Merge pull request #287 from tm16-medma/patch-1

Update ovis-compose.yml

README.md

@@ -23,7 +23,6 @@ This repository is the starting point for any information and tools you will nee
     - [File structure](#file-structure)
     - [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed)
     - [Loading data](#loading-data)
-    - [Metadata feedback](#metadata-feedback)
 4. [Things you should know](#things-you-should-know)
     - [Auto-Updates](#auto-updates)
     - [Auto-Backups](#auto-backups)
@@ -155,8 +154,7 @@ Pay special attention to:
 Clone the bridgehead repository:
 ```shell
 sudo mkdir -p /srv/docker/
-sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
-sudo git checkout metadata_fb # Only needed if you want to use metadata feedback
+sudo git clone -b main https://github.com/samply/bridgehead.git /srv/docker/bridgehead
 ```
 
 Then, run the installation script:
@@ -349,26 +347,6 @@ Normally, you will need to build your own ETL to feed the Bridgehead. However, t
 
 You can find the profiles for generating FHIR in [Simplifier](https://simplifier.net/bbmri.de/~resources?category=Profile).
 
-### Metadata feedback
-
-The Bridgehead comes with a tool that allows you to associate metadata with samples. Multiple arbitrary text strings are allowed. A typical use case would be publications based on research using a sample. Here, one could lay down the DOI of the publication in the sample.
-
-Full details of the system can be found [here](https://github.com/samply/feedback-deployment). To avail yourself of this feature, you need to
-
-- Use the bbmri project.
-- work with the ```metadata_fb``` branch of the Bridgehead repository.
-- Build the feedback-agent Docker container (more details [here](https://github.com/samply/feedback-agent/)).
-- Build the feedback-agent-ui Docker container (more details [here](https://github.com/samply/feedback-agent-ui/)).
-
-The following extra environment variables need to be added to your ```/etc/bridgehead/bbmri.conf``` file:
-
-``` code
-ENABLE_EXPORTER=true
-ENABLE_FEEDBACK_AGENT=true
-FEEDBACK_HUB_URL=<URL for central feedback hub backend API>
-FOCUS_RETRY_COUNT=256
-```
-
 ## Things you should know
 
 ### Auto-Updates

bbmri/modules/eric-compose.yml

@@ -22,7 +22,6 @@ services:
       BROKER_URL: ${ERIC_BROKER_URL}
       PROXY_ID: ${ERIC_PROXY_ID}
       APP_focus_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
-      APP_feedback-agent_KEY: ${FEEDBACK_AGENT_BEAM_SECRET}
       PRIVKEY_FILE: /run/secrets/proxy.pem
       ALL_PROXY: http://forward_proxy:3128
       TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs

bbmri/modules/exporter-compose.yml

@@ -1,67 +0,0 @@
-version: "3.7"
-
-services:
-  exporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
-    container_name: bridgehead-ccp-exporter
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      LOG_LEVEL: "INFO"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      CROSS_ORIGINS: "https://${HOST}"
-      EXPORTER_DB_USER: "exporter"
-      EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}"
-      EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
-      HTTP_RELATIVE_PATH: "/ccp-exporter"
-      SITE: "${SITE_ID}"
-      HTTP_SERVLET_REQUEST_SCHEME: "https"
-      OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
-      - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
-      - "traefik.http.routers.exporter_ccp.tls=true"
-      - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
-      - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
-    volumes:
-      - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
-
-  exporter-db:
-    image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
-    container_name: bridgehead-ccp-exporter-db
-    environment:
-      POSTGRES_USER: "exporter"
-      POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}"
-      POSTGRES_DB: "exporter"
-    volumes:
-      # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
-      - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
-
-  reporter:
-    image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
-    container_name: bridgehead-ccp-reporter
-    environment:
-      JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
-      LOG_LEVEL: "INFO"
-      CROSS_ORIGINS: "https://${HOST}"
-      HTTP_RELATIVE_PATH: "/ccp-reporter"
-      SITE: "${SITE_ID}"
-      EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
-      EXPORTER_URL: "http://exporter:8092"
-      LOG_FHIR_VALIDATION: "false"
-      HTTP_SERVLET_REQUEST_SCHEME: "https"
-
-    # In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
-    # However, in the first executions in the CCP sites, this volume seems to be very important. A report is
-    # a process that can take several hours, because it depends on the exporter.
-    # There is a risk that the bridgehead restarts, losing the already created export.
-
-    volumes:
-      - "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
-      - "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
-      - "traefik.http.routers.reporter_ccp.tls=true"
-      - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
-      - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"

