feature: add osiris2fhir in cce and minor fixes

WIP: enable osiris2fhir in PSCC for GR (#372 )
enable osiris2fhir in PSCC for GR
2026-04-17 18:30:14 +02:00 · 2026-03-17 13:35:58 +01:00 · 2026-02-24 12:09:39 +01:00 · 2026-02-20 09:27:47 +01:00 · 2026-02-10 16:04:33 +01:00 · 2026-02-10 11:21:36 +01:00
17 changed files with 108 additions and 42 deletions
--- a/bbmri/modules/directory-sync.sh
+++ b/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
--- a/cce/modules/lens-compose.yml
+++ b/cce/modules/lens-compose.yml
@@ -3,6 +3,8 @@ services:
  lens:
    container_name: lens_federated-search
    image: samply/cce-explorer:main
+    environment:
+      PUBLIC_SPOT_URL: https://${HOST}/prod
    labels:
      - "traefik.http.services.lens.loadbalancer.server.port=3000"
      - "traefik.enable=true"
--- a/cce/modules/osiris2fhir-setup.sh
+++ b/cce/modules/osiris2fhir-setup.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+if [ -n "$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
--- a/ccp/docker-compose.yml
+++ b/ccp/docker-compose.yml
@@ -22,8 +22,7 @@ services:
      - "traefik.http.routers.blaze_ccp.tls=true"

  focus:
-    #image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
-    image: ghcr.io/samply/focus:fix-exporter-v2
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
    container_name: bridgehead-focus
    environment:
    - API_KEY=${FOCUS_BEAM_SECRET_SHORT}
--- a/itcc/docker-compose.yml
+++ b/itcc/docker-compose.yml
@@ -15,7 +15,7 @@ services:
      - "blaze-data:/app/data"
    labels:
      - "traefik.enable=true"
-      - "traefik.http.routers.blaze_itcc.rule=PathPrefix(`/itcc-localdatamanagement`)"
+      - "traefik.http.routers.blaze_itcc.rule=Host(`${HOST}`) && 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"
@@ -34,7 +34,6 @@ services:
      EPSILON: 0.28
      QUERIES_TO_CACHE: '/queries_to_cache.conf'
      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
-      CQL_PROJECTS_ENABLED: "itcc"
    volumes:
      - /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
    depends_on:
--- a/itcc/modules/itcc-omics-ingest.sh
+++ b/itcc/modules/itcc-omics-ingest.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+if [ -n "$ENABLE_OMICS" ];then
+  OVERRIDE+=" -f ./$PROJECT/modules/itcc-omics-ingest.yaml"
+  GENERATE_API_KEY="$(generate_simple_password 'omics')"
+fi
--- a/itcc/modules/itcc-omics-ingest.yaml
+++ b/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"
--- a/itcc/modules/lens-compose.yml
+++ b/itcc/modules/lens-compose.yml
@@ -1,33 +1,47 @@
 version: "3.7"
 services:
-  landing:
-    container_name: lens_federated-search
-    image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID}
+  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: ${PUBLIC_ENVIRONMENT}
    labels:
      - "traefik.enable=true"
-      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
-      - "traefik.http.services.landing.loadbalancer.server.port=80"
-      - "traefik.http.routers.landing.tls=true"
+      - "traefik.http.routers.itcc.rule=Host(`${HOST}`) && PathPrefix(`/`)"
+      - "traefik.http.routers.itcc.entrypoints=websecure"
+      - "traefik.http.services.itcc.loadbalancer.server.port=3000"
+      - "traefik.http.routers.itcc.tls=true"

