@js4cytoscape/ndex-client 0.4.3-alpha.0 → 0.4.3-alpha.10

package/package.json

@@ -1,10 +1,10 @@
 {
   "name": "@js4cytoscape/ndex-client",
-  "version": "0.4.3-alpha.0",
+  "version": "0.4.3-alpha.10",
   "description": "NDEx client library",
   "repository": {
     "type": "git",
-    "url": "https://github.com/cytoscape/js4cytoscape.git"
+    "url": "git+https://github.com/cytoscape/js4cytoscape.git"
   },
   "bugs": {
     "url": "https://github.com/cytoscape/js4cytoscape/issues"
@@ -28,6 +28,9 @@
     "node": ">=12.16.1"
   },
   "dependencies": {
-    "axios": "^0.26.0"
+    "axios": "^1.4.0"
+  },
+  "devDependencies": {
+    "@microsoft/tsdoc": "^0.14.2"
   }
 }

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

@@ -6,10 +6,13 @@ const CX1_HEADER = {
   }]
 };
 
+/**
+ * NDEx client class.
+ */
 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 +20,11 @@ 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;
@@ -94,14 +101,15 @@ class NDEx {
     }
 
     _setAuthHeader(config) {
+      
+      if (config['headers'] === undefined) {config['headers'] = {};}
+      config['headers']['setAuthHeader'] = false;
+
       if (this._authType === 'b') {
         config ['auth'] = { username: this.username,
           password: this.password};
       } else if (this.authenticationType === 'g') {
-        const idToken =  this._getIdToken();
-
-        if (config['headers'] === undefined) {config['headers'] = {};}
-        config['headers']['Authorization'] = 'Bearer ' + idToken;
+        config['headers']['Authorization'] = 'Bearer ' + this._getIdToken();
       }
     }
 
@@ -376,6 +384,32 @@ class NDEx {
       return this._httpGetProtectedObj('network/' + uuid + '/summary', parameters);
     }
 
+    getNetworkV3Summary(uuid, accessKey,fmt) {
+      let parameters =  {format:  fmt != null? fmt : "FULL"}
+
+      if (accessKey != null) {
+        parameters ['accesskey'] = accessKey;
+      }
+
+      return this._httpGetV3ProtectedObj('networks/' + uuid + '/summary', parameters);
+    }
+
+    getAttributesOfSelectedNodes(uuid, {ids: nodeIds, attributeNames: names},accessKey) {
+      let parameters = {
+      };
+
+      if (accessKey != null) {
+        parameters ['accesskey'] = accessKey;
+      }
+
+      let data = {
+        "ids": nodeIds,
+        "attributeNames": names,
+      };
+  
+      return this._httpPostV3ProtectedObj('/search/networks/' + uuid + '/nodes', parameters, data);
+    }
+
     createNetworkFromRawCX(rawCX, parameters) {
       return new Promise((resolve, reject) =>{
         this._httpPostProtectedObj('network', parameters, rawCX).then(
@@ -459,7 +493,7 @@ class NDEx {
       return this._httpPostProtectedObj('search/network', params, data);
     }
 
-    neighborhoodQuery(uuid, searchTerms, saveResult, parameters) {
+    neighborhoodQuery(uuid, searchTerms, saveResult, parameters, outputCX2 = false) {
       let params = {};
 
       if (saveResult !== undefined && saveResult === true) {params.save = true;}
@@ -480,12 +514,18 @@ class NDEx {
         if (parameters.directOnly !== undefined) {
           data.directOnly = parameters.directOnly;
         }
+        if ( parameters.nodeIds !=null) {
+          data.nodeIds = parameters.nodeIds;
+        } 
       }
+      if( outputCX2)
+        return this._httpPostV3ProtectedObj('search/network/' + uuid + '/query', params, data);
+
       return this._httpPostProtectedObj('search/network/' + uuid + '/query', params, data);
 
     }
 
-    interConnectQuery(uuid, searchTerms, saveResult, parameters) {
+    interConnectQuery(uuid, searchTerms, saveResult, parameters, outputCX2 = false) {
       let params = {};
 
       if (saveResult !== undefined && saveResult === true) {params.save = true;}
@@ -499,7 +539,13 @@ class NDEx {
         if (parameters.errorWhenLimitIsOver !== undefined) {
           data.errorWhenLimitIsOver = parameters.errorWhenLimitIsOver;
         }
+        if ( parameters.nodeIds !=null) {
+          data.nodeIds = parameters.nodeIds;
+        }
       }
+      if (outputCX2)
+         return this._httpPostV3ProtectedObj('search/networks/' + uuid + '/interconnectquery', params, data);
+         
       return this._httpPostProtectedObj('search/network/' + uuid + '/interconnectquery', params, data);
 
     }
@@ -520,6 +566,16 @@ class NDEx {
       return this._httpPostProtectedObj('batch/network/summary', parameter, uuidList);
     }
 
+    getNetworkSummariesV3ByUUIDs(uuidList, accessKey,fmt) {
+      let parameter =  {format:  fmt == undefined ? "FULL" : fmt}
+
+      if(accessKey != null) 
+        parameter['accesskey']= accessKey;
+
+      return this._httpPostV3ProtectedObj('batch/networks/summary', parameter, uuidList);
+    }
+
+
     getNetworkPermissionsByUUIDs(uuidList) {
       return this._httpPostProtectedObj('batch/network/permission', undefined, uuidList);
     }
@@ -750,15 +806,19 @@ class NDEx {
     });
   }
 
+  updateNetworkFromRawCX2(uuid, rawCX2) {
+    return this._httpPutV3Obj('networks/'+uuid, undefined, rawCX2);
+  }
+
   createCyWebWorkspace(workspace) {
     return new Promise((resolve, reject)=> {
       this._httpPostV3ProtectedObj('workspaces', undefined, workspace).then(
         (response) => {
-          let uuidr = response.split('/');
+         // let uuidr = response.split('/');
 
-          let uuid = uuidr[uuidr.length - 1];
+         // let uuid = uuidr[uuidr.length - 1];
 
-          return resolve(uuid);
+          return resolve(response);
         },
         (err) => {reject(err);}
       );
@@ -786,5 +846,19 @@ class NDEx {
     return this._httpPutV3Obj('workspaces/'+workspaceId+'/networkids', undefined, networkIds);
   }
 
+  getUserCyWebWorkspaces() {
+    return new Promise((resolve, reject) => {
+      this.getSignedInUser().then((user) => {
+        this._httpGetV3ProtectedObj('users/'+ user.externalId + '/workspaces', {}).then(
+          (workspaceArray) => {resolve(workspaceArray);}, (err) => {reject(err);}
+        );
+      }, (err) => {reject(err);});
+
+    });
+  }
+
+  signInFromIdToken(idToken) {
+   return this._httpPostV3ProtectedObj('users/signin', undefined, {idToken: idToken});
+  }
 }
   module.exports = { NDEx };