bbmri/modules/exporter-setup.sh

@@ -1,9 +0,0 @@
-#!/bin/bash -e
-
-if [ "$ENABLE_EXPORTER" == true ]; then
-  log INFO "Exporter setup detected -- will start Exporter service."
-  OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml"
-  EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
-  EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
-  POSTGRES_TAG=15.6-alpine
-fi

bbmri/modules/exporter.md

@@ -1,15 +0,0 @@
-# Exporter and Reporter
-
-
-## Exporter
-The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
-It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
-
-## Exporter-DB
-It is a database to save queries for its execution in the exporter. 
-The exporter manages also the different executions of the same query in through the database.
-
-## Reporter
-This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
-It is compatible with different template engines as Groovy, Thymeleaf,...
-It is perfect to generate a document as our traditional CCP quality report.

bbmri/modules/feedback-agent-compose.yml

@@ -1,59 +0,0 @@
-version: "3.7"
-
-services:
-  feedback-agent-ui:
-    image: "samply/feedback-agent-ui"
-    environment:
-      - VUE_APP_EXPORTER_URL=https://localhost/ccp-exporter
-      - VUE_APP_FB_BACKEND_URL=http://localhost:8072
-    labels:
-     - traefik.enable=true
-     # HTTPS
-     - traefik.http.routers.feedback_agent_ui_ccp_https.rule=PathPrefix(`/ccp-feedback-agent-ui`)
-     - traefik.http.services.feedback_agent_ui_ccp_https.loadbalancer.server.port=8096
-     - traefik.http.routers.feedback_agent_ui_ccp_https.entrypoints=websecure
-     - traefik.http.routers.feedback_agent_ui_ccp_https.tls=true
-  feedback-agent:
-    image: "samply/feedback-agent"
-    environment:
-      - SPRING_DATASOURCE_URL=jdbc:postgresql://feedback-agent-db:5432/compose-postgres
-      - SPRING_DATASOURCE_USERNAME=compose-postgres
-      - SPRING_DATASOURCE_PASSWORD=${FEEDBACK_AGENT_DB_PASSWORD}
-      - SPRING_JPA_HIBERNATE_DDL_AUTO=update
-      - BEAM_PROXY_URI=http://beam-proxy-eric:8081
-      - FEEDBACK_HUB_URL=${FEEDBACK_HUB_URL}
-      - BLAZE_BASE_URL=http://blaze:8080/fhir
-      - FEEDBACK_AGENT_SECRET=${FEEDBACK_AGENT_BEAM_SECRET}
-      - FEEDBACK_AGENT_BEAM_ID=feedback-agent.${ERIC_PROXY_ID}
-      - FEEDBACK_HUB_BEAM_ID=feedback-hub.feedback-central.${ERIC_BROKER_ID}
-      - EXPORTER_API_KEY=${EXPORTER_API_KEY}
-      - CORS_ALLOWED_ORIGINS="https://${HOST}
-    networks:
-      # Only needed for local testing.
-      - feedback
-      - default
-    labels:
-     - traefik.enable=true
-     # HTTPS
-     - traefik.http.routers.feedback_agent_ccp_https.rule=PathPrefix(`/ccp-feedback-agent`)
-     - traefik.http.services.feedback_agent_ccp_https.loadbalancer.server.port=8072
-     - traefik.http.routers.feedback_agent_ccp_https.entrypoints=websecure
-     - traefik.http.middlewares.feedback_agent_ccp_https_strip.stripprefix.prefixes=/ccp-feedback-agent
-     - traefik.http.routers.feedback_agent_ccp_https.middlewares=feedback_agent_ccp_https_strip
-     - traefik.http.routers.feedback_agent_ccp_https.tls=true
-  feedback-agent-db:
-    image: 'postgres:13.1-alpine'
-    container_name: feedback-agent-db
-    environment:
-      - POSTGRES_USER=compose-postgres
-      - POSTGRES_PASSWORD=${FEEDBACK_AGENT_DB_PASSWORD}
-
-# This is needed when you run both agent and hub locally in a test
-# environment. Not necessary in production, though it probably won't
-# cause any problems.
-networks:
-  # Network to connect agent and hub.
-  feedback:
-    name: feedback
-    driver: bridge
-

