@js4cytoscape/ndex-client 0.5.0-alpha.8 → 0.6.0-alpha.1

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@js4cytoscape/ndex-client",
-  "version": "0.5.0-alpha.8",
-  "description": "NDEx client library",
+  "version": "0.6.0-alpha.1",
+  "description": "NDEx client library - Modern TypeScript implementation",
   "repository": {
     "type": "git",
     "url": "git+https://github.com/cytoscape/js4cytoscape.git"
@@ -10,36 +10,94 @@
     "url": "https://github.com/cytoscape/js4cytoscape/issues"
   },
   "homepage": "https://github.com/cytoscape/js4cytoscape",
-  "main": "./dist/ndexClient.common.js",
-  "module": "src/index.js",
+  "main": "./dist/index.js",
+  "module": "./dist/index.mjs",
+  "umd": "./dist/index.umd.js",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/index.mjs",
+      "require": "./dist/index.js"
+    }
+  },
   "files": [
     "dist",
-    "src"
+    "src",
+    "README.md",
+    "LICENSE"
   ],
   "scripts": {
-    "watch:js": "webpack --watch",
-    "build": "webpack --mode=development",
-    "build-prod": "webpack --mode=production",
-    "test": "nyc mocha --require @babel/register"
+    "dev": "tsup --watch",
+    "build": "tsup",
+    "build:docs": "typedoc",
+    "docs:api": "npm run build:docs",
+    "docs:site": "cd docs-site && npm install && npm run build",
+    "docs:serve": "cd docs-site && npm run start",
+    "docs:build": "npm run docs:api && npm run docs:site",
+    "docs:clean": "rimraf docs docs-site/build docs-site/docs/api",
+    "test": "npm run test:unit",
+    "test:unit": "jest --config jest.unit.config.js",
+    "test:integration": "jest --config jest.integration.config.js",
+    "test:all": "npm run test:unit && npm run test:integration",
+    "test:watch": "npm run test:unit -- --watch",
+    "test:coverage": "npm run test:unit -- --coverage",
+    "test:ci": "npm run test:all -- --coverage",
+    "debug:integration": "node --inspect-brk ./node_modules/.bin/jest --config jest.integration.config.js --runInBand --no-cache",
+    "debug:unit": "node --inspect-brk ./node_modules/.bin/jest --config jest.unit.config.js --runInBand --no-cache",
+    "debug:client": "node --inspect-brk debug-response.js",
+    "lint": "eslint src __tests__ --ext .ts,.js --fix",
+    "format": "prettier --write \"src/**/*.{ts,js}\" \"__tests__/**/*.{ts,js}\"",
+    "type-check": "tsc --noEmit",
+    "clean": "rimraf dist coverage",
+    "prepare": "npm run build",
+    "changeset": "changeset",
+    "release": "changeset publish"
   },
   "author": "Jing Chen",
   "license": "MIT",
   "engines": {
-    "node": ">=12.16.1"
+    "node": ">=16.0.0"
   },
+  "keywords": [
+    "ndex",
+    "network",
+    "cytoscape",
+    "bioinformatics",
+    "graph",
+    "cx2",
+    "typescript"
+  ],
   "dependencies": {
-    "axios": "^1.6.8"
+    "axios": "^1.11.0"
   },
   "devDependencies": {
-    "@microsoft/tsdoc": "^0.14.2",
-    "@babel/core": "^7.14.6",
-    "@babel/preset-env": "^7.14.5",
-    "@babel/register": "^7.14.5",
-    "babel-plugin-istanbul": "^6.0.0"
-  },
-  "babel": {
-    "presets": [
-      "@babel/preset-env"
-    ]
+    "@changesets/cli": "^2.27.1",
+    "@types/jest": "^29.5.12",
+    "@types/node": "^20.11.25",
+    "@typescript-eslint/eslint-plugin": "^7.1.1",
+    "@typescript-eslint/parser": "^7.1.1",
+    "eslint": "^8.57.0",
+    "eslint-config-prettier": "^9.1.0",
+    "eslint-plugin-prettier": "^5.1.3",
+    "glob": "^7.2.0",
+    "jest": "^29.7.0",
+    "jest-environment-jsdom": "^29.7.0",
+    "nock": "^13.5.4",
+    "prettier": "^3.2.5",
+    "rimraf": "^5.0.5",
+    "ts-jest": "^29.1.2",
+    "tsup": "^8.0.2",
+    "typedoc": "^0.25.12",
+    "typedoc-plugin-markdown": "^3.17.1",
+    "typescript": "^5.4.2"
+  },
+  "peerDependencies": {
+    "cytoscape": "^3.0.0"
+  },
+  "peerDependenciesMeta": {
+    "cytoscape": {
+      "optional": true
+    }
   }
 }

