@datagrok/peptides 0.8.9 → 0.8.13

package/jest.config.js

@@ -0,0 +1,33 @@
+module.exports = {
+  "roots": [
+    "<rootDir>/src"
+  ],
+  "testMatch": [
+    "**/__jest__/**/*.test.+(ts|tsx)"
+  ],
+  moduleFileExtensions: [
+    'ts',
+    'js',
+  ],
+  "transform": {
+    "^.+\\.(ts|tsx)$": "ts-jest"
+  },
+  transformIgnorePatterns: ['^.+\\.js$'],
+  globals: {
+    'ts-jest': {
+      'tsconfig': {
+          "target": "es6",
+          "module": "es2020",
+      }
+    }
+  },
+  reporters: [
+    "default",
+    [
+      "./node_modules/jest-html-reporter",
+      {
+        "includeConsoleLog": true
+      }
+    ]
+  ]
+}

package/package.json

@@ -1,64 +1,77 @@
 {
-	"name": "@datagrok/peptides",
-	"version": "0.8.9",
-	"description": "",
-	"dependencies": {
-		"@biowasm/aioli": ">=2.4.0",
-		"@datagrok-libraries/bio": ">=0.0.4",
-		"@datagrok-libraries/ml": ">=0.0.14",
-		"@datagrok-libraries/statistics": ">=0.1.5",
-		"@datagrok-libraries/utils": ">=0.0.22",
-		"cash-dom": "latest",
-		"d3": "latest",
-		"datagrok-api": ">=0.123.0",
-		"dayjs": "latest",
-		"file-loader": "^6.2.0",
-		"jstat": "^1.9.5",
-		"logojs-react": "^2.1.1",
-		"rxjs": "^6.5.5"
-	},
-	"devDependencies": {
-		"@types/d3": "^7.0.0",
-		"@types/jquery": "^3.5.6",
-		"@typescript-eslint/eslint-plugin": "latest",
-		"@typescript-eslint/parser": "latest",
-		"css-loader": "^5.2.4",
-		"eslint": "latest",
-		"eslint-config-google": "latest",
-		"style-loader": "^2.0.0",
-		"ts-loader": "latest",
-		"typescript": "latest",
-		"webpack": "latest",
-		"webpack-cli": "latest"
-	},
-	"sources": [
-		"common/ngl_viewer/ngl.js"
-	],
-	"scripts": {
-		"link-api": "npm link datagrok-api",
-		"link-utils": "npm link @datagrok-libraries/utils",
-		"link-statistics": "npm link @datagrok-libraries/statistics",
-		"link-ml": "npm link @datagrok-libraries/ml",
-		"link-bio": "npm link @datagrok-libraries/bio",
-		"link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/statistics link @datagrok-libraries/ml @datagrok-libraries/bio",
-		"install-dependencies": "npm install",
-		"debug-peptides": "grok publish --rebuild",
-		"release-peptides": "grok publish --rebuild --release",
-		"build-peptides": "webpack",
-		"build": "webpack",
-		"debug-peptides-dev": "grok publish dev --rebuild",
-		"release-peptides-dev": "grok publish dev --rebuild --release",
-		"debug-peptides-public": "grok publish public --rebuild",
-		"release-peptides-public": "grok publish public --rebuild --release",
-		"debug-peptides-local": "grok publish local --rebuild",
-		"release-peptides-local": "grok publish local --rebuild --release",
-		"lint": "eslint \"./src/**/*.ts\"",
-		"lint-fix": "eslint \"./src/**/*.ts\" --fix"
-	},
-	"canEdit": [
-		"Developers"
-	],
-	"canView": [
-		"All users"
-	]
+  "name": "@datagrok/peptides",
+  "version": "0.8.13",
+  "description": "",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/datagrok-ai/public.git",
+    "directory": "packages/Peptides"
+  },
+  "dependencies": {
+    "@biowasm/aioli": ">=2.4.0",
+    "@datagrok-libraries/bio": "^0.0.5",
+    "@datagrok-libraries/ml": ">=0.0.16 <0.1.21",
+    "@datagrok-libraries/statistics": "^0.1.6",
+    "@datagrok-libraries/utils": "^0.1.2",
+    "cash-dom": "latest",
+    "d3": "latest",
+    "datagrok-api": "^0.148.6",
+    "dayjs": "latest",
+    "file-loader": "^6.2.0",
+    "jstat": "^1.9.5",
+    "logojs-react": "^2.1.1",
+    "rxjs": "^6.5.5"
+  },
+  "devDependencies": {
+    "@types/d3": "^7.0.0",
+    "@types/jquery": "^3.5.6",
+    "@typescript-eslint/eslint-plugin": "latest",
+    "@typescript-eslint/parser": "latest",
+    "css-loader": "^5.2.4",
+    "eslint": "latest",
+    "eslint-config-google": "latest",
+    "style-loader": "^2.0.0",
+    "ts-loader": "latest",
+    "typescript": "latest",
+    "webpack": "latest",
+    "webpack-cli": "latest",
+    "@types/jest": "latest",
+    "jest": "latest",
+    "jest-html-reporter": "latest",
+    "puppeteer": "^13.1.2",
+    "ts-jest": "^27.1.2"
+  },
+  "sources": [
+    "common/ngl_viewer/ngl.js"
+  ],
+  "scripts": {
+    "link-api": "npm link datagrok-api",
+    "link-utils": "npm link @datagrok-libraries/utils",
+    "link-statistics": "npm link @datagrok-libraries/statistics",
+    "link-ml": "npm link @datagrok-libraries/ml",
+    "link-bio": "npm link @datagrok-libraries/bio",
+    "link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/statistics link @datagrok-libraries/ml @datagrok-libraries/bio",
+    "install-dependencies": "npm install",
+    "debug-peptides": "grok publish --rebuild",
+    "release-peptides": "grok publish --rebuild --release",
+    "build-peptides": "webpack",
+    "build": "webpack",
+    "debug-peptides-dev": "grok publish dev --rebuild",
+    "release-peptides-dev": "grok publish dev --rebuild --release",
+    "debug-peptides-public": "grok publish public --rebuild",
+    "release-peptides-public": "grok publish public --rebuild --release",
+    "debug-peptides-local": "grok publish local --rebuild",
+    "release-peptides-local": "grok publish local --rebuild --release",
+    "lint": "eslint \"./src/**/*.ts\"",
+    "lint-fix": "eslint \"./src/**/*.ts\" --fix",
+    "test": "set HOST=dev && jest",
+    "test-dev": "set HOST=dev && jest",
+    "test-local": "set HOST=localhost && jest"
+  },
+  "canEdit": [
+    "Developers"
+  ],
+  "canView": [
+    "All users"
+  ]
 }

