Merge pull request #108 from RationAI/development

Improve module for wsi-service communication.

CHANGELOG.md

@@ -3,6 +3,9 @@
 The changelog file describes changes made since v2.0.0, which made significant changes
 to the versions 1.x.x.
 
+### Unreleased 2.1.1
+**Features:** standalone wsi tile source module.
+
 ### 2.1.0
 **Features:** new system for module/plugin building, improvements of annotation listing features,
 support for generic annotation visual style changes.

modules/empaia-wsi-tile-source/README.md

@@ -1,24 +1,3 @@
 # Standalone WSI Service
 
-Implementation of OpenSeadragon Tile Source access to the standalone WSI service.
-
-> [!CAUTION]
-> This module collides with different empaia slide service access (e.g. `EmpationAPI`) - the protocols used
-> are the same and only one will be used (without user control over which one).
-
-Modified by RationAI, the WSI service can read proprietary WSI file formats
-in the standalone mode, accessing WSIs by their standalone IDs (generated via the service local path mapper),
-or accessing the files directly by a file path (must replace `/` chars with `>` for `/slides` endpoint).
-
-Also supports multifile access on the API extension `/files`.
-
-### Usage
-
-You need to provide an URL to the WSI server that uses empaia API, for example:
-````json
-   "image_group_server": "http://localhost:8080",
-   "image_group_protocol": "`${path}/v3/batch/info?slides=${data}`",
-   "image_group_preview": "`${path}/v3/batch/thumbnail/max_size/250/250?slides=${data}`",
-   "data_group_server": "http://localhost:8080",
-   "data_group_protocol": "`${path}/v3/batch/info?slides=${data.join(\",\")}`",
-````
+Deprecated. Use rationai-wsi-tile-source instead.

modules/empaia-wsi-tile-source/tile-source.js

@@ -26,7 +26,7 @@ OpenSeadragon.EmpaiaStandaloneV3TileSource = class extends OpenSeadragon.TileSou
     supports( data, url ) {
         if (url && Array.isArray(data)) {
             //multi-tile or single tile access
-            let match = url.match(/^(\/?[^\/].*\/v3\/batch)\/info/i);
+            let match = url.match(/^(\/?[^\/].*\/v3\/files)\/info/i);
             if (match) {
                 data = data || [{}];
                 data[0].tilesUrl = match[1];
@@ -159,11 +159,13 @@ OpenSeadragon.EmpaiaStandaloneV3TileSource = class extends OpenSeadragon.TileSou
     }
 
     _getInfo(url, tilesUrl) {
-        fetch(url).then(res => {
+        fetch(url).then(async res => {
+            const text = await res.text();
+            const json = JSON.parse(text);
             if (res.status !== 200) {
-                throw new HTTPError("Empaia standalone failed to fetch image info!", res, res.error);
+                throw new HTTPError("Empaia standalone failed to fetch image info!", json, res.error);
             }
-            return res.json();
+            return json;
         }).then(imageInfo => {
             const data = this.configure(imageInfo, url, null);
             // necessary TileSource props that wont get set manually
@@ -208,7 +210,7 @@ OpenSeadragon.EmpaiaStandaloneV3TileSource = class extends OpenSeadragon.TileSou
         level = this.maxLevel-level; //OSD assumes max level is biggest number, query vice versa,
 
         if (this.multifetch) {
-            //endpoint batch/tile/level/[L]/tile/[X]/[Y]/?paths=path,list,separated,by,commas
+            //endpoint files/tile/level/[L]/tile/[X]/[Y]/?paths=path,list,separated,by,commas
             return `${tiles}/tile/level/${level}/tile/${x}/${y}?slides=${this.fileId}`
         }
         //endpoint slides/[SLIDE]/tile/level/[L]/tile/[X]/[Y]/