package/src/CyNDEx.js.bak

@@ -0,0 +1,178 @@
+const CY_REST_BASE_URL = 'http://127.0.0.1';
+
+import { default as axios } from 'axios';
+
+class CyNDEx {
+
+  constructor(port = 1234) {
+    this._port = port;
+  }
+  get port() { return this._port; }
+
+  static get cyRestBaseURL() {
+    return CY_REST_BASE_URL;
+  }
+
+  setNDExServer(ndexServer) {
+    if (ndexServer !== undefined && ndexServer != null && ndexServer !== '') {
+      this._ndexServer = ndexServer;
+    }
+  }
+
+  getNDExServer() {
+    return this._ndexServer ? this._ndexServer : 'https://www.ndexbio.org';
+  }
+
+  setGoogleAuth(googleAuthObj) {
+    if (googleAuthObj !== undefined) {
+      this._googleAuth = googleAuthObj;
+      this._authType = 'g'; // valid values are 'g','b' or undefined
+    }
+  }
+
+  setAuthToken(authToken) {
+    if (authToken !== undefined ) {
+      this._authToken = authToken;
+      this._authType = 'g'; // valid values are 'g','b' or undefined
+    }
+  }
+
+  setBasicAuth(username, password) {
+    if (username !== undefined && username != null && username !== '') {
+      this._username = username;
+      this._password = password;
+      this._authType = 'b';
+    }
+  }
+
+  cyRestURL() {
+    return CY_REST_BASE_URL + ':' + this._port;
+  }
+
+  _getIdToken() {
+    return this._authToken ? this._authToken : this._googleAuth.getAuthInstance().currentUser.get().getAuthResponse().id_token;
+  }
+
+  _getAuthorizationFields() {
+    switch (this._authType) {
+      case 'b' : return {
+        username : this._username,
+        password : this._password
+      };
+      case 'g' : return {
+        idToken : this._getIdToken()
+      };
+      default : return {};
+    }
+  }
+
+  _httpGet(url) {
+
+    const baseURL = this.cyRestURL();
+
+    return new Promise(function (resolve, reject) {
+      axios({
+        method: 'get',
+        url: url,
+        baseURL: baseURL
+      }).then((response) => {
+        if (response.status === 200) {
+          return resolve(response.data);
+        }
+        return reject(response);
+      },
+        (response) => { return reject(response); }
+      );
+    });
+  }
+
+  _httpPut(url, parameters, data) {
+    return this._http('put', url, parameters, data);
+  }
+
+  _httpPost(url, parameters, data) {
+    return this._http('post', url, parameters, data);
+  }
+
+  _http(method, url, parameters, data) {
+
+    const baseURL = this.cyRestURL();
+
+    let config = {
+      method: method,
+      url: url,
+      baseURL: baseURL
+    };
+
+    if (parameters !== undefined) {
+      config['params'] = parameters;
+    }
+
+    config.data = data;
+    return new Promise(function (resolve, reject) {
+      axios(config).then((response) => {
+        if (response.status >= 200 && response.status <= 299) {
+          return resolve(response.data);
+        }
+        return reject(response);
+      },
+        (response) => {
+          return reject(response);
+        }
+      );
+    });
+
+  }
+
+  getCyNDExStatus() {
+    return this._httpGet('/cyndex2/v1');
+  }
+
+  getCytoscapeNetworkSummary(suid = 'current') {
+    return this._httpGet('/cyndex2/v1/networks/' + suid);
+  }
+
+  postNDExNetworkToCytoscape(uuid, accessKey, createView = undefined) {
+    const importParams = {
+      serverUrl: this.getNDExServer() + '/v2',
+      uuid: uuid,
+      accessKey: accessKey,
+      createView: createView
+    };
+
+    const authorizationFields = this._getAuthorizationFields();
+
+    return this._httpPost('/cyndex2/v1/networks', undefined, Object.assign(importParams, authorizationFields));
+  }
+
+  postCXNetworkToCytoscape(cx) {
+    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',
+    };
+
+    const authorizationFields = this._getAuthorizationFields();
+
+    return this._httpPost('/cyndex2/v1/networks/' + suid, undefined, Object.assign(saveParams, authorizationFields));
+  }
+
+  putCytoscapeNetworkInNDEx(suid = 'current', uuid) {
+    const saveParams = {
+      serverUrl: this.getNDExServer() + '/v2',
+      uuid: uuid
+    };
+
+    const authorizationFields = this._getAuthorizationFields();
+
+    return this._httpPut('/cyndex2/v1/networks/' + suid, undefined, Object.assign(saveParams, authorizationFields));
+  }
+}
+
+export default CyNDEx ;

