Merge branch 'master' into feat/faro

data/config/acct.json

@@ -112,7 +112,7 @@
       "title": "ACCOuNT Data Commons",
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website provides a centralized, cloud-based discovery portal for African American pharmacogenomics data and aims to accelerate discovery of novel genetic variants in African Americans related to clinically actionable cardiovascular phenotypes.",
-      "contact": "If you have any questions about access or the registration process, please contact support@datacommons.io"
+      "contact": "If you have any questions about access or the registration process, please contact support@gen3.org"
     }
   },
   "featureFlags": {

data/config/anvil.json

@@ -102,7 +102,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     },
     "categorical9Colors": [
       "#035C94",

data/config/bpa.json

@@ -116,7 +116,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website combines liquid biopsy data from academic, government, and industry partners and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for the treatment and prevention of cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "bpa-support@datacommons.io"
+      "email": "bpa-support@gen3.org"
     },
     "certs": {
       "security_quiz": {

data/config/canine.json

@@ -119,7 +119,7 @@
       "subTitle": "explore, analyze, and share research data",
       "text": "This website analyzes and shares genomic architecture of modern dog breeds and runs analysis for canine cancer to create clean, easy to navigate visualizations for data-driven discovery for canine cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     }
   },
   "featureFlags": {

data/config/dcf.json

@@ -132,7 +132,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     }
   },
   "featureFlags": {

data/config/default.json

@@ -132,7 +132,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     },
     "certs": {
       "security_quiz": {

data/config/gtex.json

@@ -123,7 +123,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "This website supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io",
+      "email": "support@gen3.org",
       "image": "stage-icons/stage-gene"
     },
     "footerLogos": [

data/config/ibdgc.json

@@ -75,7 +75,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "The Inflammatory Bowel Disease Genetics Consortium Data Commons supports the management, analysis, and sharing of genetic data to support the vision and mission of the IBD genetics consortium.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     }
   },
   "featureFlags": {

data/config/ncrdc-demo.json

@@ -112,7 +112,7 @@
       "subTitle": "explore, analyze, and share research data",
       "text": "The Data Common Frameworks (DCF) supports the management, analysis and sharing of many different types of biomedical data for the research community with the goal of accelerating research in the molecular basis for disease and matching targeted therapies that factor in each patient's unique biology.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     }
   },
   "featureFlags": {

data/config/ndh.json

@@ -114,7 +114,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "The website combines government datasets from 3 divisions of NIAID to create clean, easy to navigate visualizations for data-driven discovery within Allergy and Infectious Diseases.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     },
     "footerLogos": [
       {

data/config/va.json

@@ -125,7 +125,7 @@
       "subTitle": "Explore, Analyze, and Share Data",
       "text": "The Veterans Data Commons supports the management, analysis and sharing of veteran oncologic data for the research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for precision oncology.",
       "contact": "If you have any questions about access or the registration process, please contact ",
-      "email": "support@datacommons.io"
+      "email": "support@gen3.org"
     },
     "footerLogos": [
       {

docs/portal_config.md

@@ -52,7 +52,7 @@ Below is an example, with inline comments describing what each JSON block config
   "components": {
     "appName": "Gen3 Generic Data Commons", // required; title of commons that appears on the homepage
     "metaDescription": "", // optional; meta description used by search engines
-    "banner": [ // optional; banner displayed accross top of all of data portal
+    "banner": [ // optional; banner displayed across top of all of data portal
       {
         "type": "info", // Type of Alert styles, options: success, info, warning, error
         "message": "I'm a banner", // message to be displayed
@@ -150,9 +150,9 @@ Below is an example, with inline comments describing what each JSON block config
       "subTitle": "Explore, Analyze, and Share Data", // optional; subtitle for login page
       "text": "This is a generic Gen3 data commons.", // optional; text on the login page
       "contact": "If you have any questions about access or the registration process, please contact ", // optional; text for the contact section of the login page
-      "email": "support@datacommons.io", // optional; email for contact
+      "email": "support@gen3.org", // optional; email for contact
       "image": "gene", // optional; images displayed on the login page
-      "hideNavLink": false// optional default false; hide login link in main naviagion
+      "hideNavLink": false// optional default false; hide login link in main navigation
     },
    "systemUse" : { // optional; will show a Use Message in a popup, to inform users of the use policy of the commons. It will display a message which requires acceptance before a user can use the site.
       "systemUseTitle" : "", // required; Title of the popup dialog
@@ -730,7 +730,7 @@ Below is an example, with inline comments describing what each JSON block config
   "connectSrcCSPWhitelist": [ // optional; Array of urls to add to the header CSP (Content-Security-Policy) connect-src 'self'
     "https://example.s3.amazonaws.com" // full url to be added
   ],
-  "analysisTools": [ // analysis apps to be diplayed at the /analysis/ page.
+  "analysisTools": [ // analysis apps to be displayed at the /analysis/ page.
     {
       "appId": "myAppId", // Optional. Can be used to ensure the app path after the /analysis/ subpath is fixed, e.g. URL https://SERVER-DOMAIN/analysis/myAppId. If not set, then "title" (below) is used.
       "title": "My app title", // App title/name, also displayed on the App card in the /analysis page

src/Analysis/GWASApp/Components/JobInputModal/WorkflowLimitsModalErrorMessage/WorkflowLimitsModalErrorMessage.jsx

