xOpat Deployment

To deploy xOpat, we need to configure it statically,

1. Clone repository and install development dependencies:

   git clone https://github.com/RationAI/xopat.git
   cd xopat
   npm install
   

2. Create env.json in env directory (can be also created - but unpersonalised - by using grunt env):

   Note

   This env.json file is suitable for WSI-Server. If you have your own image server you need to configure your own.

   env.json

   {
   "core": {
       // This configuration file supports JSON with comments
       "gateway": "/",
       // Active configuration key from 'client'
       "active_client": "localhost",
       "client": {
           "localhost": {
               // Viewer url, so that it is accessible at domain+path url
               "domain": "http://localhost:8000",
               "path": "/",
               // The default image server used. Configures an OpenSeadragon protocol using here URL of the service
               "image_group_server": "http://localhost:8080",
               "image_group_protocol": "`${path}/v3/slides/info?slide_id=${data}`",
               "image_group_preview": "`${path}/v3/slides/thumbnail/max_size/250/250?slide_id=${data}`",
               "data_group_server": "http://localhost:8080",
               // This endpoint needs to ask for array of data items (get me tile level 5 x3 y0 for this slide list)
               "data_group_protocol": "`${path}/v3/files/info?paths=${data.join(\",\")}`",
               "headers": {},
               "js_cookie_expire": 365,
               "js_cookie_path": "/",
               "js_cookie_same_site": "",
               "js_cookie_secure": "",
               "secureMode": false
           }
       },
       // Setup can configure much more default parameters for the viewer
       "setup": {
           "locale": "en",
           "theme": "auto"
       },
       // OpenSeadragon library origin
       "openSeadragonPrefix": "https://cdn.jsdelivr.net/npm/openseadragon@4.1.1/build/openseadragon/",
       "openSeadragon": "openseadragon.min.js"
   },
   // We do not re-define any plugin configuration
   "plugins": {},
   // We force-load module for communication with WSI-Service
   "modules": {
       "empaia-wsi-tile-source": {  // the module id
           "permaLoad": true        // the built-in parameter for force-loading
       }
   }
   }
   

   3. run server node:

   npm run s-node
   

Now you should see xOpat running. However, to open the viewer, you must tell it what data is to be viewed in a what way, and possibly also other things (active plugins and their configuration, etc.).

Accessing WSIs

The simples way of opening a slide is through URL parameters.

1. Go to image server deployment and inspect "cases" to the url: http://localhost:8080/v3/cases
2. Fetch desired case ID and use it to get its slides: http://localhost:8080/v3/cases/slides?case_id=*CASE_ID
3. Find desired slide ID and add it to the xOpat deployment url: http://localhost:9000/?slides=*SLIDE_ID*

Now you should have working xOpat instance.