package/src/NDEx.js

@@ -394,6 +394,10 @@ class NDEx {
       return this._httpGetV3ProtectedObj('networks/' + uuid + '/summary', parameters);
     }
 
+    getNetworkDOI(uuid, key, email){
+      return this._httpGetV3ProtectedObj('networks/' + uuid + '/DOI', {key: key, email: email});
+    }
+
     getAttributesOfSelectedNodes(uuid, {ids: nodeIds, attributeNames: names},accessKey) {
       let parameters = {
       };
@@ -425,6 +429,10 @@ class NDEx {
       });
     }
 
+    copyNetwork(uuid){
+      return this._httpPostV3ProtectedObj('networks/'+uuid+'/copy', undefined, {});
+    }
+
     updateNetworkFromRawCX(uuid, rawcx) {
       return this._httpPutObj('network/' + uuid, undefined, rawcx);
     }
@@ -585,11 +593,19 @@ class NDEx {
     }
 
     moveNetworks(networkIds, folderId){
-      return this._httpPostV3ProtectedObj('batch/networks/move', undefined, {targetFolder:folderId, networks: networkIds});
+      if(Object.isArray(networkIds)){
+        return this._httpPostV3ProtectedObj('batch/networks/move', undefined, {targetFolder:folderId, networks: networkIds});
+      }else{
+        throw new Error('Invalid networkIds');
+      }
     }
 
     setNetworksVisibility(files, visibility){
-      return this._httpPostV3ProtectedObj('batch/networks/visibility', undefined, {files: files, visibility: visibility});
+      if(this._validateShareData(files)){ 
+        return this._httpPostV3ProtectedObj('batch/networks/visibility', undefined, {items: files, visibility: visibility});
+      }else{
+        throw new Error('Invalid share data');
+      }
     }
 
     /* network set functions */
@@ -869,6 +885,18 @@ class NDEx {
    return this._httpPostV3ProtectedObj('users/signin', undefined, {idToken: idToken});
   }
 
+  // Permission and AccessKey APIs
+
+  //Todo:permission APIs
+
+  getAccessKey(uuid){
+    return this._httpGetProtectedObj('network/'+uuid+'/accesskey', {});
+  }
+
+  updateAccessKey(uuid, action){
+    return this._httpPutObj('network/'+uuid+'/accesskey', {action: action});
+  }
+
   // V3-Files APIs
   copyFile(fromUuid, toPath, type, accessKey) {
     let parameters = {};
@@ -891,29 +919,77 @@ class NDEx {
     return this._httpDeleteV3Obj('files/trash', undefined);
   }
 