bbmri/modules/feedback-agent-setup.sh

@@ -1,8 +0,0 @@
-#!/bin/bash
-
-if [ "$ENABLE_FEEDBACK_AGENT" == true ]; then
-  OVERRIDE+=" -f ./$PROJECT/modules/feedback-agent-compose.yml"
-  FEEDBACK_AGENT_BEAM_SECRET="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-  FEEDBACK_AGENT_DB_PASSWORD="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-fi
-

bbmri/modules/feedback-agent.md

@@ -1,6 +0,0 @@
-# Metadata feedback agent
-
-This component can be used to choose the sample to be associated
-with a given piece of metadata (generally the ID of a publication
-relating to research done with the sample).
-

ccp/modules/ovis-compose.yml

@@ -0,0 +1,112 @@
+version: '3.7'
+
+services:
+
+  ovis-traefik-forward-auth:
+      image: quay.io/oauth2-proxy/oauth2-proxy:latest
+      environment:
+        - http_proxy=${http_proxy:-http://forward_proxy:3128}
+        - https_proxy=${https_proxy:-http://forward_proxy:3128}
+        - OAUTH2_PROXY_PROVIDER=oidc
+        - OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
+        - OAUTH2_PROXY_OIDC_ISSUER_URL=${OAUTH_ISSUER_URL}
+        - OAUTH2_PROXY_CLIENT_ID=${OAUTH_CLIENT_ID}
+        - OAUTH2_PROXY_CLIENT_SECRET=${OAUTH_CLIENT_SECRET}
+        - OAUTH2_PROXY_COOKIE_SECRET=${AUTHENTICATION_SECRET}
+        - OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST:-localhost}
+        - OAUTH2_PROXY_COOKIE_REFRESH=4m
+        - OAUTH2_PROXY_COOKIE_EXPIRE=24h
+        - OAUTH2_PROXY_HTTP_ADDRESS=:4180
+        - OAUTH2_PROXY_REVERSE_PROXY=true
+        - OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST:-localhost}
+        - OAUTH2_PROXY_UPSTREAMS=static://202
+        - OAUTH2_PROXY_EMAIL_DOMAINS=*
+        #- OAUTH2_PROXY_ALLOWED_GROUPS=app-ovis
+        #- OAUTH2_PROXY_ERRORS_TO_INFO_LOG=true
+        - OAUTH2_PROXY_CODE_CHALLENGE_METHOD=S256
+        # For some reason, login.verbis.dkfz.de does not have a "groups" scope but this comes automatically through a
+        # scope called microprofile-jwt. Remove the following line once we have a "groups" scope.
+        - OAUTH2_PROXY_SCOPE=openid profile email
+        # Pass Authorization Header and some user information to spot
+        - OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
+        - OAUTH2_PROXY_SET_XAUTHREQUEST=true
+      labels:
+        - "traefik.enable=true"
+        - "traefik.http.middlewares.ovis-traefik-forward-auth.forwardauth.address=http://ovis-traefik-forward-auth:4180"
+        - "traefik.http.middlewares.ovis-traefik-forward-auth.forwardauth.authResponseHeaders=Authorization, X-Forwarded-User, X-Auth-Request-User, X-Auth-Request-Email"
+        - "traefik.http.services.ovis-traefik-forward-auth.loadbalancer.server.port=4180"