  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_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: ${FOCUS_BEAM_SECRET_SHORT}
--- a/itcc/vars
+++ b/itcc/vars
@@ -6,6 +6,7 @@ FOCUS_RETRY_COUNT=${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 $PROJECT/modules/*.sh
 do
--- a/kr/docker-compose.yml
+++ b/kr/docker-compose.yml
@@ -12,7 +12,8 @@ services:
      BASE_URL: "http://bridgehead-kr-blaze:8080"
      JAVA_TOOL_OPTIONS: "-Xmx${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: ${BLAZE_CQL_CACHE_CAP:-32}
      ENFORCE_REFERENTIAL_INTEGRITY: "false"
    volumes:
      - "blaze-data:/app/data"
--- a/kr/modules/export-and-qb.curl-templates
+++ b/kr/modules/export-and-qb.curl-templates
@@ -1,6 +0,0 @@
-# Full Excel Export
-curl --location --request POST 'https://${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'
--- a/kr/modules/lens-compose.yml
+++ b/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.services.landing.loadbalancer.server.port=80"
-      - "traefik.http.routers.landing.tls=true"
+      - "traefik.http.routers.lens.rule=Host(`${HOST}`)"
+      - "traefik.http.routers.lens.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_ID: ${SITE_ID}
-      BEAM_BROKER_ID: ${BROKER_ID}
-      BEAM_APP_ID: "focus"
-      PROJECT_METADATA: "kr_supervisors"
+      BEAM_PROXY_URL: http://beam-proxy:8081
+      BEAM_APP_ID: "spot.${SITE_ID}.${BROKER_ID}"
+      CORS_ORIGIN: "https://${HOST}"
+      SITES: ${SITES}
+      TRANSFORM: LENS
+      PROJECT: kr
+      BIND_ADDR: 0.0.0.0:8055
    depends_on:
      - "beam-proxy"
    labels:
      - "traefik.enable=true"
-      - "traefik.http.services.spot.loadbalancer.server.port=8080"
+      - "traefik.http.services.spot.loadbalancer.server.port=8055"
      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
+      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowheaders=content-type"
      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${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"
+      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth"
+
+  beam-proxy:
+    environment:
+      APP_spot_KEY: ${FOCUS_BEAM_SECRET_SHORT}
--- a/kr/modules/obds2fhir-rest-compose.yml
+++ b/kr/modules/obds2fhir-rest-compose.yml
@@ -3,7 +3,7 @@ version: "3.7"
 services:
  obds2fhir-rest:
    container_name: bridgehead-obds2fhir-rest
-    image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
+    image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main
    environment:
      IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
      MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
--- a/kr/vars
+++ b/kr/vars
@@ -3,7 +3,7 @@ BROKER_URL=https://${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

--- a/lib/functions.sh
+++ b/lib/functions.sh
@@ -327,7 +327,7 @@ function sync_secrets() {
        -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
        -e PROXY_ID=$proxy_id \
        -e BROKER_URL=$broker_url \
-        -e OIDC_PROVIDER=secret-sync-central.test-secret-sync.$broker_id \
+        -e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
        -e SECRET_DEFINITIONS=$secret_sync_args \
        docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest

--- a/pscc/modules/osiris2fhir-compose.yml
+++ b/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: ${LOCAL_SALT}
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.osiris2fhir.rule=PathPrefix(`/osiris2fhir`)"
+      - "traefik.http.middlewares.osiris2fhir_strip.stripprefix.prefixes=/osiris2fhir"
+      - "traefik.http.services.osiris2fhir.loadbalancer.server.port=8080"
+      - "traefik.http.routers.osiris2fhir.tls=true"
+      - "traefik.http.routers.osiris2fhir.middlewares=osiris2fhir_strip,auth"
--- a/pscc/modules/osiris2fhir-setup.sh
+++ b/pscc/modules/osiris2fhir-setup.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+if [ -n "$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
Author	SHA1	Message	Date
Pierre Delpy	5e9590736b	feature: add osiris2fhir in cce and minor fixes	2026-03-17 13:35:58 +01:00
Pierre Delpy	c1de9b8314	WIP: enable osiris2fhir in PSCC for GR (#372 ) enable osiris2fhir in PSCC for GR	2026-02-24 12:09:39 +01:00
DavidCroftDKFZ	9d3ec957a2	Activate Directory token login (#371 ) Right now, Directory sync will only be activated if a username has been specified. It also needs to run if a login token has been specified, hence the change in this commit.	2026-02-20 09:27:47 +01:00
Martin Jurk	7a9f80537b	sites moved to etc itcc.comf (#369 )	2026-02-10 16:04:33 +01:00
Pierre Delpy	bff06a6bb0	fix kr deployment (#370 )	2026-02-10 11:21:36 +01:00
Martin Jurk	6923ead6ce	feat: itcc lens2 (#365 )	2026-01-28 14:28:09 +01:00
Manoj Waikar	7dc9e2e663	Changes to make deployed CCE explorer work properly. (#368 ) * Changes to make deployed CCE explorer work properly. In the lens environment section in services: - add PUBLIC_SPOT_URL value	2026-01-13 10:42:10 +01:00
Jan	85cfc2514d	update beam proxy server used for oauth enrollment (#366 )	2025-12-11 11:33:29 +01:00