorer
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
+    image: ghcr.io/samply/itcc-explorer:fix-setup
+    environment:
+      HOST: "0.0.0.0"
+      BIND_ADDR: "0.0.0.0:3000"
+      PUBLIC_ENVIRONMENT: ${PUBLIC_ENVIRONMENT}
     labels:
+      - "traefik.http.routers.lens.rule=Host(`${HOST}`)"
       - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
+      - "traefik.http.services.landing.loadbalancer.server.port=3000"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
       - "traefik.http.routers.landing.tls=true"
 
   spot:
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
+    image: samply/rustyspot:latest
     environment:
+      HTTP_PROXY: ${HTTP_PROXY_URL}
+      HTTPS_PROXY: ${HTTPS_PROXY_URL}
+      NO_PROXY: beam-proxy
       BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
-      BEAM_URL: http://beam-proxy:8081
+      BEAM_PROXY_URL: http://beam-proxy:8081
       BEAM_PROXY_ID: ${SITE_ID}
       BEAM_BROKER_ID: ${BROKER_ID}
-      BEAM_APP_ID: "focus"
+      BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
-      PROJECT_METADATA: "itcc"
+      CORS_ORIGIN: "https://${HOST}"
+      SITES: ${SITES}
+      TRANSFORM: LENS
+      PROJECT: "itcc"
+      BIND_ADDR: 0.0.0.0:8055
     depends_on:
       - "beam-proxy"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
+      - "traefik.http.services.spot.loadbalancer.server.port=8055"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${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,auth"
+
+  beam-proxy:
+    environment:
+      APP_spot_KEY: ${FOCUS_BEAM_SECRET_SHORT}

itcc/vars

@@ -6,6 +6,8 @@ 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
+SITES=itcc-inform,itcc-ither,itcc-mappyacts,itcc-profyle,itcc-smpaeds,itcc-zero
 
 for module in $PROJECT/modules/*.sh
 do