+        - "traefik.http.routers.oauth2.rule=Host(`${HOST:-localhost}`) && PathPrefix(`/oauth2-ovis/`)"
+        - "traefik.http.routers.oauth2.tls=true"
+
+  fhir-transformer:
+    image: docker.verbis.dkfz.de/ovis/adt-mon-gql-fhir-transformer:latest
+    restart: on-failure
+    environment:
+      - FHIR_SERVER_URL=${FHIR_SERVER_URL:-http://bridgehead-ccp-blaze:8080/fhir}
+      - FHIR_USERNAME=${FHIR_USERNAME}
+      - FHIR_PASSWORD=${FHIR_PASSWORD}
+    volumes:
+      - /var/cache/bridgehead/ccp/ovis/shared_data:/app/output
+
+  mongo:
+    image: mongo:${MONGO_VER:-latest}
+    restart: always
+    command: mongod
+      - /var/cache/bridgehead/ccp/ovis/mongo/init/init.js:/docker-entrypoint-initdb.d/init.js
+
+  backend:
+    image: docker.verbis.dkfz.de/ovis/adt-mon-gql-backend:latest
+    restart: always
+    user: root
+    working_dir: /app
+    environment:
+      - APOLLO_PORT=${APOLLO_PORT:-4001}
+      - CREDOS_PORT=${CREDOS_PORT:-4000}
+      - MONGO_VER=latest
+      - CORS_ORIGIN=*
+      - DB=${DB:-onc_test}
+      - ADRESS=${ADRESS:-mongodb://mongo:27017}
+    depends_on:
+      - mongo
+      - fhir-transformer
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:${APOLLO_PORT:-4001}/health"]
+      interval: 5s
+      timeout: 3s
+      retries: 5
+      start_period: 10s
+    entrypoint: >
+      sh -c "
+        # First run the initialization process
+        while [ ! -f /shared/omock.json ]; do
+          echo 'Waiting for omock.json...'
+          sleep 5
+        done;
+        mkdir -p ./prep &&
+        cp /shared/omock.json ./prep/omock.json &&
+        node ./mgDB/prep/preprocessor.mjs &&
+        echo 'Processing complete' &&
+        exec node --watch index.js"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.ovis-backend.rule=Host(`${HOST:-localhost}`) && PathPrefix(`/graphql`)"
+      - "traefik.http.routers.ovis-backend.tls=true"
+      - "traefik.http.services.ovis-backend.loadbalancer.server.port=${APOLLO_PORT:-4001}"
+    volumes:
+      - /var/cache/bridgehead/ccp/ovis/shared_data:/shared
+
+  frontend:
+    image: docker.verbis.dkfz.de/ovis/adt-mon-gql-frontend:latest
+    restart: always
+    environment:
+      - PUBLIC_GRAPHQL_URL=https://${HOST:-localhost}/graphql
+    depends_on:
+      backend:
+        condition: service_healthy
+    working_dir: /app
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.ovis-frontend.tls=true"
+      - "traefik.http.routers.ovis-frontend.rule=Host(`${HOST:-localhost}`)"
+      - "traefik.http.routers.ovis-frontend.middlewares=traefik-forward-auth"
+      - "traefik.http.services.ovis-frontend.loadbalancer.server.port=5173"

