@js4cytoscape/ndex-client 0.3.2 → 0.4.3-alpha.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@js4cytoscape/ndex-client",
-  "version": "0.3.2",
+  "version": "0.4.3-alpha.1",
   "description": "NDEx client library",
   "repository": {
     "type": "git",
@@ -28,6 +28,6 @@
     "node": ">=12.16.1"
   },
   "dependencies": {
-    "axios": "^0.26.0"
+    "axios": "^1.3.4"
   }
 }

package/src/CyNDEx.js

@@ -20,7 +20,7 @@ class CyNDEx {
   }
 
   getNDExServer() {
-    return this._ndexServer ? this._ndexServer : 'http://public.ndexbio.org';
+    return this._ndexServer ? this._ndexServer : 'https://www.ndexbio.org';
   }
 
   setGoogleAuth(googleAuthObj) {
@@ -149,6 +149,10 @@ class CyNDEx {
     return this._httpPost('/cyndex2/v1/networks/cx', undefined, cx);
   }
 
+  postCX2NetworkToCytoscape(cx2_string, title, collection_name) {
+    return this._httpPost('/v1/networks',{ 'format': 'cx2', 'collection': collection_name, 'title':title}, cx2_string);
+  }
+
   postCytoscapeNetworkToNDEx(suid = 'current') {
     const saveParams = {
       serverUrl: this.getNDExServer() + '/v2',

package/src/NDEx.js

@@ -9,7 +9,7 @@ const CX1_HEADER = {
 class NDEx {
     constructor(hostprefix) {
       if (hostprefix === undefined || hostprefix === null || hostprefix === '') {
-        throw new Error('NDEx server endpoint base URL is required in client constructor.');
+        throw new Error('NDEx server host name or endpoint base URL is required in client constructor.');
       }
 
       // axios needs http to be at the front of the url.
@@ -17,7 +17,11 @@ class NDEx {
       // with an ambiguous reason
       let httpRegex = new RegExp("^(http|https)://", "i");
       if (!httpRegex.test(hostprefix)) {
-        throw new Error(`"http://" or "https://" must be prefixed to the input url: ${hostprefix}`);
+        // throw new Error(`"http://" or "https://" must be prefixed to the input url: ${hostprefix}`);
+        // we assume it is a host name
+        if ( hostprefix.indexOf('/') > -1 )
+             throw new Error ('"/" are not allowed in host name.');
+         hostprefix = "https://"+ hostprefix + "/v2"; 
       }
 
       this._host = hostprefix;
@@ -176,11 +180,11 @@ class NDEx {
       return this._httpPostProtectedObjAux(this._v3baseURL,URL,parameters, data);
     }
 
-    _httpPutObj(URL, parameters, data) {
+    _httpPutObjAux(prefix, URL, parameters, data) {
       let config = {
         method: 'put',
         url: URL,
-        baseURL: this.host
+        baseURL: prefix
       };
 
       this._setAuthHeader(config);
@@ -204,11 +208,28 @@ class NDEx {
       });
     }
 
+    _httpPutObj(URL,parameters, data) {
+      return this._httpPutObjAux(this.host,URL, parameters, data);
+    }
+
+    _httpPutV3Obj(URL,parameters,data) {
+      return this._httpPutObjAux(this._v3baseURL,URL,parameters,data);
+    }
+
+
     _httpDeleteObj(URL, parameters, data) {
+       return this._httpDeleteObjAux(this.host,URL,parameters, data);
+    }
+    
+    _httpDeleteV3Obj(URL, parameters) {
+       return this._httpDeleteObjAux(this._v3baseURL, URL, parameters, undefined);
+    }
+
+    _httpDeleteObjAux(prefix, URL, parameters, data) {
       let config = {
         method: 'delete',
         url: URL,
-        baseURL: this.host
+        baseURL: prefix
       };
 
       this._setAuthHeader(config);
@@ -733,5 +754,41 @@ class NDEx {
     });
   }
 
+  createCyWebWorkspace(workspace) {
+    return new Promise((resolve, reject)=> {
+      this._httpPostV3ProtectedObj('workspaces', undefined, workspace).then(
+        (response) => {
+          let uuidr = response.split('/');
+
+          let uuid = uuidr[uuidr.length - 1];
+
+          return resolve(uuid);
+        },
+        (err) => {reject(err);}
+      );
+    });
+
+  }
+
+  getCyWebWorkspace(workspaceId) {
+    return this._httpGetV3ProtectedObj('workspaces/'+ workspaceId, {});
+    }
+
+  deleteCyWebWorkspace(workspaceId) {
+    return this._httpDeleteV3Obj('workspaces/'+ workspaceId, undefined);
+  }
+
+  updateCyWebWorkspace(workspaceId, workspaceObj) {
+    return this._httpPutV3Obj('workspaces/'+workspaceId, undefined, workspaceObj);
+  }
+
+  updateCyWebWorkspaceName(workspaceId, newName) {
+    return this._httpPutV3Obj('workspaces/'+workspaceId+'/name', undefined, {'name': newName});
+  }
+
+  updateCyWebWorkspaceNetworks(workspaceId, networkIds) {
+    return this._httpPutV3Obj('workspaces/'+workspaceId+'/networkids', undefined, networkIds);
+  }
+
 }
   module.exports = { NDEx };