modules/rationai-wsi-tile-source/README.md

@@ -0,0 +1,29 @@
+# Standalone WSI Service
+
+Implementation of OpenSeadragon Tile Source access to the standalone WSI service.
+
+Modified by RationAI, the WSI service can read proprietary WSI file formats
+in the standalone mode, accessing WSIs by their IDs (dependent on the mapper usage).
+
+Also supports multifile access on the API extension `/files`.
+
+### Usage
+Configure the default viewer ENV
+````json
+   "image_group_server": "http://localhost:8080",
+   "image_group_protocol": "{url: `$${path}/v3/files/info?paths=$${data}`, type: 'empaia-standalone'}",
+   "image_group_preview": "`${path}/v3/batch/thumbnail/max_size/250/250?slides=${data}`",
+   "data_group_server": "http://localhost:8080",
+   "data_group_protocol": "{url:`$${path}/v3/files/info?paths=$${data.join(\",\")}`, type: 'empaia-standalone'}",
+````
+or provide particular strings in the ``protocol`` for sessions.
+
+You can also just set an URL to the WSI server, for example:
+````json
+   "image_group_server": "http://localhost:8080",
+   "image_group_protocol": "`${path}/v3/batch/info?slides=${data}`",
+   "image_group_preview": "`${path}/v3/batch/thumbnail/max_size/250/250?slides=${data}`",
+   "data_group_server": "http://localhost:8080",
+   "data_group_protocol": "`${path}/v3/batch/info?slides=${data.join(\",\")}`",
+````
+But this approach has its limitations.

modules/rationai-wsi-tile-source/tile-source.js

@@ -1,12 +1,12 @@
 // noinspection JSUnresolvedVariable
 
 /**
- * @class EmpaiaStandaloneV3TileSource
+ * @class RationaiStandaloneV3TileSource
  * @memberof OpenSeadragon
  * @extends OpenSeadragon.TileSource
  * @param {object} options configuration either empaia info response or list of these objects
  */
-OpenSeadragon.EmpaiaStandaloneV3TileSource = class extends OpenSeadragon.TileSource {
+OpenSeadragon.RationaiStandaloneV3TileSource = class extends OpenSeadragon.TileSource {
 
     constructor(options) {
         super(options);
@@ -52,7 +52,7 @@ OpenSeadragon.EmpaiaStandaloneV3TileSource = class extends OpenSeadragon.TileSou
 
         if (!url || !Array.isArray(data) || typeof data !== "object") return false;
         //multi-tile or single tile access
-        let match = url.match(/^(\/?[^\/].*\/v3\/batch)\/info/i);
+        let match = url.match(/^(\/?[^\/].*\/v3\/files)\/info/i);
         if (match) {
             data = data || [{}];
             data[0].tilesUrl = match[1];
@@ -199,7 +199,7 @@ OpenSeadragon.EmpaiaStandaloneV3TileSource = class extends OpenSeadragon.TileSou
     getImageInfo(url) {
         if (!this._handlesOwnImageLoadLogics) return super.getImageInfo(url);
 
-        let match = url.match(/^(\/?[^\/].*\/v3\/batch)\/info/i);
+        let match = url.match(/^(\/?[^\/].*\/v3\/files)\/info/i);
         if (match) {
             this._setDownloadHandler(true);
             return this._getInfo(url, match[1]);
@@ -215,11 +215,13 @@ OpenSeadragon.EmpaiaStandaloneV3TileSource = class extends OpenSeadragon.TileSou
     _getInfo(url, tilesUrl) {
         fetch(url, {
             headers: this.ajaxHeaders || {}
-        }).then(res => {
+        }).then(async res => {
+            const text = await res.text();
+            const json = JSON.parse(text);
             if (res.status !== 200) {
-                throw new HTTPError("Empaia standalone failed to fetch image info!", res, res.error);
+                throw new HTTPError("Empaia standalone failed to fetch image info!", json, res.error);
             }
-            return res.json();
+            return json;
         }).then(imageInfo => {
             const data = this.configure(imageInfo, url, null);
             // necessary TileSource props that wont get set manually
@@ -264,11 +266,11 @@ OpenSeadragon.EmpaiaStandaloneV3TileSource = class extends OpenSeadragon.TileSou
         level = this.maxLevel-level; //OSD assumes max level is biggest number, query vice versa,
 
         if (this.multifetch) {
-            //endpoint batch/tile/level/[L]/tile/[X]/[Y]/?paths=path,list,separated,by,commas
-            return `${tiles}/tile/level/${level}/tile/${x}/${y}?slides=${this.fileId}`
+            //endpoint files/tile/level/[L]/tile/[X]/[Y]/?paths=id,list,separated,by,commas
+            return `${tiles}/tile/level/${level}/tile/${x}/${y}?paths=${this.fileId}`
         }
-        //endpoint slides/[SLIDE]/tile/level/[L]/tile/[X]/[Y]/
-        return `${tiles}/tile/level/${level}/tile/${x}/${y}?slide=${this.fileId}`
+        //endpoint slides/tile/level/[L]/tile/[X]/[Y]/?slide_id=id
+        return `${tiles}/tile/level/${level}/tile/${x}/${y}?slide_id=${this.fileId}`
     }
 
     _setDownloadHandler(isMultiplex) {