ccp/modules/ovis-setup.sh

@@ -0,0 +1,108 @@
+#!/bin/bash -e
+
+if [ -n "$ENABLE_OVIS" ];then
+    # Setup MongoDB initialization directory if it doesn't exist
+    mkdir -p "/var/cache/bridgehead/ccp/ovis/mongo/init"
+    
+    # Generate MongoDB initialization script directly
+    cat > "/var/cache/bridgehead/ccp/ovis/mongo/init/init.js" << 'EOF'
+db = db.getSiblingDB("test_credos");
+db.createCollection("user");
+db.user.insertMany([{
+    "_id": "OVIS-Root",
+    "createdAt": new Date(),
+    "createdBy": "system",
+    "role": "super-admin",
+    "status": "active",
+    "pseudonymization": false,
+    "darkMode": false,
+    "colorTheme": "CCCMunich",
+    "language":  "de",
+}]);
+
+db = db.getSiblingDB("onc_test");
+db.createCollection("user");
+db.user.insertMany([{
+    "_id": "OVIS-Root",
+    "createdAt": new Date(),
+    "createdBy": "system",
+    "role": "super-admin",
+    "status": "active",
+    "pseudonymization": false,
+    "darkMode": false,
+    "colorTheme": "CCCMunich",
+    "language":  "de",
+}]);
+
+db.ops.insertMany([
+    {"OPSC_4":"1-40","OPS_Gruppen_Text":"Biopsie ohne Inzision an Nervensystem und endokrinen Organen "},
+    {"OPSC_4":"1-44","OPS_Gruppen_Text":"Biopsie ohne Inzision an den Verdauungsorganen"},
+    {"OPSC_4":"1-40","OPS_Gruppen_Text":"Biopsie ohne Inzision an anderen Organen und Geweben"},
+    {"OPSC_4":"1-50","OPS_Gruppen_Text":"Biopsie an Haut, Mamma, Knochen und Muskeln durch Inzision"},
+    {"OPSC_4":"1-51","OPS_Gruppen_Text":"Biopsie an Nervengewebe, Hypophyse, Corpus pineale durch Inzision und Trepanation von Schädelknochen "},
+    {"OPSC_4":"1-55","OPS_Gruppen_Text":"Biopsie an anderen Verdauungsorganen, Zwerchfell und (Retro-)Peritoneum durch Inzision "},
+    {"OPSC_4":"1-56","OPS_Gruppen_Text":"Biopsie an Harnwegen und männlichen Geschlechtsorgannen durch Inzision"},
+    {"OPSC_4":"1-58","OPS_Gruppen_Text":"Biopsie an anderen Organen durch Inzision "},
+    {"OPSC_4":"1-63","OPS_Gruppen_Text":"Diagnostische Endoskopie des oberen Verdauungstraktes"},
+    {"OPSC_4":"1-65","OPS_Gruppen_Text":"Diagnostische Endoskopie des unteren Verdauungstraktes"},
+    {"OPSC_4":"1-69","OPS_Gruppen_Text":"Diagnostische Endoskopie durch Inzision und intraoperativ "},
+    {"OPSC_4":"5-01","OPS_Gruppen_Text":"Inzision (Trepanation) und Exzision an Schädel, Gehirn und Hirnhäuten"},
+    {"OPSC_4":"5-02","OPS_Gruppen_Text":"Andere Operationen  an Schädel, Gehirn und Hirnhäuten"},
+    {"OPSC_4":"5-03","OPS_Gruppen_Text":"Operationen an Rückenmark, Rückenmarkhäuten und Spinalkanal"},
+    {"OPSC_4":"5-05","OPS_Gruppen_Text":"Andere Operationen an Nerven und Nervenganglien "},
+    {"OPSC_4":"5-06","OPS_Gruppen_Text":"Operationen an Schilddrüse und Nebenschilddrüse "},
+    {"OPSC_4":"5-07","OPS_Gruppen_Text":"Operationen an anderen endokrinen Drüsen "},
+    {"OPSC_4":"5-20","OPS_Gruppen_Text":"Andere Operationen an Mittel- und Innenohr "},
+    {"OPSC_4":"5-25","OPS_Gruppen_Text":"Operationen an der Zunge "},
+    {"OPSC_4":"5-31","OPS_Gruppen_Text":"Andere Larynxoperationen und Operationen an der Trachea "},
+    {"OPSC_4":"5-32","OPS_Gruppen_Text":"Exzision und Resektion an Lunge und Bronchus "},
+    {"OPSC_4":"5-33","OPS_Gruppen_Text":"Andere Operationen an Lunge und Bronchus"},
+    {"OPSC_4":"5-34","OPS_Gruppen_Text":"Operationen an Brustwand, Pleura, Mediastinum und Zwerchfell "},
+    {"OPSC_4":"5-37","OPS_Gruppen_Text":"Rhythmuschirurgie und andere Operationen an Herz und Perikard"},
