refactor and clean up

bbmri/modules/eric-compose.yml

@@ -11,7 +11,6 @@ services:
       BLAZE_URL: "http://blaze:8080/fhir/"
       BEAM_PROXY_URL: http://beam-proxy-eric:8081
       RETRY_COUNT: ${FOCUS_RETRY_COUNT}
-      OBFUSCATE_BBMRI_ERIC_WAY: "true"
     depends_on:
       - "beam-proxy-eric"
       - "blaze"

cce/modules/lens-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 services:
   lens:
     container_name: lens_federated-search
-    image: samply/cce-explorer:main
+    image: ghcr.io/samply/cce-explorer:pr-1
     labels:
       - "traefik.http.services.lens.loadbalancer.server.port=3000"
       - "traefik.enable=true"
@@ -36,9 +36,4 @@ services:
       - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
       - "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}
-      
+      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"

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
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
+    container_name: lens_itcc_explorer
+    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=80"
+      - "traefik.http.services.landing.loadbalancer.server.port=3000"
       - "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: ${BROKER_ID}
-      BEAM_APP_ID: "focus"
-      PROJECT_METADATA: "itcc"
+      BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
+      CORS_ORIGIN: "https://${HOST}"
+      SITES: ${SITES}
+      TRANSFORM: LENS
+      PROJECT: "itcc"
+      BIND_ADDR: 0.0.0.0:8055
     depends_on:
       - "beam-proxy"
     labels:
       - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
+      - "traefik.http.services.spot.loadbalancer.server.port=8055"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
       - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
-      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
+      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)"
+      - "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

lib/functions.sh

@@ -337,8 +337,8 @@ function sync_secrets() {
 }
 
 function secret_sync_gitlab_token() {
-    if [[ "$PROJECT" != "ccp" && "$PROJECT" != "bbmri" ]]; then
-        log "INFO" "Not running Secret Sync for project $PROJECT"
+    if [[ "$PROJECT" != "dktk" && "$PROJECT" != "bbmri" ]]; then
+        log "INFO" "Not running Secret Sync for project minimal"
         return
     fi
     # Map the origin of the git repository /etc/bridgehead to the prefix recognized by Secret Sync

pscc/root.crt.pem

@@ -1,20 +1,20 @@
 -----BEGIN CERTIFICATE-----
-MIIDNTCCAh2gAwIBAgIUVC1Y1tx0q5PNR33gArAyyBm8PMQwDQYJKoZIhvcNAQEL
-BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjUxMTAzMTQxODQ5WhcNMzUx
-MTAxMTQxOTE5WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
-AQEBBQADggEPADCCAQoCggEBAMB1yd7zkh7Io/ReQYindBcAdA1b4ogdVnrdSLRN
-N3zLSh6jN5KIXgs34BdRXx0so0m96q+9xlgacTXGRBn1Tu5SKMRyXdxnCLMzHAYU
-rNKhqF5HeZCYkVyh/tsAyFfDwZDVzsdX64V+0r5+raev2X0gJnlgmF83DIKjkVUS
-2+c+3BnXa9LOdXks0qygJjvaFyi+5MA3DinLnmMLCQ3yAvaZYWyP3xCnGIoVrZFq
-a+YioMCmHrbByuXPoZsXcFY7Z85LQkCtSVt1dH4kkN2/JehXG099nqwMqO8FpLZZ
-xG7/U3P/slX1MMLs97nqRCRoW7Cha2ci1NBYLll+34ekhxMCAwEAAaN7MHkwDgYD
-VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFJHTpnuyIGHw
-yvC/mmh+S/JKYVrAMB8GA1UdIwQYMBaAFJHTpnuyIGHwyvC/mmh+S/JKYVrAMBYG
-A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQAeDc/k28yb
-I5MLC/LdaA+MKsW2FWF9HT+tsbtltTaQIRnnkwfU/40Ius3gzUU5z+kPqq5+kxhy
-3T646Rbau85Zw24gdNmiVKAAG5ntKoQ7XnyR/06PYyXNGLqnb6aKvbcIPoWtU/+2
-8f5hHdQ/4271aHws7dKcBNWu9V5WmxMZ3YTfnBR5lEda+DhVwHqtmun8EpSbwthD
-aLLIOHJpetr+KWUVFHQdGbO23Qg1Else0Akcn5Gzf/sKkVCVxjHE6jeo4ZwHtstG
-KMoff+ETC+DL5kMZ4CV5VaQ4HxVK7N0qiUxmijWe+EyRZseum1c0s2OEi2L52Q9K
-P4N3yD4ed4p/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 -----END CERTIFICATE-----

pscc/vars

@@ -1,4 +1,4 @@
-BROKER_ID=broker.pscc.org
+BROKER_ID=test-no-real-data.broker.samply.de
 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)"

versions/acceptance

@@ -1,6 +1,6 @@
 FOCUS_TAG=develop
 BEAM_TAG=develop
-BLAZE_TAG=0.32
+BLAZE_TAG=main
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=develop
 MTBA_TAG=develop

versions/test

@@ -1,6 +1,6 @@
 FOCUS_TAG=develop
 BEAM_TAG=develop
-BLAZE_TAG=0.32
+BLAZE_TAG=main
 POSTGRES_TAG=15.13-alpine
 TEILER_DASHBOARD_TAG=develop
-MTBA_TAG=develop
+MTBA_TAG=develop