@js4cytoscape/ndex-client 0.6.0-alpha.1 → 0.6.0-alpha.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@js4cytoscape/ndex-client",
-  "version": "0.6.0-alpha.1",
+  "version": "0.6.0-alpha.3",
   "description": "NDEx client library - Modern TypeScript implementation",
   "repository": {
     "type": "git",
@@ -12,7 +12,8 @@
   "homepage": "https://github.com/cytoscape/js4cytoscape",
   "main": "./dist/index.js",
   "module": "./dist/index.mjs",
-  "umd": "./dist/index.umd.js",
+  "unpkg": "./dist/index.global.js",
+  "jsdelivr": "./dist/index.global.js",
   "types": "./dist/index.d.ts",
   "exports": {
     ".": {
@@ -23,7 +24,6 @@
   },
   "files": [
     "dist",
-    "src",
     "README.md",
     "LICENSE"
   ],
@@ -32,16 +32,23 @@
     "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:site": "cd docs-root/guide && npm install && npm run build",
+    "docs:serve": "cd docs-root/guide && npm run start",
     "docs:build": "npm run docs:api && npm run docs:site",
-    "docs:clean": "rimraf docs docs-site/build docs-site/docs/api",
+    "docs:clean": "rimraf docs-root/api docs-root/guide/build",
     "test": "npm run test:unit",
     "test:unit": "jest --config jest.unit.config.js",
-    "test:integration": "jest --config jest.integration.config.js",
+    "test:integration": "npm run test:integration:all",
+    "test:integration:node": "jest --config jest.integration.node.config.js",
+    "test:integration:browser": "jest --config jest.integration.browser.config.js",
+    "test:integration:all": "npm run test:integration:node && npm run test:integration:browser",
+    "test:integration:parallel": "jest --config jest.integration.node.config.js & jest --config jest.integration.browser.config.js",
     "test:all": "npm run test:unit && npm run test:integration",
     "test:watch": "npm run test:unit -- --watch",
+    "test:watch:integration:node": "npm run test:integration:node -- --watch",
+    "test:watch:integration:browser": "npm run test:integration:browser -- --watch",
     "test:coverage": "npm run test:unit -- --coverage",
+    "test:coverage:integration": "npm run test:integration:node -- --coverage && npm run test:integration:browser -- --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",
@@ -57,7 +64,7 @@
   "author": "Jing Chen",
   "license": "MIT",
   "engines": {
-    "node": ">=16.0.0"
+    "node": ">=18"
   },
   "keywords": [
     "ndex",
@@ -69,7 +76,8 @@
     "typescript"
   ],
   "dependencies": {
-    "axios": "^1.11.0"
+    "axios": "^1.11.0",
+    "form-data": "^4.0.4"
   },
   "devDependencies": {
     "@changesets/cli": "^2.27.1",
@@ -88,8 +96,9 @@
     "rimraf": "^5.0.5",
     "ts-jest": "^29.1.2",
     "tsup": "^8.0.2",
-    "typedoc": "^0.25.12",
-    "typedoc-plugin-markdown": "^3.17.1",
+    "typedoc": "^0.28.12",
+    "typedoc-material-theme": "^1.4.0",
+    "typedoc-plugin-markdown": "^4.8.1",
     "typescript": "^5.4.2"
   },
   "peerDependencies": {

package/src/CyNDEx.js

@@ -1,178 +0,0 @@
-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/CyNDEx.js.bak

@@ -1,178 +0,0 @@
-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 ;