@@ -7,7 +7,7 @@ import {
 import { components } from '../../../../../params';
 import './WorkflowLimitsModalErrorMessage.css';
 
-const supportEmail = components.login?.email || 'support@datacommons.io';
+const supportEmail = components.login?.email || 'support@gen3.org';
 
 const WorkflowLimitsModalErrorMessage = ({
   status,

src/Analysis/GWASApp/Components/JobInputModal/WorkflowLimitsModalErrorMessage/WorkflowLimitsModalErrorMessage.test.jsx

@@ -37,7 +37,7 @@ describe('WorkflowLimitsModalErrorMessage', () => {
 
   test(`renders limit reached message when status is "success",
     workflowLimitInfoIsValid is true, and workFlowLimitExceeded is true`, async () => {
-    const supportEmail = components.login?.email || 'support@datacommons.io';
+    const supportEmail = components.login?.email || 'support@gen3.org';
     render(
       <WorkflowLimitsModalErrorMessage
         {...defaultProps}

src/Analysis/GWASResults/Views/Home/HomeTable/ActionsDropdown/ActionsDropdown.jsx

@@ -31,7 +31,7 @@ const ActionsDropdown = ({ record }) => {
     });
   };
 
-  const supportEmail = components.login?.email || 'support@datacommons.io';
+  const supportEmail = components.login?.email || 'support@gen3.org';
   const checkWorkflowLimit = async () => {
     try {
       const data = await fetchMonthlyWorkflowLimitInfo();

src/Analysis/SharedUtils/WorkflowLimitsDashboard/WorkflowLimitsDashboard.jsx

@@ -12,7 +12,7 @@ import LoadingErrorMessage from '../LoadingErrorMessage/LoadingErrorMessage';
 import './WorkflowLimitsDashboard.css';
 
 const WorkflowLimitsDashboard = React.memo(() => {
-  const supportEmail = components.login?.email || 'support@datacommons.io';
+  const supportEmail = components.login?.email || 'support@gen3.org';
   const refetchInterval = 5000;
 
   const { data, status } = useQuery(

src/Analysis/SharedUtils/WorkflowLimitsDashboard/WorkflowLimitsDashboard.test.jsx

@@ -21,7 +21,7 @@ const testDataExceeds = {
   workflow_limit: 50,
 };
 
-const supportEmail = components.login?.email || 'support@datacommons.io';
+const supportEmail = components.login?.email || 'support@gen3.org';
 
 const testJSX = () => (
   <QueryClientProvider client={mockedQueryClient}>

src/Discovery/Discovery.css

@@ -1,6 +1,6 @@
 .discovery-container {
   background-color: #f2f2f2;
-  padding: 30px 32px;
+  padding: 0 32px 30px 32px;
   min-height: calc(100vh - 221px);
   display: flex;
   flex-direction: column;
@@ -503,9 +503,9 @@
   font-weight: bold;
 }
 
-#discovery-page-accessibility-links {
-  top: 129px;
-  padding-right: 16px;
+.discovery-page-accessibility-links {
+  display: flex;
+  justify-content: flex-end;
 }
 
 .discovery-hidden-link {

src/Discovery/Discovery.tsx

@@ -1,5 +1,6 @@
 import React, {
   useState, useEffect, ReactNode, useMemo,
+  useRef,
 } from 'react';
 import * as JsSearch from 'js-search';
 import jsonpath from 'jsonpath';
@@ -236,6 +237,8 @@ const Discovery: React.FunctionComponent<Props> = (props: Props) => {
       || config.features.search.tagSearchDropdown.collapseOnDefault === undefined),
   );
   const [visibleResources, setVisibleResources] = useState([]);
+  const [discoveryTopPadding, setDiscoveryTopPadding] = useState(30);
+  const discoveryAccessibilityLinksRef = useRef(null);
 
   const handleSearchChange = (ev) => {
     const { value } = ev.currentTarget;
@@ -340,6 +343,13 @@ const Discovery: React.FunctionComponent<Props> = (props: Props) => {
     }
   });
 