+    {"OPSC_4":"5-38","OPS_Gruppen_Text":"Inzision, Exzision und Verschluß von Blutgefäßen "},
+    {"OPSC_4":"5-39","OPS_Gruppen_Text":"Andere Operationen an Blutgefäßen "},
+    {"OPSC_4":"5-40","OPS_Gruppen_Text":"Operationen am Lymphgewebe "},
+    {"OPSC_4":"5-41","OPS_Gruppen_Text":"Operationen an Milz und Knochenmark "},
+    {"OPSC_4":"5-42","OPS_Gruppen_Text":"Operationen am Ösophagus "},
+    {"OPSC_4":"5-43","OPS_Gruppen_Text":"Inzision, Exzision und Resektion am Magen "},
+    {"OPSC_4":"5-44","OPS_Gruppen_Text":"Erweiterte Magenresektion und andere Operationen am Magen "},
+    {"OPSC_4":"5-45","OPS_Gruppen_Text":"Inzision, Exzision, Resektion und Anastomose an Dünn- und Dickdarm "},
+    {"OPSC_4":"5-46","OPS_Gruppen_Text":"Andere Operationen an Dünn- und Dickdarm "},
+    {"OPSC_4":"5-47","OPS_Gruppen_Text":"Operationen an der Appendix "},
+    {"OPSC_4":"5-48","OPS_Gruppen_Text":"Operationen am Rektum "},
+    {"OPSC_4":"5-49","OPS_Gruppen_Text":"Operationen am Anus "},
+    {"OPSC_4":"5-50","OPS_Gruppen_Text":"Operationen an der Leber "},
+    {"OPSC_4":"5-51","OPS_Gruppen_Text":"Operationen an Gallenblase und Gallenwegen "},
+    {"OPSC_4":"5-52","OPS_Gruppen_Text":"Operationen am Pankreas "},
+    {"OPSC_4":"5-53","OPS_Gruppen_Text":"Verschluß abdominaler Hernien "},
+    {"OPSC_4":"5-54","OPS_Gruppen_Text":"Andere Operationen in der Bauchregion "},
+    {"OPSC_4":"5-55","OPS_Gruppen_Text":"Operationen an der Niere "},
+    {"OPSC_4":"5-56","OPS_Gruppen_Text":"Operationen am Ureter "},
+    {"OPSC_4":"5-57","OPS_Gruppen_Text":"Operationen an der Harnblase "},
+    {"OPSC_4":"5-59","OPS_Gruppen_Text":"Andere Operationen an den Harnorganen "},
+    {"OPSC_4":"5-60","OPS_Gruppen_Text":"Operationen an Prostata und Vesiculae seminales "},
+    {"OPSC_4":"5-61","OPS_Gruppen_Text":"Operationen an Skrotum und Tunica vaginalis testis"},
+    {"OPSC_4":"5-62","OPS_Gruppen_Text":"Operationen am Hoden "},
+    {"OPSC_4":"5-65","OPS_Gruppen_Text":"Operationen am Ovar "},
+    {"OPSC_4":"5-68","OPS_Gruppen_Text":"Inzision, Exzision und Exstirpation des Uterus "},
+    {"OPSC_4":"5-70","OPS_Gruppen_Text":"Operationen an Vagina und Douglasraum "},
+    {"OPSC_4":"5-71","OPS_Gruppen_Text":"Operationen an der Vulva "},
+    {"OPSC_4":"5-85","OPS_Gruppen_Text":"Operationen an Muskeln, Sehnen, Faszien und Schleimbeuteln"},
+    {"OPSC_4":"5-87","OPS_Gruppen_Text":"Exzision und Resektion der Mamma "},
+    {"OPSC_4":"5-89","OPS_Gruppen_Text":"Operationen an Haut und Unterhaut "},
+    {"OPSC_4":"5-90","OPS_Gruppen_Text":"Operative Wiederherstellung und Rekonstruktion von Haut und Unterhaut"},
+    {"OPSC_4":"5-91","OPS_Gruppen_Text":"Andere Operationen an Haut und Unterhaut "},
+    {"OPSC_4":"5-93","OPS_Gruppen_Text":"Angaben zum Transplantat und zu verwendeten Materialien"},
+    {"OPSC_4":"5-98","OPS_Gruppen_Text":"Spezielle Operationstechniken und Operationen bei speziellen Versorgungssituationen "},
+    {"OPSC_4":"8-13","OPS_Gruppen_Text":"Manipulation am Harntrakt"},
+    {"OPSC_4":"8-14","OPS_Gruppen_Text":"Therapeutische Kathedirisierung, Aspiration, Punktion und Spülung "},
+    {"OPSC_4":"8-15","OPS_Gruppen_Text":"Therapeutische Aspiration und Entleerung durch Punktion "},
+    {"OPSC_4":"8-17","OPS_Gruppen_Text":"Spülung (Lavage) "},
+    {"OPSC_4":"8-19","OPS_Gruppen_Text":"Verbände "},
+    {"OPSC_4":"8-77","OPS_Gruppen_Text":"Maßnahmen im Rahmen der Reanimation "},
+    {"OPSC_4":"8-92","OPS_Gruppen_Text":"Neurologisches Monitoring "},
+])
+EOF
+    
+    OVERRIDE+=" -f ./$PROJECT/modules/ovis-compose.yml"
+fi

