Merge pull request #169 from hms-dbmi/gic-bch-dev

GIC Release 1.4.0

CHANGELOG.md

@@ -2,6 +2,12 @@
 
 All notable changes to this project will be documented in this file. As our fork has diverged from AWS SWB mainline branch, we are noting the SWB version and the lab version together, as <swb version>\_<lab version>, starting from SWB mainline, 5.0.0.
 
+## [5.0.0_1.4.0](https://github.com/hms-dbmi/service-workbench-on-aws/compare/v5.0.0_1.3.2...v5.0.0_1.4.0) (01/25/2024)
+* Parameterize user register TOS acceptance.
+* Add comma separated study whitelist in stage file.
+* Add Jira support widget.
+* Add dropdown to help link if more than one url is given.
+
 ## [5.0.0_1.3.2](https://github.com/hms-dbmi/service-workbench-on-aws/compare/v5.0.0_1.3.1...v5.0.0_1.3.2) (12/21/2023)
 - Update register page email regex validation: validatorjs schema regex fields need slashes before and after the regex, or else it returns a validation error.
 

addons/addon-base-ui/packages/base-ui/src/helpers/settings.js

@@ -30,6 +30,10 @@ const branding = {
     title: process.env.REACT_APP_USER_REGISTRATION_TITLE,
     summary: process.env.REACT_APP_USER_REGISTRATION_SUMMARY,
     success: process.env.REACT_APP_USER_REGISTRATION_SUCCESS,
+    tosRequired: process.env.REACT_APP_USER_REGISTRATION_TOS_REQUIRED === 'true',
+  },
+  tos: {
+    onLanding: process.env.REACT_APP_TOS_LINK_ON_LANDING === 'true',
   },
   main: {
     title: process.env.REACT_APP_BRAND_MAIN_TITLE,

addons/addon-custom/packages/main/lib/schemas/register-user.json

@@ -27,5 +27,5 @@
       "pattern": "\\d{4}-[01]\\d-[0-3]\\dT[0-2]\\d:[0-5]\\d:[0-5]\\d\\.\\d+([+-][0-2]\\d:[0-5]\\d|Z)"
     }
   },
-  "required": ["email", "firstName", "lastName", "acceptedTerms"]
+  "required": ["email", "firstName", "lastName"]
 }

addons/addon-custom/packages/main/src/extend/withAuth.js

@@ -56,8 +56,12 @@ function RegisterLogin(enableCustomRegister) {
             Register
           </Button>
         )}
-        <Link to="/legal">Terms of Service</Link>
-        <br />
+        {branding.tos.onLanding && (
+          <>
+            <Link to="/legal">Terms of Service</Link>
+            <br />
+          </>
+        )}
         {branding.main.loginWarning}
       </>
     );

addons/addon-custom/packages/main/src/parts/App.js

@@ -18,7 +18,7 @@ import { Switch, Redirect, withRouter } from 'react-router-dom';
 import { action, decorate, computed } from 'mobx';
 import { inject, observer } from 'mobx-react';
 import { getEnv } from 'mobx-state-tree';
-import { Menu } from 'semantic-ui-react';
+import { Menu, Dropdown, DropdownMenu, DropdownItem } from 'semantic-ui-react';
 
 import { getRoutes, getMenuItems, getDefaultRouteLocation } from '@aws-ee/base-ui/dist/helpers/plugins-util';
 import MainLayout from '@aws-ee/base-ui/dist/parts/MainLayout';
@@ -73,14 +73,42 @@ class RegisterApp extends React.Component {
     }
   }
 
-  openHelp() {
-    window.open(branding.page.help, '_blank');
+  openHelp(url) {
+    return () => window.open(url, '_blank');
+  }
+
+  getLinks() {
+    const helpLinks = (branding.page.help || '').split(',').filter(x => x);
+    if (helpLinks.length < 2) {
+      return helpLinks;
+    }
+    return helpLinks.reduce((items, link) => {
+      const [text, ...urlParts] = link.split('=');
+      const url = urlParts.join('='); // if there are query params then we need to rebuild the url
+      if (!text || !url) {
+        console.error(`Poorly formed help link was provided: "${link}"`, 'Expected: "Text=URL"');
+        return items;
+      }
+      return [...items, { text, url }];
+    }, []);
   }
 
