v1 mainzelliste

cce/modules/lens-compose.yml

@@ -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/id-management-compose.yml

@@ -0,0 +1,37 @@
+version: "3.7"
+
+services:
+  patientlist:
+    image: docker.verbis.dkfz.de/bridgehead/mainzelliste
+    container_name: bridgehead-patientlist
+    environment:
+      - TOMCAT_REVERSEPROXY_FQDN=${HOST}
+      - TOMCAT_REVERSEPROXY_SSL=true
+      - ML_SITE=${IDMANAGEMENT_FRIENDLY_ID}
+      - ML_DB_PASS=${PATIENTLIST_POSTGRES_PASSWORD}
+      - ML_API_KEY=${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
+      - ML_UPLOAD_API_KEY=${IDMANAGER_UPLOAD_APIKEY}
+      # Add Variables from /etc/patientlist-id-generators.env
+      - PATIENTLIST_SEEDS_TRANSFORMED
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.patientlist.rule=PathPrefix(`/patientlist`)"
+      - "traefik.http.services.patientlist.loadbalancer.server.port=8080"
+      - "traefik.http.routers.patientlist.tls=true"
+    depends_on:
+      - patientlist-db
+
+  patientlist-db:
+    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
+    container_name: bridgehead-patientlist-db
+    environment:
+      POSTGRES_USER: "mainzelliste"
+      POSTGRES_DB: "mainzelliste"
+      POSTGRES_PASSWORD: ${PATIENTLIST_POSTGRES_PASSWORD}
+    volumes:
+      - "patientlist-db-data:/var/lib/postgresql/data"
+      # NOTE: Add backups here. This is only imported if /var/lib/bridgehead/data/patientlist/ is empty!!!
+      - "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"
+
+volumes:
+  patientlist-db-data:

itcc/modules/id-management-setup.sh

@@ -0,0 +1,54 @@
+#!/bin/bash -e
+
+function idManagementSetup() {
+	if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
+		log INFO "id-management setup detected -- will start id-management (mainzelliste)."
+		OVERRIDE+=" -f ./itcc/modules/id-management-compose.yml"
+
+		# Auto Generate local Passwords
+		PATIENTLIST_POSTGRES_PASSWORD="$(echo \"id-management-module-db-password-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+		IDMANAGER_LOCAL_PATIENTLIST_APIKEY="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+
+		# Transform Seeds Configuration to pass it to the Mainzelliste Container
+		PATIENTLIST_SEEDS_TRANSFORMED="$(declare -p PATIENTLIST_SEEDS | tr -d '\"' | sed 's/\[/\[\"/g' | sed 's/\]/\"\]/g')"
+
+		# Ensure old ids are working !!!
+		export IDMANAGEMENT_FRIENDLY_ID=$(legacyIdMapping "$SITE_ID")
+
+	fi
+}
+
+# Transform into single string array, e.g. 'dktk-test' to 'dktk test'
+# Usage: transformToSingleStringArray 'dktk-test' -> 'dktk test'
+function transformToSingleStringArray() {
+	echo "${1//-/ }";
+}
+
+# Ensure all Words are Uppercase
+# Usage: transformToUppercase 'dktk test' -> 'Dktk Test'
+function transformToUppercase() {
+	result="";
+	for word in $1; do
+		result+=" ${word^}";
+	done
+	echo "$result";
+}
+
+# Handle all execeptions from the norm (e.g LMU, TUM)
+# Usage: applySpecialCases 'Muenchen Lmu Test' -> 'Muenchen LMU Test'
+function applySpecialCases() {
+	result="$1";
+	result="${result/Lmu/LMU}";
+	result="${result/Tum/TUM}";
+	result="${result/Dktk Test/Teststandort}";
+	echo "$result";
+}
+
+# Transform current siteids to legacy version
+# Usage: legacyIdMapping "dktk-test" -> "DktkTest"
+function legacyIdMapping() {
+	single_string_array=$(transformToSingleStringArray "$1");
+	uppercase_string=$(transformToUppercase "$single_string_array");
+	normalized_string=$(applySpecialCases "$uppercase_string");
+	echo "$normalized_string" | tr -d ' '
+}

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 +1,46 @@
 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:
       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

nngm/docker-compose.yml

@@ -22,8 +22,7 @@ services:
       - "traefik.http.routers.blaze_nngm.tls=true"
 
   focus:
-    #image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
-    image: ghcr.io/samply/focus:feature-nngm-v2
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
     container_name: bridgehead-focus
     environment:
     - API_KEY=${FOCUS_BEAM_SECRET_SHORT}