dhki/vars

@@ -17,4 +17,12 @@ do
 done
 
 idManagementSetup
-obds2fhirRestSetup
+obds2fhirRestSetup
+
+for module in modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done
+
+transfairSetup

modules/transfair-compose.yml

@@ -0,0 +1,51 @@
+
+services:
+  transfair:
+    image: docker.verbis.dkfz.de/cache/samply/transfair:latest
+    container_name: bridgehead-transfair
+    environment:
+      # NOTE: Those 3 variables need only to be passed if their set, otherwise transfair will complain about empty url values
+      - INSTITUTE_TTP_URL
+      - INSTITUTE_TTP_API_KEY
+      - PROJECT_ID_SYSTEM
+      - FHIR_REQUEST_URL=${FHIR_REQUEST_URL}
+      - FHIR_INPUT_URL=${FHIR_INPUT_URL}
+      - FHIR_OUTPUT_URL=${FHIR_OUTPUT_URL:-http://blaze:8080}
+      - FHIR_REQUEST_CREDENTIALS=${FHIR_REQUEST_CREDENTIALS}
+      - FHIR_INPUT_CREDENTIALS=${FHIR_INPUT_CREDENTIALS}
+      - FHIR_OUTPUT_CREDENTIALS=${FHIR_OUTPUT_CREDENTIALS}
+      - EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID}
+      - DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
+      - RUST_LOG=${RUST_LOG:-info}
+    volumes:
+      - /var/cache/bridgehead/${PROJECT}/transfair:/transfair
+
+  transfair-input-blaze:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    container_name: bridgehead-transfair-input-blaze
+    environment:
+      BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx1024m"
+      DB_BLOCK_CACHE_SIZE: 1024
+      CQL_EXPR_CACHE_SIZE: 8
+      ENFORCE_REFERENTIAL_INTEGRITY: "false"
+    volumes:
+      - "transfair-input-blaze-data:/app/data"
+    profiles: ["transfair-input-blaze"]
+
+  transfair-request-blaze:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
+    container_name: bridgehead-transfair-requests-blaze
+    environment:
+      BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx1024m"
+      DB_BLOCK_CACHE_SIZE: 1024
+      CQL_EXPR_CACHE_SIZE: 8
+      ENFORCE_REFERENTIAL_INTEGRITY: "false"
+    volumes:
+      - "transfair-request-blaze-data:/app/data"
+    profiles: ["transfair-request-blaze"]
+
+volumes:
+  transfair-input-blaze-data:
+  transfair-request-blaze-data:

modules/transfair-setup.sh

@@ -0,0 +1,22 @@
+#!/bin/bash -e
+
+function transfairSetup() {
+    if [[ -n "$INSTITUTE_TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
+        echo "Starting transfair."
+	    OVERRIDE+=" -f ./modules/transfair-compose.yml"
+	    if [ -n "$FHIR_INPUT_URL" ]; then
+		    log INFO "TransFAIR input fhir store set to external $FHIR_INPUT_URL"
+	    else
+		    log INFO "TransFAIR input fhir store not set writing to internal blaze"
+		    FHIR_INPUT_URL="http://transfair-input-blaze:8080"
+		    OVERRIDE+=" --profile transfair-input-blaze"
+	    fi
+	    if [ -n "$FHIR_REQUEST_URL" ]; then
+		    log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL"
+	    else
+		    log INFO "TransFAIR request fhir store not set writing to internal blaze"
+		    FHIR_REQUEST_URL="http://transfair-requests-blaze:8080"
+		    OVERRIDE+=" --profile transfair-request-blaze"
+	    fi
+    fi
+}