+  permanentlyDeleteFile(fileId) {
+    return this._httpDeleteV3Obj('files/trash/'+fileId, undefined);
+  }
+
   restoreFile(networkIds, folderIds, shortcutIds) {
     return this._httpPostV3ProtectedObj('files/trash/restore', undefined, {networks: networkIds, folders: folderIds, shortcuts: shortcutIds});
   }
   // Sharing  
   //add, remove, update member
+  _validateShareData(data) {
+    // Check if data is an object and has files property
+    if (typeof data !== 'object' || data === null || data.files === undefined) {
+      throw new Error('Data must be an object with a "files" property');
+    }
+    
+    // Check if files is an object
+    if (typeof data.files !== 'object' || data.files === null) {
+      throw new Error('The "files" property must be an object');
+    }
+    
+    // Check each key-value pair in files
+    const validValues = ['NETWORK', 'FOLDER', 'SHORTCUT'];
+    
+    for (const [uuid, fileType] of Object.entries(data.files)) {
+      // Validate UUID format (basic validation)
+      if (!/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(uuid)) {
+        throw new Error(`Invalid UUID format: ${uuid}`);
+      }
+      
+      // Validate file type
+      if (!validValues.includes(fileType)) {
+        throw new Error(`Invalid file type for ${uuid}: ${fileType}. Must be one of: ${validValues.join(', ')}`);
+      }
+    }
+  }
+  _validateMemberData(data){
+    if(typeof data !== 'object' || data === null || data.members === undefined){
+      throw new Error('Data must be an object with a "members" property');
+    }
+    const validValues = ['READ', 'WRITE'];
+    for (const [uuid, permission] of Object.entries(data.members)) {
+      if (!validValues.includes(permission)) {
+        throw new Error(`Invalid permission for ${uuid}: ${permission}. Must be one of: ${validValues.join(', ')}`);
+      }
+      if(typeof uuid !== 'string' || !/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(uuid)){
+        throw new Error(`Invalid UUID format: ${uuid}`);
+      }
+    }
+    
+  }
+
   updateMember(files, members){
-    return this._httpPostV3ProtectedObj('files/sharing/members', undefined, {files: files, members: members});
+    if(this._validateShareData(files) && this._validateMemberData(members)){
+      return this._httpPostV3ProtectedObj('files/sharing/members', undefined, {files: files, members: members});
+    }else{
+      throw new Error('Invalid share data');
+    }
   }
 
   listMembers(files){
     return this._httpGetV3ProtectedObj('files/sharing/members/list', files);
   }
 
-  _validateShareData(data){
-    // must be object
-    if (typeof data !== 'object') {
-      throw new Error('Data must be an object');
-    }
-    
-  }
+
 
   transferOwnership(files, newOwner){
-    return this._httpPostV3ProtectedObj('files/sharing/transfer_ownership', undefined, {files: files, new_owner: newOwner});
+    if(this._validateShareData(files)){
+      return this._httpPostV3ProtectedObj('files/sharing/transfer_ownership', undefined, {files: files, new_owner: newOwner});
+    } else {
+      throw new Error('Invalid share data');
+    }
   }
 
   listShares(limit){
@@ -925,11 +1001,19 @@ class NDEx {
   }
   
   share(files){
-    return this._httpPostV3ProtectedObj('files/sharing/share', undefined, {files: files});
+    if(this._validateShareData(files)){
+      return this._httpPostV3ProtectedObj('files/sharing/share', undefined, {files: files});
+    }else{
+      throw new Error('Invalid share data');
+    }
   }
 
   unshare(files){
-    return this._httpPostV3ProtectedObj('files/sharing/unshare', undefined, {files: files});
+    if(this._validateShareData(files)){
+      return this._httpPostV3ProtectedObj('files/sharing/unshare', undefined, {files: files});
+    }else{
+      throw new Error('Invalid share data');
+    }
   }
 
   // Folder
@@ -972,7 +1056,7 @@ class NDEx {
     return this._httpGetV3ProtectedObj('files/folders/' + folderId + '/count', parameters);
   }
 
-  getFolderList(folderId, accessKey, format) {
+  getFolderList(folderId, accessKey, format, type) {
     let parameters = {};
 
     if (accessKey !== undefined) {
@@ -981,6 +1065,9 @@ class NDEx {
     if (format !== undefined) {
       parameters['format'] = format;
     }
+    if (type !== undefined) {
+      parameters['type'] = type;
+    }
     return this._httpGetV3ProtectedObj('files/folders/' + folderId + '/list', parameters);
   }