@datagrok/sequence-translator 0.0.5 → 0.0.9

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

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
-  "friendlyName": "SequenceTranslator",
-  "version": "0.0.5",
+  "friendlyName": "Sequence Translator",
+  "version": "0.0.9",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/utils": "^0.1.0",
@@ -23,7 +23,10 @@
     "debug-sequencetranslator-public": "grok publish public --rebuild",
     "release-sequencetranslator-public": "grok publish public --rebuild --release",
     "debug-sequencetranslator-local": "grok publish local --rebuild",
-    "release-sequencetranslator-local": "grok publish local --rebuild --release"
+    "release-sequencetranslator-local": "grok publish local --rebuild --release",
+    "test": "set HOST=dev && jest",
+    "test-dev": "set HOST=dev && jest",
+    "test-local": "set HOST=localhost && jest"
   },
   "devDependencies": {
     "@typescript-eslint/eslint-plugin": "^4.29.1",
@@ -32,6 +35,11 @@
     "eslint": "^7.32.0",
     "eslint-config-google": "^0.14.0",
     "webpack": "^5.31.0",
-    "webpack-cli": "^4.6.0"
+    "webpack-cli": "^4.6.0",
+    "@types/jest": "latest",
+    "jest": "latest",
+    "jest-html-reporter": "latest",
+    "puppeteer": "^13.1.2",
+    "ts-jest": "^27.1.2"
   }
 }

package/setup.cmd

@@ -8,4 +8,4 @@ call npm link datagrok-api
 cd ../../packages/SequenceTranslator
 call npm install
 call npm link datagrok-api @datagrok-libraries/utils
-webpack
+webpack

package/src/ICDs.ts

@@ -0,0 +1,3 @@
+export const ICDS = `DISPLAY
+NO DATA
+`;

package/src/IDPs.ts

@@ -0,0 +1,3 @@
+export const IDPS = `DISPLAY
+NO DATA
+`;

package/src/__jest__/remote.test.ts

@@ -0,0 +1,49 @@
+/**
+ * @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 () => {
+  let 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 ?? 'SequenceTranslator';
+  console.log(`Testing ${target_package} package`);
+
+  //console.log(require('root-require')('package.json').version);
+  let r = await page.evaluate((target_package):Promise<object> => {
+    return new Promise<object>((resolve, reject) => {
+      (<any>window).grok.functions.eval(target_package + ':test()').then((df: any) => {
+        let cStatus = df.columns.byName('success');
+        let cMessage = df.columns.byName('result');
+        let cCat = df.columns.byName('category');
+        let cName = df.columns.byName('name');
+        let failed = false;
+        let report = '';
+        for (let i = 0; i < df.rowCount; i++)
+          if (!cStatus.get(i)) {
+            report += `${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) {
+  let response = await fetch(`${url}/users/login/dev/${key}`, {method: 'POST'});
+  let 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) {
+  let response = await fetch(`${url}/admin/plugins/admin/settings`, {headers: {Authorization: token}});
+  let 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 {
+  let urls: Indexable = {};
+  for (let server in conf.servers) {
+    urls[conf['servers'][server]['url']] = conf['servers'][server];
+  }
+  return urls;
+}
+
+export function getDevKey(hostKey: string): {url: string, key: string} {
+  let config = yaml.load(fs.readFileSync(confPath, 'utf8')) as any;
+  let host = hostKey == '' ? config.default : hostKey;
+  host = host.trim();
+  let 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 ?? '';
+  let cfg = getDevKey(url);
+  url = cfg.url;
+
+  let key = cfg.key;
+  let token = await getToken(url, key);
+  url = await getWebUrl(url, token);
+  console.log(`Using web root: ${url}`);
+
+  let browser = await puppeteer.launch({
+    args: ['--disable-dev-shm-usage', '--disable-features=site-per-process'],
+    ignoreHTTPSErrors: true,
+  });
+
+  let page = await browser.newPage();
+  await page.goto(`${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 }

package/src/defineAxolabsPattern.ts

@@ -138,10 +138,7 @@ export function defineAxolabsPattern() {
         updateSvgScheme();
         updateOutputExamples();
       });
-      let isOverhang = false;
-      if (asBases[i].value.slice(-3) == '(o)')
-        isOverhang = true;
-      else
+      if (asBases[i].value.slice(-3) != '(o)')
         nucleotideCounter++;
 
       asModificationItems.append(
@@ -184,10 +181,7 @@ export function defineAxolabsPattern() {
         updateSvgScheme();
         updateOutputExamples();
       });
-      let isOverhang = false;
-      if (ssBases[i].value.slice(-3) == '(o)')
-        isOverhang = true;
-      else
+      if (ssBases[i].value.slice(-3) != '(o)')
         nucleotideCounter++;
 
       ssModificationItems.append(

package/src/package-test.ts

@@ -1,8 +1,9 @@
 import * as DG from 'datagrok-api/dg';
-import {runTests} from '@datagrok-libraries/utils/src/test';
+import {runTests, tests} from '@datagrok-libraries/utils/src/test';
 import './tests/smiles-tests';
 
 export const _package = new DG.Package();
+export {tests}
 
 //name: test
 //output: dataframe result