@js4cytoscape/ndex-client 0.3.2

package/package.json

@@ -0,0 +1,33 @@
+{
+  "name": "@js4cytoscape/ndex-client",
+  "version": "0.3.2",
+  "description": "NDEx client library",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/cytoscape/js4cytoscape.git"
+  },
+  "bugs": {
+    "url": "https://github.com/cytoscape/js4cytoscape/issues"
+  },
+  "homepage": "https://github.com/cytoscape/js4cytoscape",
+  "main": "./dist/ndexClient.common.js",
+  "module": "src/index.js",
+  "files": [
+    "dist",
+    "src"
+  ],
+  "scripts": {
+    "watch:js": "webpack --watch",
+    "build": "webpack --mode=development",
+    "build-prod": "webpack --mode=production",
+    "test": "nyc mocha"
+  },
+  "author": "Jing Chen",
+  "license": "MIT",
+  "engines": {
+    "node": ">=12.16.1"
+  },
+  "dependencies": {
+    "axios": "^0.26.0"
+  }
+}

package/src/CyNDEx.js

@@ -0,0 +1,174 @@
+const CY_REST_BASE_URL = 'http://127.0.0.1';
+
+const axios = require('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 : 'http://public.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);
+  }
+
+  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));
+  }
+}
+
+module.exports = { CyNDEx };