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DevOps Documentation

Prequisites

  • Yarn
  • Docker
  • nginx
  • nodejs
  • mysql

How we deploy the application on the VMs:

The deploy process will be explain to deploy on linux virtual machines, if you are using azure, aws… the process will be diferente. Consult the Deployment | OHIF to see more information.

To deploy the dockers on VM some adjusts have to be done, in the dockers compose or in the configurations of the connection to the servides.

The deploy diagram is the following:

Deploy the Server

First thing to do, is put the server up. The server will be on a docker container, as the following:

version: '3.5'

services:
  orthanc:
    image: jodogne/orthanc-plugins:1.9.7
    hostname: orthanc
    volumes:
      # Nginx config
      - ./config/nginx.conf:/usr/local/openresty/nginx/conf/nginx.conf:ro
      # Config
      - ./config/orthanc.json:/etc/orthanc/orthanc.json:ro
      # Persist data
      - ./volumes/orthanc-db/:/var/lib/orthanc/db/
    ports:
      - '8082:4242' # DICOM
      - '8083:8042' # Web
    restart: unless-stopped
    networks:
      - all

networks:
  all:
    ipam:
      driver: default
      config:f        - subnet: 10.1.0.0/16

In our server machine, we only have 10 ports open to the network, because of that in our docker-compose file we configure the orthanc server ports to be 8082, and 8083, that are mapped to 8762 to 8769 in mednat network. Because of virtual machines configuration the last 7 lines of the docker-compose file are required, as well as the following configuration on the /etc/docker/daemon.json file:

{ "bip": "10.2.0.1/16” }

After this, we are able to run the docker-compose file, and have the Orthanc Server online. The server is accessed from outside through http://mednat.ieeta.pt:8763, on UA network, as explained before.

The next step is do add DICOM images to the server, for that we used the Welcome to The Cancer Imaging Archive - The Cancer Imaging Archive (TCIA) to download some studies to put on our server.

In order to resolve, CORS problems that eventually happen, it is important to have a nginx configuration file that give Cross-Origin Resource Sharing. So we install nginx on virtual machine, and put the following nginx configuration file. And then the CORS problem may be resolved.

server {
    listen 8085;

    # CORS Magic
    add_header 'Access-Control-Allow-Origin' '*';
    add_header 'Access-Control-Allow_Credentials' 'true';
    add_header 'Access-Control-Allow-Headers' 'Authorization,Accept,Origin,DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range';
    add_header 'Access-Control-Allow-Methods' 'GET,POST,OPTIONS,PUT,DELETE,PATCH';

    location / {

        if ($request_method = 'OPTIONS') {
            add_header 'Access-Control-Allow-Origin' '*';
            add_header 'Access-Control-Allow_Credentials' 'true';
            add_header 'Access-Control-Allow-Headers' 'Authorization,Accept,Origin,DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range>
            add_header 'Access-Control-Allow-Methods' 'GET,POST,OPTIONS,PUT,DELETE,PATCH';
            add_header 'Access-Control-Max-Age' 1728000;
            add_header 'Content-Type' 'text/plain charset=UTF-8';
            add_header 'Content-Length' 0;
            return 204;
        }

        proxy_pass         http://127.0.0.1:8083;
        proxy_set_header   Host $host;
        proxy_set_header   X-Real-IP $remote_addr;
        proxy_set_header   X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header   X-Forwarded-Host $server_name;

        # CORS Magic
        add_header 'Access-Control-Allow-Origin' '*';
        add_header 'Access-Control-Allow_Credentials' 'true';
        add_header 'Access-Control-Allow-Headers' 'Authorization,Accept,Origin,DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Ran>
        add_header 'Access-Control-Allow-Methods' 'GET,POST,OPTIONS,PUT,DELETE,PATCH';
    }
}

Deploy the Viewer

To deploy the Viewer on the virtual machine, there are some steps to take: Configure connection to Server, at platform/viewer/public/config/docker_openresty-orthanc.js Run the docker-compose file, at platform/viewer/.recipes/OpenResty-Orthanc/docker-compose.yml.

