With minichris-cube-dev.sh

.gitignore

@@ -1,3 +1,4 @@
 node_modules/
 .vagrant/
 .idea/
+/docker-compose-cube-dev.env

README.md

@@ -206,7 +206,7 @@ _miniChRIS_ does not replace `make.sh`. However, for most users
 looking for how to run _ChRIS_ and have it "just work," _miniChRIS_
 is right for you.
 
-- _miniChRIS_ has 109 lines of shell code --- *ChRIS_ultron_backEnd* has 3,200
+- _miniChRIS_ has 140 lines of shell code (103 lines in `test.sh`) --- *ChRIS_ultron_backEnd* has 3,200
 - _miniChRIS_ does not create files on host outside of named docker volumes
 - `make.sh` runs arbitrary `chmod 755` and `chmod -R 777` on the host filesystem.
 - _miniChRIS_ is fully containerized.
@@ -232,3 +232,16 @@ is right for you.
 `./minichris.sh` takes 30-60 seconds on a decent laptop (quad-core, 16 GB, SSD)
 and takes 2-3 minutes in [Github Actions' Ubuntu VMs](https://github.com/FNNDSC/miniChRIS/actions).
 It is strongly recommended that you use an SSD!
+
+
+## For [ChRIS_ultron_backEnd](https://github.com/FNNDSC/ChRIS_ultron_backEnd) Development
+
+We can use `minichris-cube-dev.sh` for [ChRIS_ultron_backEnd](https://github.com/FNNDSC/ChRIS_ultron_backEnd) development:
+
+* Copy `docker-compose-cube-dev.env.tmpl` to `docker-compose-cube-dev.env` and setup your `ChRIS_ultron_backEnd` path.
+* `./minichris-cube-dev.sh`
+* We can use the same `unmake.sh` to shutdown the docker containers.
+
+### _CAVEAT_ for mac or linux/arm64 users:
+  * Some docker images are not available yet. You need to compile the docker images on your own and tag the images as specified in `docker-compose-cube-dev.yml`.
+  * `oxidicom` seems not compilable in the aarch64 environment (because of [openjp2](https://crates.io/crates/openjp2)). Please comment out the `oxidicom` block in `docker-compose-cube-dev.yml`.