package/src/__jest__/remote.test.ts

@@ -0,0 +1,50 @@
+/**
+ * @jest-environment jsdom
+ */
+
+import * as utils from './test-node';
+import puppeteer from 'puppeteer';
+
+const P_START_TIMEOUT: number = 100000;
+let browser: puppeteer.Browser;
+let page: puppeteer.Page;
+
+beforeAll(async () => {
+  const out = await utils.getBrowserPage(puppeteer);
+  browser = out.browser;
+  page = out.page;
+}, P_START_TIMEOUT);
+
+afterAll(async () => {
+  await browser.close();
+});
+
+it('TEST', async () => {
+  const target_package:string = process.env.TARGET_PACKAGE ?? 'Peptides';
+  console.log(`Testing ${target_package} package`);
+
+  //console.log(require('root-require')('package.json').version);
+  const r = await page.evaluate((target_package):Promise<object> => {
+    return new Promise<object>((resolve, reject) => {
+      (<any>window).grok.functions.eval(target_package + ':test()').then((df: any) => {
+        const cStatus = df.columns.byName('success');
+        const cMessage = df.columns.byName('result');
+        const cCat = df.columns.byName('category');
+        const cName = df.columns.byName('name');
+        let failed = false;
+        let report = '';
+        for (let i = 0; i < df.rowCount; i++) {
+          if (!cStatus.get(i)) {
+            report += `${cCat.get(i)}.${cName.get(i)}: ${cMessage.get(i)}\n`;
+            failed = true;
+          }
+        }
+        resolve({report, failed});
+      }).catch((e: any) => reject(e));
+    });
+  }, target_package);
+  // @ts-ignore
+  console.log(r.report);
+  // @ts-ignore
+  expect(r.failed).toBe(false);
+}, 100000);