As explained before, we have our server running on http://mednat.ieeta.pt:8765, so the Viewer needs to know where is suppose to query the studies. As said before, at platform/viewer/public/config/ docker_openresty-orthanc.js, configuration file should look like this:

window.config = {
  routerBasename: '/',
  showStudyList: true,
  servers: {
    // This is an array, but we'll only use the first entry for now
    dicomWeb: [
      {
        name: 'Orthanc',
        wadoUriRoot: 'http://mednat.ieeta.pt:8765/wado',
         qidoRoot: 'http://mednat.ieeta.pt:8765/dicom-web',
         wadoRoot: 'http://mednat.ieeta.pt:8765/dicom-web',
        qidoSupportsIncludeField: false,
        imageRendering: 'wadors',
        thumbnailRendering: 'wadors',
        // requestOptions: {
        // undefined to use JWT + Bearer auth
        // auth: 'orthanc:orthanc',
        // },
      },
    ],
  },
};

After this, we are able to see our docker-compose file, firstly we build the React application with a Dockerfile, and then using nginx put it on 8084 port, which in mednat means 8754 port.

version: '3.5'

services:
  # Exposed server that's handling incoming web requests
  # Underlying image: openresty/openresty:alpine-fat
  ohif_viewer:
    build:
      # Project root
      context: ./../../../../
      # Relative to context
      dockerfile: ./platform/viewer/.recipes/OpenResty-Orthanc/dockerfile
    image: webapp:latest
    container_name: webapp
    volumes:
      # Nginx config
      - ./config/nginx.conf:/usr/local/openresty/nginx/conf/nginx.conf:ro
      # Logs
      - ./logs/nginx:/var/logs/nginx
    ports:
      - '8083:443' # SSL
      - '8084:80' # Web
    restart: on-failure
    networks:
      - all

networks:
 all:
  ipam:
   driver: default
   config:
    - subnet: 10.1.0.0/16

The docker-compose is supported by a Dockerfile, in the same path, that will build the application.

# Stage 1: Build the application

FROM node:lts-slim as builder

RUN mkdir /usr/src/app
WORKDIR /usr/src/app

ENV APP_CONFIG=config/docker_openresty-orthanc.js
ENV PATH /usr/src/app/node_modules/.bin:$PATH

COPY package.json /usr/src/app/package.json
COPY yarn.lock /usr/src/app/yarn.lock

ADD . /usr/src/app/
RUN yarn install
RUN yarn run build

# Stage 2: Bundle the built application into a Docker container
# which runs openresty (nginx) using Alpine Linux
# LINK: https://hub.docker.com/r/openresty/openresty
FROM openresty/openresty:1.19.9.1-4-alpine-fat

RUN mkdir /var/log/nginx
RUN apk add --no-cache openssl
RUN apk add --no-cache openssl-dev
RUN apk add --no-cache git
RUN apk add --no-cache gcc

RUN luarocks install lua-resty-openidc

RUN luarocks install lua-resty-jwt
RUN luarocks install lua-resty-session
RUN luarocks install lua-resty-http

# Copy build output to image
COPY --from=builder /usr/src/app/platform/viewer/dist /var/www/html

ENTRYPOINT ["/usr/local/openresty/nginx/sbin/nginx", "-g", "daemon off;"]

The nginx file is the following:

worker_processes 2;
error_log   /var/logs/nginx/mydomain.error.log;
pid /var/run/nginx.pid;
include /usr/share/nginx/modules/*.conf; # See /usr/share/doc/nginx/README.dynamic.

events {
    worker_connections 1024; ## Default: 1024
    use epoll; # http://nginx.org/en/docs/events.html
    multi_accept on; # http://nginx.org/en/docs/ngx_core_module.html#multi_accept
}

