DICOM files

[CGDogan]

Subpullrequests: camicroscope/SlideLoader#68 camicroscope/iipImage#17

1. Allow .dcm extension
2. Use caMicroscope/image-decoders, our new repo, as the base Dockerfile that builds OpenSlide. If needed, FROM camicroscope/image-decoders can replaced with apt-get install libopenslide0.

Before merging, Tony and Nan don't have access to caMicroscope Docker so @birm could you please publish an image of currnet https://github.com/camicroscope/image-decoders to Docker Hub so that we can change the images to be downloaded from camicroscope rather than currently my repo for easy testing.

caMicroscope.yml for testing my three pullrequests:

version: '3'

services:
  mongo:
    image: mongo:4.2-bionic
    container_name: ca-mongo
    restart: always
    logging:
      options:
          max-file: "5"
          max-size: "10m"
    volumes:
      - ./db:/data/db
  back:
    build:
      context: "https://github.com/cgdogan/caracal.git#patch-2"
      args:
        viewer: "v3.10.2"
    depends_on:
      - "mongo"
    ports:
      - "4010:4010"
    container_name: ca-back
    restart: always
    logging:
      options:
          max-file: "5"
          max-size: "10m"
    volumes:
      - ./images/:/images/
      - ./config/login.html:/src/static/login.html
      - ./jwt_keys/:/src/keys/
      - ./config/routes.json:/src/routes.json
      - ./config/contentSecurityPolicy.json:/src/contentSecurityPolicy.json
    environment:
      JWK_URL: "https://www.googleapis.com/oauth2/v3/certs"
      IIP_PATH: "http://ca-iip:8080/fcgi-bin/iipsrv.fcgi"
      MONGO_URI: "mongodb://ca-mongo"
      DISABLE_SEC: "true"
      GENERATE_KEY_IF_MISSING: "true"
  iip:
    build: "https://github.com/CGDogan/iipimage.git#earlydcm"
    container_name: ca-iip
    logging:
      options:
          max-file: "5"
          max-size: "10m"
    restart: always
    volumes:
      - ./images/:/images/
  loader:
    build: "https://github.com/CGDogan/SlideLoader.git#earlydcm"
    container_name: ca-load
    restart: always
    logging:
      options:
          max-file: "5"
          max-size: "10m"
    volumes:
      - ./images/:/images/

What do you think?

[birm]

This looks good to me, I'll have to more carefully review/consider the corresponding PRs before merging though!

[birm]

Re container, is this what you expected? https://hub.docker.com/layers/camicroscope/image-decoders/latest/images/sha256-485bc08d511febb71cd7bbe7028a48259eba9a1be1d9e8430ccb61f3d722e94f?context=repo

[CGDogan]

Yes, thanks, I have now updated the subpullrequests to use it

[birm]

I think that we can merge all of these PRs now. @tcpan do you agree?