   appMenuItems() {
+    const links = this.getLinks();
     return (
       <>
-        {branding.page.help && <Menu.Item onClick={this.openHelp}>Help</Menu.Item>}
+        {links.length === 1 && <Menu.Item onClick={this.openHelp(links[0])}>Help</Menu.Item>}
+        {links.length > 1 && (
+          <Dropdown item text="Help">
+            <DropdownMenu>
+              {links.map(({ text, url }) => (
+                <DropdownItem key={text} onClick={this.openHelp(url)}>
+                  {text}
+                </DropdownItem>
+              ))}
+            </DropdownMenu>
+          </Dropdown>
+        )}
         <TermsModal // Clickable Terms menu item
           trigger={<Menu.Item>Terms of Service</Menu.Item>}
           closeOnDimmerClick

addons/addon-custom/packages/main/src/parts/Register.js

@@ -83,6 +83,32 @@ class Register extends React.Component {
     };
   }
 
+  renderTOS() {
+    return (
+      <>
+        {this.terms.value !== termsState.unset.value && <Icon name={this.terms.icon} color={this.terms.color} />}
+        {this.terms.label} &nbsp;
+        <TermsModal
+          trigger={
+            <button
+              id="terms-modal"
+              className="link"
+              type="button"
+              ref={ref => {
+                this.termsModalButton = ref;
+              }}
+            >
+              Terms of Service
+            </button>
+          }
+          closeOnDimmerClick
+          acceptAction={this.setTerms(termsState.accepted)}
+          declineAction={this.setTerms(termsState.declined)}
+        />
+      </>
+    );
+  }
+
   renderRegisterationForm() {
     return (
       <Form size="large" loading={this.loading} onSubmit={this.handleSubmit}>
@@ -101,40 +127,16 @@ class Register extends React.Component {
 
             {this.renderField('email')}
           </div>
+          {branding.register.tosRequired && <div className="center mt2">{this.renderTOS()}</div>}
           <div className="center mt3">
-            {this.terms.value !== termsState.unset.value && <Icon name={this.terms.icon} color={this.terms.color} />}
-            {this.terms.label} &nbsp;
-            <TermsModal
-              trigger={
-                <button
-                  id="terms-modal"
-                  className="link"
-                  type="button"
-                  ref={ref => {
-                    this.termsModalButton = ref;
-                  }}
-                >
-                  Terms of Service
-                </button>
-              }
-              closeOnDimmerClick
-              acceptAction={this.setTerms(termsState.accepted)}
-              declineAction={this.setTerms(termsState.declined)}
-            />
-          </div>
-          <div className="mt3 center">
             <div>
               <Form.Field>
                 {this.errors.form && (
                   <div className="mb1">
                     <Label prompt>{this.errors.form}</Label>
                   </div>
                 )}
-                <Form.Button
-                  id="register-submit"
-                  disabled={this.terms.value !== termsState.accepted.value}
-                  color="green"
-                >
+                <Form.Button id="register-submit" disabled={this.submitDisabled()} color="green">
                   Create a new Service Workbench account
                 </Form.Button>
               </Form.Field>
@@ -145,6 +147,10 @@ class Register extends React.Component {
     );
   }
 
+  submitDisabled() {
+    return branding.register.tosRequired ? this.terms.value !== termsState.accepted.value : false;
+  }
+
   renderConfirmation() {
     return (
       <div>
@@ -207,20 +213,24 @@ class Register extends React.Component {
         return;
       }
 
-      // Validate that the terms have been accepted
-      if (this.terms.value !== termsState.accepted.value) {
+      // Validate that the terms have been accepted, if required
+      let acceptedTerms;
+      if (branding.register.tosRequired && this.terms.value !== termsState.accepted.value) {
         runInAction(() => {
           this.errors.form = termsErrorText;
           this.formProcessing = false;
         });
         return;
       }
+      if (branding.register.tosRequired) {
+        acceptedTerms = new Date().toISOString();
+      }
 
       const result = await registerUser({
         firstName: this.user.firstName,
         lastName: this.user.lastName,
         email: this.user.email,
-        acceptedTerms: new Date().toISOString(),
+        acceptedTerms,
       });
       // if we encounter an error then don't continue to process the form and instead display a message
       if (result.error) {

main/config/settings/example.yml

@@ -157,5 +157,11 @@ HostedZoneId: 'Z02455261RJ9QQPVHFZGA'
 #userRegistrationSuccess: "<p>Your Service Workbench account has been successfully created. What you should expect next:</p><ol><li>The Service Workbench administrator will review your account.</li><li>Once your account is activated, you can login to Service Workbench and start your research.</li></ol>"
 #loginWarning: "WARNING: You are entering a secure environment."
 