# Core Modules Docs:
# http://nginx.org/en/docs/http/ngx_http_core_module.html
http {
    include    '/usr/local/openresty/nginx/conf/mime.types';
    default_type application/octet-stream;

    keepalive_timeout 65;
    keepalive_requests 100000;
    tcp_nopush on;
    tcp_nodelay on;

    # lua_ settings
    #
    lua_package_path '/usr/local/openresty/lualib/?.lua;;';
    lua_shared_dict discovery 1m; # cache for discovery metadata documents
    lua_shared_dict jwks 1m;      # cache for JWKs
    # lua_ssl_trusted_certificate /etc/ssl/certs/ca-certificates.crt;

    variables_hash_max_size 2048;
    server_names_hash_bucket_size 128;
    server_tokens off;

    resolver 8.8.8.8 valid=30s ipv6=off;
    resolver_timeout 11s;

    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
                      '$status $body_bytes_sent "$http_referer" '
                      '"$http_user_agent" "$http_x_forwarded_for"';

    # Nginx `listener` block
    server {
        listen [::]:80 default_server;
        listen 80;
        # listen      443 ssl;
        access_log  /var/logs/nginx/mydomain.access.log;

        # Domain to protect
        server_name 127.0.0.1 localhost; # mydomain.com;
        proxy_intercept_errors off;
        # ssl_certificate /etc/letsencrypt/live/mydomain.co.uk/fullchain.pem;
        # ssl_certificate_key /etc/letsencrypt/live/mydomain.co.uk/privkey.pem;
        gzip on;
        gzip_types text/css application/javascript application/json image/svg+xml;
        gzip_comp_level 9;
        etag on;

        # https://github.com/bungle/lua-resty-session/issues/15
        set $session_check_ssi off;
        lua_code_cache on;
        set $session_secret Eeko7aeb6iu5Wohch9Loo1aitha0ahd1;
        set $session_storage cookie;

        server_tokens off; # Hides server version num

        # Reverse Proxy for `orthanc` admin
        #
        location /pacs-admin/ {

          proxy_http_version 1.1;

          proxy_set_header Host               $host;
          proxy_set_header X-Real-IP          $remote_addr;
          proxy_set_header X-Forwarded-For    $proxy_add_x_forwarded_for;
          proxy_set_header X-Forwarded-Proto  $scheme;

          expires           0;
          add_header        Cache-Control private;

          proxy_pass        http://mednat.ieeta.pt:8765;
        }

        # Reverse Proxy for `orthanc` APIs (including DICOMWeb)
        #
        location /pacs/ {

          proxy_http_version 1.1;

          proxy_set_header Host               $host;
          proxy_set_header X-Real-IP          $remote_addr;
          proxy_set_header X-Forwarded-For    $proxy_add_x_forwarded_for;
          proxy_set_header X-Forwarded-Proto  $scheme;

          expires           0;
          add_header        Cache-Control private;

          proxy_pass        http://mednat.ieeta.pt:8765/;

          # By default, this endpoint is protected by CORS (cross-origin-resource-sharing)
          # You can add headers to allow other domains to request this resource.
          # See the "Updating CORS Settings" example below
        }

        # Do not cache sw.js, required for offline-first updates.
        location /sw.js {
          add_header Cache-Control "no-cache";
          proxy_cache_bypass $http_pragma;
          proxy_cache_revalidate on;
          expires off;
          access_log off;
        }

        # Single Page App
        # Try files, fallback to index.html
        #
        location / {
          alias  /var/www/html/;
          index index.html;
          try_files $uri $uri/ /index.html;
          add_header Cache-Control "no-store, no-cache, must-revalidate";
        }

        # EXAMPLE: Redirect server error pages to the static page /40x.html
        #
        # error_page 404 /404.html;
        #     location = /40x.html {
        # }

        # EXAMPLE: Redirect server error pages to the static page /50x.html
        #
        # error_page 500 502 503 504 /50x.html;
        #    location = /50x.html {
        # }
    }
}

Now, we are able to run docker-compose file, and after that the Viewer will be accessed from http://mednat.ieeta.pt/8754.