docker-compose-cube-dev.env.tmpl

@@ -0,0 +1 @@
+CUBE_SRC=${CHRIS_ULTRON_BACKEND_DIR}

docker-compose-cube-dev.yml

@@ -0,0 +1,334 @@
+# an ephemeral instance of ChRIS backend services for local development
+#
+# warning: /var/run/docker.sock is mounted into some services (notably pman)
+
+services:
+  chrisomatic:
+    image: ghcr.io/fnndsc/chrisomatic:0.8.2
+    profiles:
+      - tools
+    volumes:
+      - "./chrisomatic.yml:/chrisomatic.yml:ro"
+      - "/var/run/docker.sock:/var/run/docker.sock:rw"
+    userns_mode: host
+    depends_on:
+      - chris
+    networks:
+      - local
+
+  db_migrate:
+    image: ghcr.io/fnndsc/cube:5.0.0
+    command:
+      - sh
+      - -c
+      - pip install -r /opt/ChRIS_ultron_backEnd/requirements/production.txt && python manage.py migrate --noinput
+    env_file: secrets.env
+    volumes:
+      - chris_files:/data:rw
+      - ${CUBE_SRC}/chris_backend:/opt/app-root/src
+      - ${CUBE_SRC}:/opt/ChRIS_ultron_backEnd
+    depends_on:
+      db:
+        condition: service_healthy
+    networks:
+      - local
+
+  chris:
+    container_name: chris
+    image: ghcr.io/fnndsc/cube:5.0.0
+    command:
+      - sh
+      - -c
+      - pip install -r /opt/ChRIS_ultron_backEnd/requirements/production.txt && gunicorn -b 0.0.0.0:8000 -w 4 config.wsgi:application
+    ports:
+      - "8000:8000"
+    volumes:
+      - chris_files:/data:rw
+      - ${CUBE_SRC}/chris_backend:/opt/app-root/src
+      - ${CUBE_SRC}:/opt/ChRIS_ultron_backEnd
+    depends_on:
+      db_migrate:
+        condition: service_completed_successfully
+      queue:
+        condition: service_started
+    networks:
+      - local
+    env_file: secrets.env
+    labels:
+      org.chrisproject.role: "ChRIS_ultron_backEnd"
+      org.chrisproject.miniChRIS: "miniChRIS"
+  worker:
+    image: ghcr.io/fnndsc/cube:5.0.0
+    command:
+      - sh
+      - -c
+      - pip install -r /opt/ChRIS_ultron_backEnd/requirements/production.txt && celery -A core worker -c 4 -l info -Q main1,main2
+    volumes:
+      - chris_files:/data:rw
+      - ${CUBE_SRC}/chris_backend:/opt/app-root/src
+      - ${CUBE_SRC}:/opt/ChRIS_ultron_backEnd
+    env_file: secrets.env
+    depends_on:
+      db_migrate:
+        condition: service_completed_successfully
+      queue:
+        condition: service_started
+      pfcon:
+        condition: service_started
+    restart: unless-stopped
+    networks:
+      - local
+  worker_periodic:
+    image: ghcr.io/fnndsc/cube:5.0.0
+    command:
+      - sh
+      - -c
+      - pip install -r /opt/ChRIS_ultron_backEnd/requirements/production.txt && celery -A core worker -c 2 -l info -Q periodic
+    volumes:
+      - chris_files:/data:rw
+      - ${CUBE_SRC}/chris_backend:/opt/app-root/src
+      - ${CUBE_SRC}:/opt/ChRIS_ultron_backEnd
+    env_file: secrets.env
+    depends_on:
+      db_migrate:
+        condition: service_completed_successfully
+      queue:
+        condition: service_started
+    restart: unless-stopped
+    networks:
+      - local
+  scheduler:
+    image: ghcr.io/fnndsc/cube:5.0.0
+    command:
+      - sh
+      - -c
+      - pip install -r /opt/ChRIS_ultron_backEnd/requirements/production.txt && celery -A core beat -l info --scheduler django_celery_beat.schedulers:DatabaseScheduler
+    volumes:
+      - chris_files:/data:rw
+      - ${CUBE_SRC}/chris_backend:/opt/app-root/src
+      - ${CUBE_SRC}:/opt/ChRIS_ultron_backEnd
+    env_file: secrets.env
+    depends_on:
+      db_migrate:
+        condition: service_completed_successfully
+      queue:
+        condition: service_started
+    restart: unless-stopped
+    networks:
+      - local
+  db:
+    image: docker.io/library/postgres:16
+    env_file: secrets.env
+    restart: unless-stopped
+    volumes:
+      - db_data:/var/lib/postgresql/data
+    networks:
+      - local
+    healthcheck:
+      test: ["CMD", "pg_isready"]
+      interval: 2s
+      timeout: 4s
+      retries: 3
+      start_period: 60s
+  queue:
+    image: docker.io/library/rabbitmq:3
+    restart: unless-stopped
+    networks:
+      - local
+
+  pfcon:
+    container_name: pfcon
+    image: ghcr.io/fnndsc/pfcon:5.2.2
+    environment:
+      COMPUTE_SERVICE_URL: http://pman:5010/api/v1/
+      SECRET_KEY: secret
+      PFCON_USER: pfcon