-# URL for help link
+# Require the TOS to be accepted before registration can occur.
+#tosRequired: true
+
+# Should the TOS link be enabled on the landing page.
+#tosLinkOnLanding: true
+
+# URL for help link. Can be empty, a single url, or a list like, "Some Link=https://www.google.com/?q=what,Other Link=https://www.example.com/"
 #helpUrl: about:blank

main/solution/backend/config/infra/functions.yml

@@ -20,6 +20,7 @@ openDataScrapeHandler:
     APP_STUDY_DATA_BUCKET_NAME: ${self:custom.settings.studyDataBucketName}
     APP_CUSTOM_USER_AGENT: ${self:custom.settings.customUserAgent}
     APP_IS_APP_STREAM_ENABLED: ${self:custom.settings.isAppStreamEnabled}
+    APP_OPEN_DATA_SCRAPE_WHITELIST: ${self:custom.settings.openDataScrapeWhitelist}
 
   events:
     - schedule:

main/solution/backend/config/settings/.defaults.yml

@@ -321,3 +321,6 @@ dataSourceReachabilityHandlerRoleArn: 'arn:aws:iam::${self:custom.settings.awsAc
 
 # The stack name of the 'backend' serverless service
 backendStackName: ${self:custom.settings.namespace}-backend
+
+# custom list of open studies to include when scraping that are not part in the filtered tag list
+openDataScrapeWhitelist: ''

main/solution/backend/src/lambdas/open-data-scrape-handler/__tests__/handler-impl.test.js

@@ -113,33 +113,83 @@ describe('fetchOpenData', () => {
     sha: 'abc2',
   };
 
+  const whitelistStudy = {
+    name: 'Study 3',
+    description: 'Example study 3',
+    tags: ['other-tag'],
+    resources: [
+      {
+        description: 'Description for Study 3',
+        arn: 'arn:aws:s3:::study3',
+        region: 'us-east-1',
+        type: 'S3 Bucket',
+      },
+    ],
+    id: 'study-3',
+    sha: 'abc2',
+  };
+
   it('has invalid study (Invalid ARN)', async () => {
     const fileUrls = ['firstFileUrl'];
     const requiredTags = ['genetic'];
+    const studyWhitelist = [];
     const fetchFile = jest.fn();
     fetchFile.mockReturnValueOnce(invalidStudy);
 
-    const result = await fetchOpenData({ fileUrls, requiredTags, log: consoleLogger, fetchFile });
+    const result = await fetchOpenData({ fileUrls, requiredTags, studyWhitelist, log: consoleLogger, fetchFile });
     expect(result).toEqual([]);
   });
 
   it('has one valid study', async () => {
     const fileUrls = ['firstFileUrl'];
     const requiredTags = ['genetic'];
+    const studyWhitelist = [];
     const fetchFile = jest.fn();
     fetchFile.mockReturnValueOnce(validStudy);
 
-    const result = await fetchOpenData({ fileUrls, requiredTags, log: consoleLogger, fetchFile });
+    const result = await fetchOpenData({ fileUrls, requiredTags, studyWhitelist, log: consoleLogger, fetchFile });
     expect(result).toEqual([validStudyOpenData]);
   });
 
   it('has one valid study and one invalid study (Invalid ARN)', async () => {
-    const fileUrls = ['firstFileUrl'];
+    const fileUrls = ['firstFileUrl', 'fileUrl2'];
     const requiredTags = ['genetic'];
+    const studyWhitelist = [];
     const fetchFile = jest.fn();
     fetchFile.mockReturnValueOnce(validStudy).mockReturnValueOnce(invalidStudy);
 
