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": "/",
                   // Named slide-protocol registry. Each entry is a backtick template
                   // resolving a scalar DataID to a tile-source URL; the server URL is
                   // embedded directly in the template. The `default_*_protocol` keys
                   // pick which entry is used by default for background / visualization
                   // slides. Protocols can also be added at runtime by plugins via
                   // `window.SLIDE_PROTOCOLS.register(...)` — e.g. the dicom plugin
                   // registers a "dicom" factory protocol that builds a DICOMWebTileSource.
                   "slide_protocols": {
                       "wsi_service": "`http://localhost:8080/v3/slides/info?slide_id=${data}`"
                   },
                   "default_background_protocol":    "wsi_service",
                   "default_visualization_protocol": "wsi_service",
                   "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"
           }
       },
       // We do not re-define any plugin configuration
       "plugins": {},
       // We force-load module for communication with WSI-Service
       "modules": {
           "rationai-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.