+  // to dynamically set the top padding for discovery panel to compensate for the height of the accessibility links
+  useEffect(() => {
+    if (discoveryAccessibilityLinksRef.current) {
+      setDiscoveryTopPadding(30 - discoveryAccessibilityLinksRef.current.clientHeight);
+    }
+  }, [setDiscoveryTopPadding]);
+
   // Set up table columns
   // -----
   const columns = config.studyColumns.map((column) => ({
@@ -647,11 +657,11 @@ const Discovery: React.FunctionComponent<Props> = (props: Props) => {
   // Disabling noninteractive-tabindex rule because the span tooltip must be focusable as per https://www.w3.org/TR/2017/REC-wai-aria-1.1-20171214/#tooltip
   /* eslint-disable jsx-a11y/no-noninteractive-tabindex */
   return (
-    <div className='discovery-container'>
+    <div className='discovery-container' style={{ paddingTop: discoveryTopPadding }}>
       {(config.features.pageTitle && config.features.pageTitle.enabled)
         && <h1 className='discovery-page-title'>{config.features.pageTitle.text || 'Discovery'}</h1>}
 
-      <DiscoveryAccessibilityLinks />
+      <DiscoveryAccessibilityLinks ref={discoveryAccessibilityLinksRef} />
 
       {/* Header with stats */}
       <div className='discovery-header'>

src/Discovery/DiscoveryAccessibilityLinks.tsx

@@ -1,4 +1,4 @@
-import React from 'react';
+import React, { forwardRef } from 'react';
 import Tooltip from 'rc-tooltip';
 
 const tooltipText = 'These accessibility links assist with keyboard navigation of the site. Selecting a link will bring tab focus to the specified page content.';
@@ -23,8 +23,8 @@ const viewLinkedElement = (elementId) => {
   });
 };
 
-const DiscoveryAccessibilityLinks = () => (
-  <div className='g3-accessibility-links' id='discovery-page-accessibility-links'>
+const DiscoveryAccessibilityLinks = forwardRef((props, ref) => (
+  <div className='discovery-page-accessibility-links' ref={ref}>
     <Tooltip
       placement='left'
       overlay={tooltipText}
@@ -80,6 +80,6 @@ const DiscoveryAccessibilityLinks = () => (
       <span>Pagination</span>
     </a>
   </div>
-);
+));
 
 export default DiscoveryAccessibilityLinks;

src/GenericAccessRequestForm/Constants/FormSpecificConstants.tsx

@@ -1,7 +1,7 @@
 import React from 'react';
 import { workspaceRegistrationConfig } from '../../localconf';
 
-const defaultEmail = 'support@datacommons.io';
+const defaultEmail = 'support@gen3.org';
 
 const StudyRegistrationAccessRequest = {
   name: 'StudyRegistration',

src/Workspace/ErrorWorkspacePlaceholder.jsx

@@ -4,7 +4,7 @@ import NotFoundSVG from '../img/not-found.svg';
 import { components } from '../params';
 
 const ErrorWorkspacePlaceholder = () => {
-  const supportEmail = components.login?.email || 'support@datacommons.io';
+  const supportEmail = components.login?.email || 'support@gen3.org';
   return (
     <div className='error-workspace-placeholder__error-msg'>
       <h1>Error opening workspace...</h1>

src/Workspace/index.jsx

@@ -458,7 +458,7 @@ class Workspace extends React.Component {
 
   handleMenuClick = async (e) => {
     if (this.state.payModel.all_pay_models[e.key].request_status === 'above limit') {
-      message.error('Selected pay model usage has exceeded its available funding. Please choose another pay model. Contact brhsupport@datacommons.io with questions.');
+      message.error('Selected pay model usage has exceeded its available funding. Please choose another pay model. Contact brhsupport@gen3.org with questions.');
       return;
     }
     await fetchWithCreds({
@@ -741,7 +741,7 @@ class Workspace extends React.Component {
                   {isPayModelAboveLimit
                     ? (
                       <Alert
-                        description='Selected pay model usage has exceeded its available funding.  Please replenish your funds or choose a different pay model. Contact brhsupport@datacommons.io if you have questions.'
+                        description='Selected pay model usage has exceeded its available funding.  Please replenish your funds or choose a different pay model. Contact brhsupport@gen3.org if you have questions.'
                         type='error'
                         banner
                         closable

src/components/ErrorPage403.jsx

@@ -5,7 +5,7 @@ import { components } from '../params';
 
 class ErrorPage403 extends React.Component {
   render() {
-    const supportEmail = components.login?.email || 'support@datacommons.io';
+    const supportEmail = components.login?.email || 'support@gen3.org';
     return (
       <div className='error-placeholder__error-msg '>
         <h1>Error accessing requested resource...</h1>

testSchema.sh

@@ -8,7 +8,6 @@ testCases=(
 bpa "data.bloodpac.org"
 dcf "nci-crdc.datacommons.io"
 gtex "gen3.biodatacatalyst.nhlbi.nih.gov"
-anvil "gen3.theanvil.io"
 genomel "genomel.bionimbus.org"
 )
 index=0