-    const result = await fetchOpenData({ fileUrls, requiredTags, log: consoleLogger, fetchFile });
+    const result = await fetchOpenData({ fileUrls, requiredTags, studyWhitelist, log: consoleLogger, fetchFile });
     expect(result).toEqual([validStudyOpenData]);
   });
+
+  it('has whitelisted study is included', async () => {
+    const fileUrls = ['firstFileUrl', 'fileUrl2', 'fileUrl3'];
+    const requiredTags = ['genetic'];
+    const studyWhitelist = ['study-3'];
+    const fetchFile = jest.fn();
+    fetchFile
+      .mockReturnValueOnce(validStudy)
+      .mockReturnValueOnce(invalidStudy)
+      .mockReturnValueOnce(whitelistStudy);
+
+    const result = await fetchOpenData({ fileUrls, requiredTags, studyWhitelist, log: consoleLogger, fetchFile });
+    expect(result).toEqual([
+      validStudyOpenData,
+      {
+        description: 'Example study 3',
+        id: 'study-3',
+        name: 'Study 3',
+        resources: [
+          {
+            arn: 'arn:aws:s3:::study3',
+            description: 'Description for Study 3',
+            region: 'us-east-1',
+            type: 'S3 Bucket',
+          },
+        ],
+        sha: 'abc2',
+        tags: ['other-tag'],
+      },
+    ]);
+  });
 });

main/solution/backend/src/lambdas/open-data-scrape-handler/handler-impl.js

@@ -42,14 +42,16 @@ if (typeof fetch !== 'function' && fetch.default && typeof fetch.default === 'fu
   fetch = fetch.default;
 }
 
-const newHandler = async ({ studyService, log = consoleLogger } = {}) => {
+const newHandler = async ({ studyService, log = consoleLogger, settings } = {}) => {
+  const whitelist = settings.get('openDataScrapeWhitelist') || '';
   const scrape = {
     githubApiUrl: 'https://api.github.com',
     rawGithubUrl: 'https://raw.githubusercontent.com',
     owner: 'awslabs',
     repository: 'open-data-registry',
     ref: 'main',
     subtree: 'datasets',
+    studyWhitelist: whitelist.split(',').filter(x => x),
     filterTags: [
       'genetic',
       'genomic',
@@ -193,15 +195,15 @@ const newHandler = async ({ studyService, log = consoleLogger } = {}) => {
   return async () => fetchAndSaveOpenData(fetchDatasetFiles, scrape, log, fetchFile, basicProjection, studyService);
 };
 
-const fetchOpenData = async ({ fileUrls, requiredTags, log, fetchFile }) => {
+const fetchOpenData = async ({ fileUrls, requiredTags, studyWhitelist, log, fetchFile }) => {
   log.info(`Fetching ${fileUrls.length} metadata files`);
   const metadata = await Promise.all(fileUrls.map(fetchFile));
 
-  log.info(`Filtering for ${requiredTags} tags and resources with valid ARNs`);
+  log.info(`Filtering for ${requiredTags} tags, ${studyWhitelist} whitelist studies, and resources with valid ARNs`);
   const validS3Arn = new RegExp(/^arn:aws:s3:.*:.*:.+$/);
-  const filtered = metadata.filter(({ tags, resources }) => {
+  const filtered = metadata.filter(({ id, tags, resources }) => {
     return (
-      requiredTags.some(filterTag => tags.includes(filterTag)) &&
+      (studyWhitelist.includes(id) || requiredTags.some(filterTag => tags.includes(filterTag))) &&
       resources.every(resource => {
         return resource.type === 'S3 Bucket' && validS3Arn.test(resource.arn);
       })
@@ -237,7 +239,13 @@ async function saveOpenData(log, simplified, studyService) {
 
 const fetchAndSaveOpenData = async (fetchDatasetFiles, scrape, log, fetchFile, basicProjection, studyService) => {
   const fileUrls = await fetchDatasetFiles();
-  const openData = await fetchOpenData({ fileUrls, requiredTags: scrape.filterTags, log, fetchFile });
+  const openData = await fetchOpenData({
+    fileUrls,
+    requiredTags: scrape.filterTags,
+    studyWhitelist: scrape.studyWhitelist,
+    log,
+    fetchFile,
+  });
 
   const simplifiedStudyData = openData.map(basicProjection);
 

main/solution/backend/src/lambdas/open-data-scrape-handler/handler.js

@@ -26,7 +26,8 @@ const initHandler = (async () => {
   await container.initServices();
   const studyService = await container.find('studyService');
   const log = await container.find('log');
-  return newHandler({ studyService, log });
+  const settings = await container.find('settings');
+  return newHandler({ studyService, log, settings });
 })();
 
 // eslint-disable-next-line import/prefer-default-export