package/src/__jest__/test-node.ts

@@ -0,0 +1,96 @@
+import * as path from 'path';
+import * as os from 'os';
+import * as fs from 'fs';
+// @ts-ignore
+import * as yaml from 'js-yaml';
+const fetch = require('node-fetch');
+
+export async function getToken(url: string, key: string) {
+  const response = await fetch(`${url}/users/login/dev/${key}`, {method: 'POST'});
+  const json = await response.json();
+  if (json.isSuccess == true)
+    return json.token;
+  else
+    throw 'Unable to login to server. Check your dev key';
+}
+
+export async function getWebUrl(url: string, token: string) {
+  const response = await fetch(`${url}/admin/plugins/admin/settings`, {headers: {Authorization: token}});
+  const json = await response.json();
+  return json.settings.webRoot;
+}
+
+const grokDir = path.join(os.homedir(), '.grok');
+const confPath = path.join(grokDir, 'config.yaml');
+
+function mapURL(conf: Config): Indexable {
+  const urls: Indexable = {};
+  for (const server in conf.servers)
+    urls[conf['servers'][server]['url']] = conf['servers'][server];
+
+  return urls;
+}
+
+export function getDevKey(hostKey: string): {url: string, key: string} {
+  const config = yaml.load(fs.readFileSync(confPath, 'utf8')) as any;
+  let host = hostKey == '' ? config.default : hostKey;
+  host = host.trim();
+  const urls = mapURL(config);
+  let key = '';
+  let url = '';
+  try {
+    let url = new URL(host).href;
+    if (url.endsWith('/')) url = url.slice(0, -1);
+    if (url in urls) key = config['servers'][urls[url]]['key'];
+  } catch (error) {
+    if (config['servers'][host] == null)
+      throw `Unknown server alias. Please add it to ${confPath}`;
+    url = config['servers'][host]['url'];
+    key = config['servers'][host]['key'];
+  }
+  return {url, key};
+}
+
+export async function getBrowserPage(puppeteer: any): Promise<{browser: any, page: any}> {
+  let url:string = process.env.HOST ?? '';
+  const cfg = getDevKey(url);
+  url = cfg.url;
+
+  const key = cfg.key;
+  const token = await getToken(url, key);
+  url = await getWebUrl(url, token);
+  console.log(`Using web root: ${url}`);
+
+  const browser = await puppeteer.launch({
+    args: ['--disable-dev-shm-usage', '--disable-features=site-per-process'],
+    ignoreHTTPSErrors: true,
+  });
+
+  const page = await browser.newPage();
+  await page.goto(`${url}/oauth/`);
+  await page.setCookie({name: 'auth', value: token});
+  await page.evaluate((token: any) => {
+    window.localStorage.setItem('auth', token);
+  }, token);
+  await page.goto(url);
+  try {
+    await page.waitForSelector('.grok-preloader');
+    await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 100000});
+  } catch (error) {
+    throw error;
+  }
+  return {browser, page};
+}
+
+
+interface Config {
+  servers: {
+    [alias: string]: {
+      url: string,
+      key: string
+    }
+  },
+  default: string,
+}
+
+interface Indexable { [key: string]: any }