+      PFCON_PASSWORD: pfcon1234
+      PFCON_INNETWORK: "true"
+      STORAGE_ENV: filesystem
+      STOREBASE_MOUNT: /var/local/storeBase
+    ports:
+      - "5005:5005"
+    volumes:
+      - chris_files:/var/local/storeBase
+    networks:
+      local:
+        aliases:
+          - pfcon.host
+      remote:
+    labels:
+      org.chrisproject.role: "pfcon"
+    user: "1001"
+
+  pman:
+    image: ghcr.io/fnndsc/pman:6.0.1
+    container_name: pman
+    environment:
+      CONTAINER_ENV: docker
+      CONTAINER_USER: "1001:"
+      ENABLE_HOME_WORKAROUND: "yes"
+      JOB_LABELS: "org.chrisproject.miniChRIS=plugininstance"
+      SECRET_KEY: secret
+      REMOVE_JOBS: "yes"
+    volumes:
+      - /var/run/docker.sock:/var/run/docker.sock:rw
+    depends_on:
+      - pfcon
+    ports:
+      - "5010:5010"
+    networks:
+      remote:
+    userns_mode: "host"
+    labels:
+      org.chrisproject.role: "pman"
+
+  chris_ui:
+    image: ghcr.io/fnndsc/chris_ui:20240410.445-c5ca2f65
+    command: sirv --host --single
+    environment:
+      REACT_APP_CHRIS_UI_URL: http://localhost:8000/api/v1/
+      REACT_APP_PFDCM_URL: http://localhost:4005/
+    ports:
+      - "8020:3000"
+
+  orthanc:
+    image: docker.io/jodogne/orthanc-plugins:1.12.3
+    volumes:
+      - ./orthanc.json:/etc/orthanc/orthanc.json:ro
+      - orthanc:/var/lib/orthanc/db
+    ports:
+      - "4242:4242"
+      - "8042:8042"
+    networks:
+      - pacs
+    profiles:
+      - pacs
+      - orthanc
+
+  pfdcm:
+    image: ghcr.io/fnndsc/pfdcm:3.1.22
+    container_name: pfdcm
+    environment:
+      MAX_WORKERS: 1
+    volumes:
+      - pfdcm:/home/dicom:rw
+      - ./pfdcm-services:/home/dicom/services:ro
+      - chris_files:/chris_files:rw
+    ports:
+      - "4005:4005"
+    networks:
+      - pacs
+    user: "1001"
+    profiles:
+      - pacs
+
+  oxidicom:
+    image: ghcr.io/fnndsc/oxidicom:v1.0.1
+    container_name: oxidicom
+    environment:
+      CHRIS_URL: http://chris:8000/api/v1/
+      CHRIS_USERNAME: chris
+      CHRIS_PASSWORD: chris1234
+      CHRIS_FILES_ROOT: /data
+      CHRIS_SCP_AET: ChRIS
+      CHRIS_PACS_ADDRESS: orthanc:4242
+      PORT: 11111
+      CHRIS_LISTENER_THREADS: 8
+      CHRIS_PUSHER_THREADS: 2
+      CHRIS_VERBOSE: "yes"
+      # OTEL_EXPORTER_OTLP_ENDPOINT: "http://otel-collector:4318"
+      # OTEL_RESOURCE_ATTRIBUTES: service.name=oxidicom-test
+    volumes:
+      - chris_files:/data:rw
+    ports:
+      - "11111:11111"
+    networks:
+      - pacs
+      - local
+    profiles:
+      - pacs
+  pfbridge:
+    image: docker.io/fnndsc/pfbridge:3.7.8
+    container_name: pfbridge
+    environment:
+      MAX_WORKERS: 1
+      PFLINK_USERNAME: pflink
+      PFLINK_PASSWORD: pflink1234
+      NAME: PFDCMLOCAL
+      PACSNAME: orthanc
+      CUBEANDSWIFTKEY: local
+    ports:
+      - "33333:33333"
+    networks:
+      local:
+      pflink:
+    profiles:
+      - pflink
+
+  pflink:
+    image: docker.io/fnndsc/pflink:4.0.6
+    container_name: pflink
+    restart: unless-stopped
+    environment:
+      PFDCM_NAME: "NOTPFDCMLOCAL" # work around for hard-coded edge case
+      PFLINK_MONGODB: "mongodb://pflink-db:27017"
+      PFLINK_PFDCM: "http://pfdcm:4005"
+      PFLINK_PORT: "4010"
+    ports:
+      - "4010:4010"
+    networks:
+      local:
+      pflink:
+    depends_on:
+      - pflink-db
+    profiles:
+      - pflink
+
+  pflink-db:
+    image: mongo
+    environment:
+      - PUID=1000
+      - PGID=1000
+    volumes:
+      - pflink-db-data:/data/db
+    restart: unless-stopped
+    networks:
+      pflink:
+    profiles:
+      - pflink
+
+  # Non-root container user workarounds
+
+  cube-nonroot-user-volume-fix:
+    image: docker.io/library/alpine:latest
+    volumes:
+      - chris_files:/data:rw
+    user: root
+    command: chmod g+rwx /data
+    restart: "no"
+
+  pfdcm-nonroot-user-volume-fix:
+    image: docker.io/library/alpine:latest
+    volumes:
+      - pfdcm:/home/dicom:rw
+    user: root
+    command: chown 1001 /home/dicom
+    restart: "no"
+
+networks:
+  local:
+    name: minichris-local
+  remote:
+  pacs:
+  monitoring:
+  pflink:
+
+volumes:
+  chris_files:
+    name: minichris-files
+  db_data:
+  orthanc:
+  pfdcm:
+  grafana_data:
+  openobserve_data:
+  pflink-db-data: