@@ -183,6 +208,18 @@ OpenAccessFileDownloadModal.propTypes = {
downloadRequestResponse: PropTypes.string.isRequired,
handleDownloadRequest: PropTypes.func.isRequired,
selectedFiles: PropTypes.arrayOf(PropTypes.shape({})).isRequired,
+ profile: PropTypes.shape({
+ userid: PropTypes.string,
+ user_metadata: PropTypes.shape({
+ userType: PropTypes.string,
+ email: PropTypes.string,
+ name: PropTypes.string,
+ }),
+ }),
+};
+
+OpenAccessFileDownloadModal.defaultProps = {
+ profile: {},
};
export default OpenAccessFileDownloadModal;
diff --git a/src/BrowseDataPage/components/selectiveDataDownloadFileBrowser.jsx b/src/BrowseDataPage/components/selectiveDataDownloadFileBrowser.jsx
new file mode 100644
index 00000000..478d11c2
--- /dev/null
+++ b/src/BrowseDataPage/components/selectiveDataDownloadFileBrowser.jsx
@@ -0,0 +1,77 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import { Link } from 'react-router-dom';
+import BrowseDataTable from '../browseDataTable';
+import BrowseDataFilter from '../browseDataFilter';
+import BootstrapSpinner from '../../lib/ui/spinner';
+
+function SelectiveDataDownloadFileBrowser({
+ profile,
+ filteredFiles,
+ fetching,
+ activeFilters,
+ onChangeFilter,
+ onResetFilters,
+ handleDownloadRequest,
+ downloadRequestResponse,
+ waitingForResponse,
+}) {
+ return (
+
+ );
+}
+
+SelectiveDataDownloadFileBrowser.propTypes = {
+ profile: PropTypes.shape({
+ user_metadata: PropTypes.shape({
+ userType: PropTypes.string,
+ email: PropTypes.string,
+ name: PropTypes.string,
+ }),
+ }),
+ filteredFiles: PropTypes.arrayOf(PropTypes.shape({})).isRequired,
+ fetching: PropTypes.bool.isRequired,
+ activeFilters: BrowseDataFilter.propTypes.activeFilters.isRequired,
+ onChangeFilter: PropTypes.func.isRequired,
+ onResetFilters: PropTypes.func.isRequired,
+ handleDownloadRequest: PropTypes.func.isRequired,
+ downloadRequestResponse: PropTypes.string.isRequired,
+ waitingForResponse: PropTypes.bool.isRequired,
+};
+
+SelectiveDataDownloadFileBrowser.defaultProps = {
+ profile: {},
+};
+
+export default SelectiveDataDownloadFileBrowser;
diff --git a/src/BrowseDataPage/components/selectiveDataDownloadFileBrowserTab.jsx b/src/BrowseDataPage/components/selectiveDataDownloadFileBrowserTab.jsx
new file mode 100644
index 00000000..1a584721
--- /dev/null
+++ b/src/BrowseDataPage/components/selectiveDataDownloadFileBrowserTab.jsx
@@ -0,0 +1,47 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+
+function SelectiveDataDownloadFileBrowserTab({
+ className,
+ id,
+ href,
+ ariaControls,
+ tabTitle,
+ tabSelectHandler,
+ onResetFilters,
+}) {
+ function handleTabSelect(e) {
+ e.preventDefault();
+ tabSelectHandler();
+ onResetFilters();
+ }
+
+ return (
+
+ );
+}
+
+SelectiveDataDownloadFileBrowserTab.propTypes = {
+ className: PropTypes.string.isRequired,
+ id: PropTypes.string.isRequired,
+ href: PropTypes.string.isRequired,
+ ariaControls: PropTypes.string.isRequired,
+ tabTitle: PropTypes.string.isRequired,
+ tabSelectHandler: PropTypes.func.isRequired,
+ onResetFilters: PropTypes.func.isRequired,
+};
+
+export default SelectiveDataDownloadFileBrowserTab;
diff --git a/src/BrowseDataPage/components/selectiveDataDownloads.jsx b/src/BrowseDataPage/components/selectiveDataDownloads.jsx
new file mode 100644
index 00000000..9649bce9
--- /dev/null
+++ b/src/BrowseDataPage/components/selectiveDataDownloads.jsx
@@ -0,0 +1,128 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import { useSelector } from 'react-redux';
+import { Link } from 'react-router-dom';
+import PageTitle from '../../lib/ui/pageTitle';
+import BrowseDataFilter from '../browseDataFilter';
+import SelectiveDataDownloadFileBrowser from './selectiveDataDownloadFileBrowser';
+
+function SelectiveDataDownloads({
+ profile,
+ filteredFiles,
+ fetching,
+ activeFilters,
+ onChangeFilter,
+ onResetFilters,
+ handleDownloadRequest,
+ downloadRequestResponse,
+ waitingForResponse,
+}) {
+ const dataDownload = useSelector((state) => state.browseData);
+
+ // set page title based on selected data
+ function renderPageTitle() {
+ let titleStr = 'Data Download';
+ if (dataDownload.pass1b06DataSelected) {
+ titleStr = 'Data Download - Endurance Training Rats';
+ }
+ if (dataDownload.pass1a06DataSelected) {
+ titleStr = 'Data Download - Acute Exercise Rats';
+ }
+ if (dataDownload.humanPrecovidSedAduDataSelected) {
+ titleStr = 'Data Download - Human Sedentary Adults';
+ }
+
+ return titleStr;
+ }
+
+ // set page summary based on selected data
+ function renderStudySummary() {
+ let summary = '';
+ if (dataDownload.pass1b06DataSelected) {
+ summary =
+ 'Experimental data from endurance trained (1 week, 2 weeks, 4 weeks or 8 weeks) compared to untrained young adult rats (6 months old).';
+ }
+ if (dataDownload.pass1a06DataSelected) {
+ summary =
+ 'Experimental data from acute exercise study on young adult rats for a comprehensive analysis of the physiological responses following a single exercise session in 6-month-old F344 rats.';
+ }
+ if (dataDownload.humanPrecovidSedAduDataSelected) {
+ summary =
+ 'Differential analysis results data for differences in changes during the acute bout, comparing the change from pre-exercise baseline at any given timepoint during the acute bout as compared to resting control.';
+ }
+
+ return summary;
+ }
+
+ // set data file list based on selected data
+ let dataFiles = [];
+ if (dataDownload.pass1b06DataSelected) {
+ dataFiles = filteredFiles.filter((item) => item.phase === 'PASS1B-06');
+ }
+ if (dataDownload.pass1a06DataSelected) {
+ dataFiles = filteredFiles.filter((item) => item.phase === 'PASS1A-06');
+ }
+ if (dataDownload.humanPrecovidSedAduDataSelected) {
+ dataFiles = filteredFiles.filter(
+ (item) => item.phase === 'HUMAN-PRECOVID-SED-ADU',
+ );
+ }
+
+ return (
+
+ );
+}
+
+SelectiveDataDownloads.propTypes = {
+ filteredFiles: PropTypes.arrayOf(PropTypes.shape({})),
+ fetching: PropTypes.bool.isRequired,
+ profile: PropTypes.shape({
+ user_metadata: PropTypes.shape({
+ userType: PropTypes.string,
+ email: PropTypes.string,
+ name: PropTypes.string,
+ userid: PropTypes.string,
+ }),
+ }),
+ activeFilters: BrowseDataFilter.propTypes.activeFilters.isRequired,
+ onChangeFilter: PropTypes.func.isRequired,
+ onResetFilters: PropTypes.func.isRequired,
+ handleDownloadRequest: PropTypes.func.isRequired,
+ downloadRequestResponse: PropTypes.string.isRequired,
+ waitingForResponse: PropTypes.bool.isRequired,
+};
+
+SelectiveDataDownloads.defaultProps = {
+ profile: {},
+ filteredFiles: [],
+};
+
+export default SelectiveDataDownloads;
diff --git a/src/BrowseDataPage/components/selectiveDataDownloadsCard.jsx b/src/BrowseDataPage/components/selectiveDataDownloadsCard.jsx
new file mode 100644
index 00000000..8214e9a0
--- /dev/null
+++ b/src/BrowseDataPage/components/selectiveDataDownloadsCard.jsx
@@ -0,0 +1,60 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import { useHistory } from 'react-router-dom';
+
+function SelectiveDataDownloadsCard({
+ cardIcon,
+ cardTitle,
+ dataSelectHandler,
+ selectedData,
+ cssSelector,
+ children,
+}) {
+ const history = useHistory();
+
+ function handleDataSelect(e) {
+ e.preventDefault();
+ dataSelectHandler();
+ history.push('/data-download/file-browser', {
+ state: { selectedData },
+ });
+ }
+
+ return (
+
+ );
+}
+
+SelectiveDataDownloadsCard.propTypes = {
+ cardIcon: PropTypes.string.isRequired,
+ cardTitle: PropTypes.string.isRequired,
+ dataSelectHandler: PropTypes.func.isRequired,
+ selectedData: PropTypes.string,
+ cssSelector: PropTypes.string,
+};
+
+SelectiveDataDownloadsCard.defaultProps = {
+ selectedData: '',
+ cssSelector: '',
+};
+
+export default SelectiveDataDownloadsCard;
diff --git a/src/BrowseDataPage/helper.jsx b/src/BrowseDataPage/helper.jsx
index cfb731a7..30204653 100644
--- a/src/BrowseDataPage/helper.jsx
+++ b/src/BrowseDataPage/helper.jsx
@@ -251,6 +251,57 @@ export const transformData = (arr) => {
item.assay = newMetabAssayVal;
}
}
+ if (
+ item.assay !== null &&
+ item.assay !== undefined &&
+ item.omics === 'Metabolomics Targeted'
+ ) {
+ let newMetabAssayVal = item.assay;
+ if (
+ newMetabAssayVal.indexOf('Acylcarnitines') !== -1 &&
+ newMetabAssayVal.indexOf('Oxylipins') !== -1
+ ) {
+ newMetabAssayVal = 'Merged';
+ item.assay = newMetabAssayVal;
+ }
+ }
+ if (item.tissue_name !== null && item.tissue_name !== undefined) {
+ let newTissueVal = item.tissue_name;
+ if (
+ newTissueVal.indexOf('Human PBMC') !== -1 ||
+ newTissueVal.indexOf('Human EDTA Packed Cells') !== -1 ||
+ newTissueVal.indexOf('Human PAXgene RNA') !== -1
+ ) {
+ newTissueVal = 'Blood';
+ item.tissue_name = newTissueVal;
+ }
+ if (
+ newTissueVal.indexOf('Human Adipose') !== -1 ||
+ newTissueVal.indexOf('Human Adipose Powder') !== -1
+ ) {
+ newTissueVal = 'Adipose';
+ item.tissue_name = newTissueVal;
+ }
+ if (
+ newTissueVal.indexOf('Human Muscle') !== -1 ||
+ newTissueVal.indexOf('Human Muscle Powder') !== -1
+ ) {
+ newTissueVal = 'Muscle';
+ item.tissue_name = newTissueVal;
+ }
+ if (newTissueVal.indexOf('Human EDTA Plasma') !== -1) {
+ newTissueVal = 'Plasma';
+ item.tissue_name = newTissueVal;
+ }
+ if (
+ newTissueVal.indexOf('EDTA Plasma') !== -1 &&
+ item.omics.indexOf('Metabolomics') !== -1 &&
+ item.study.indexOf('Acute Exercise') !== -1
+ ) {
+ newTissueVal = 'Plasma';
+ item.tissue_name = newTissueVal;
+ }
+ }
});
return tranformArray;
};
diff --git a/src/LandingPage/landingPage.jsx b/src/LandingPage/landingPage.jsx
index c57f6a75..6542e7cd 100644
--- a/src/LandingPage/landingPage.jsx
+++ b/src/LandingPage/landingPage.jsx
@@ -214,18 +214,9 @@ export function LandingPage({ isAuthenticated, profile }) {
diff --git a/src/MultiOmicsWorkingGroups/bicUpdates.jsx b/src/MultiOmicsWorkingGroups/bicUpdates.jsx
new file mode 100644
index 00000000..87b5a26a
--- /dev/null
+++ b/src/MultiOmicsWorkingGroups/bicUpdates.jsx
@@ -0,0 +1,39 @@
+import React from 'react';
+
+function BicUpdates() {
+ return (
+
+
BIC Updates
+
+ The Bioinformatics Center is committed to keeping our community informed
+ and up-to-date with the latest developments in bioinformatics resources,
+ tools, and data. To this end, we provide{' '}
+
+ monthly BIC Updates
+ {' '}
+ that encapsulate all recent advancements, new resources, and crucial
+ data updates facilitated by our center.{' '}
+
+ The archive of all the monthly BIC Updates is available here
+
+ .
+
+
+ Note: BIC Updates are disseminated monthly through email by Jane Lu. To
+ be added to the distribution list, please contact Jane at{' '}
+ motrpac-acc@aging.ufl.edu
+ .
+
+
+ );
+}
+
+export default BicUpdates;
diff --git a/src/MultiOmicsWorkingGroups/dawgPAC.jsx b/src/MultiOmicsWorkingGroups/dawgPAC.jsx
new file mode 100644
index 00000000..ecef3adf
--- /dev/null
+++ b/src/MultiOmicsWorkingGroups/dawgPAC.jsx
@@ -0,0 +1,268 @@
+import React, { useState } from 'react';
+import PropTypes from 'prop-types';
+import HtmlReportModal from './htmlReportModal';
+
+const proteomicsReportsDA = [
+ 't55-gastrocnemius_prot-ph_DEA_report.html',
+ 't55-gastrocnemius_prot-pr_DEA_report.html',
+ 't58-heart_prot-ac_DEA_report.html',
+ 't58-heart_prot-ph_DEA_report.html',
+ 't58-heart_prot-pr_DEA_report.html',
+ 't59-kidney_prot-ph_DEA_report.html',
+ 't59-kidney_prot-pr_DEA_report.html',
+ 't66-lung_prot-ph_DEA_report.html',
+ 't66-lung_prot-pr_DEA_report.html',
+ 't68-liver_prot-ac_DEA_report.html',
+ 't68-liver_prot-ph_DEA_report.html',
+ 't68-liver_prot-pr_DEA_report.html',
+ 't70-white-adipose_prot-ph_DEA_report.html',
+ 't70-white-adipose_prot-pr_DEA_report.html',
+];
+
+const proteomicsReportsQCNorm = [
+ 't55-gastrocnemius_prot-ph_qc-norm_report.html',
+ 't55-gastrocnemius_prot-pr_qc-norm_report.html',
+ 't58-heart_prot-ac_qc-norm_report.html',
+ 't58-heart_prot-ph_qc-norm_report.html',
+ 't58-heart_prot-pr_qc-norm_report.html',
+ 't59-kidney_prot-ph_qc-norm_report.html',
+ 't59-kidney_prot-pr_qc-norm_report.html',
+ 't66-lung_prot-ph_qc-norm_report.html',
+ 't66-lung_prot-pr_qc-norm_report.html',
+ 't68-liver_prot-ac_qc-norm_report.html',
+ 't68-liver_prot-ph_qc-norm_report.html',
+ 't68-liver_prot-pr_qc-norm_report.html',
+ 't70-white-adipose_prot-ph_qc-norm_report.html',
+ 't70-white-adipose_prot-pr_qc-norm_report.html',
+];
+
+const proteomics1A1CIndependentAnalyses = [
+ 't55-gastrocnemius_prot-ph_1A1C-independent-analyses_report.html',
+ 't55-gastrocnemius_prot-pr_1A1C-independent-analyses_report.html',
+ 't58-heart_prot-ac_1A1C-independent-analyses_report.html',
+ 't58-heart_prot-ph_1A1C-independent-analyses_report.html',
+ 't58-heart_prot-pr_1A1C-independent-analyses_report.html',
+ 't59-kidney_prot-ph_1A1C-independent-analyses_report.html',
+ 't59-kidney_prot-pr_1A1C-independent-analyses_report.html',
+ 't66-lung_prot-ph_1A1C-independent-analyses_report.html',
+ 't66-lung_prot-pr_1A1C-independent-analyses_report.html',
+ 't68-liver_prot-ac_1A1C-independent-analyses_report.html',
+ 't68-liver_prot-ph_1A1C-independent-analyses_report.html',
+ 't68-liver_prot-pr_1A1C-independent-analyses_report.html',
+ 't70-white-adipose_prot-ph_1A1C-independent-analyses_report.html',
+ 't70-white-adipose_prot-pr_1A1C-independent-analyses_report.html',
+];
+
+function DawgPAC({ profile }) {
+ const [selectedReport, setSelectedReport] = useState(null);
+ const [selectedReportLabel, setSelectedReportLabel] = useState(null);
+
+ const handleClickReport = (report, reportLabel) => {
+ setSelectedReport(report);
+ setSelectedReportLabel(reportLabel);
+ };
+
+ return (
+
+
+ DAWG-PAC: Data Analysis Working Group - PASS1A/1C
+
+
PASS1A/1C: Acute exercise on young adult rats
+
+ The goal of the acute exercise study on young adult rats (designated as
+ PASS1A-06) is to conduct a comprehensive analysis of the physiological
+ responses following a single exercise session in 6-month-old F344 rats.
+ The primary aim was to collect a wide range of tissue samples
+ post-exercise for high-quality analysis at chemical analysis sites.
+
+
+
+ );
+}
+
+DawgPAC.propTypes = {
+ profile: PropTypes.shape({
+ userid: PropTypes.string,
+ user_metadata: PropTypes.object,
+ }),
+};
+
+DawgPAC.defaultProps = {
+ profile: {},
+};
+
+export default DawgPAC;
diff --git a/src/MultiOmicsWorkingGroups/htmlReportModal.jsx b/src/MultiOmicsWorkingGroups/htmlReportModal.jsx
index 475951cc..6e6caa1c 100644
--- a/src/MultiOmicsWorkingGroups/htmlReportModal.jsx
+++ b/src/MultiOmicsWorkingGroups/htmlReportModal.jsx
@@ -1,7 +1,8 @@
import React, { useState, useRef } from 'react';
import PropTypes from 'prop-types';
+import { trackEvent } from '../GoogleAnalytics/googleAnalytics';
-function HtmlReportModal({ selectedReport, selectedReportLabel }) {
+function HtmlReportModal({ selectedReport, selectedReportLabel, profile }) {
const iframeRef = useRef(null);
const [iframeLoaded, setIframeLoaded] = useState(false);
@@ -29,6 +30,19 @@ function HtmlReportModal({ selectedReport, selectedReportLabel }) {
className="btn btn-primary btn-report-download ml-3"
href={`/static-assets/dawg-pac/${selectedReport}`}
download
+ onClick={(e) => {
+ // track event in Google Analytics 4
+ trackEvent(
+ 'Multi-omics Working Groups',
+ 'html_report_download',
+ profile && profile.userid
+ ? profile.userid.substring(
+ profile.userid.indexOf('|') + 1,
+ )
+ : 'anonymous',
+ selectedReport,
+ );
+ }}
>
Download Report
@@ -71,11 +85,16 @@ function HtmlReportModal({ selectedReport, selectedReportLabel }) {
HtmlReportModal.propTypes = {
selectedReport: PropTypes.string,
selectedReportLabel: PropTypes.string,
+ profile: PropTypes.shape({
+ userid: PropTypes.string,
+ user_metadata: PropTypes.object,
+ }),
};
HtmlReportModal.defaultProps = {
selectedReport: null,
selectedReportLabel: null,
+ profile: {},
};
export default HtmlReportModal;
diff --git a/src/MultiOmicsWorkingGroups/multiOmicsWorkingGroups.jsx b/src/MultiOmicsWorkingGroups/multiOmicsWorkingGroups.jsx
index 2237d76d..7d0e0f4e 100644
--- a/src/MultiOmicsWorkingGroups/multiOmicsWorkingGroups.jsx
+++ b/src/MultiOmicsWorkingGroups/multiOmicsWorkingGroups.jsx
@@ -1,70 +1,13 @@
-import React, { useState } from 'react';
+import React from 'react';
import { useSelector } from 'react-redux';
import { Redirect } from 'react-router-dom';
import { Helmet } from 'react-helmet';
import PageTitle from '../lib/ui/pageTitle';
-import HtmlReportModal from './htmlReportModal';
-
-const proteomicsReportsDA = [
- 't55-gastrocnemius_prot-ph_DEA_report.html',
- 't55-gastrocnemius_prot-pr_DEA_report.html',
- 't58-heart_prot-ac_DEA_report.html',
- 't58-heart_prot-ph_DEA_report.html',
- 't58-heart_prot-pr_DEA_report.html',
- 't59-kidney_prot-ph_DEA_report.html',
- 't59-kidney_prot-pr_DEA_report.html',
- 't66-lung_prot-ph_DEA_report.html',
- 't66-lung_prot-pr_DEA_report.html',
- 't68-liver_prot-ac_DEA_report.html',
- 't68-liver_prot-ph_DEA_report.html',
- 't68-liver_prot-pr_DEA_report.html',
- 't70-white-adipose_prot-ph_DEA_report.html',
- 't70-white-adipose_prot-pr_DEA_report.html',
-];
-
-const proteomicsReportsQCNorm = [
- 't55-gastrocnemius_prot-ph_qc-norm_report.html',
- 't55-gastrocnemius_prot-pr_qc-norm_report.html',
- 't58-heart_prot-ac_qc-norm_report.html',
- 't58-heart_prot-ph_qc-norm_report.html',
- 't58-heart_prot-pr_qc-norm_report.html',
- 't59-kidney_prot-ph_qc-norm_report.html',
- 't59-kidney_prot-pr_qc-norm_report.html',
- 't66-lung_prot-ph_qc-norm_report.html',
- 't66-lung_prot-pr_qc-norm_report.html',
- 't68-liver_prot-ac_qc-norm_report.html',
- 't68-liver_prot-ph_qc-norm_report.html',
- 't68-liver_prot-pr_qc-norm_report.html',
- 't70-white-adipose_prot-ph_qc-norm_report.html',
- 't70-white-adipose_prot-pr_qc-norm_report.html',
-];
-
-const proteomics1A1CIndependentAnalyses = [
- 't55-gastrocnemius_prot-ph_1A1C-independent-analyses_report.html',
- 't55-gastrocnemius_prot-pr_1A1C-independent-analyses_report.html',
- 't58-heart_prot-ac_1A1C-independent-analyses_report.html',
- 't58-heart_prot-ph_1A1C-independent-analyses_report.html',
- 't58-heart_prot-pr_1A1C-independent-analyses_report.html',
- 't59-kidney_prot-ph_1A1C-independent-analyses_report.html',
- 't59-kidney_prot-pr_1A1C-independent-analyses_report.html',
- 't66-lung_prot-ph_1A1C-independent-analyses_report.html',
- 't66-lung_prot-pr_1A1C-independent-analyses_report.html',
- 't68-liver_prot-ac_1A1C-independent-analyses_report.html',
- 't68-liver_prot-ph_1A1C-independent-analyses_report.html',
- 't68-liver_prot-pr_1A1C-independent-analyses_report.html',
- 't70-white-adipose_prot-ph_1A1C-independent-analyses_report.html',
- 't70-white-adipose_prot-pr_1A1C-independent-analyses_report.html',
-];
+import BicUpdates from './bicUpdates';
+import PreCAWG from './preCAWG';
+import DawgPAC from './dawgPAC';
function MultiOmicsWorkingGroups() {
- const [selectedReport, setSelectedReport] = useState(null);
- const [selectedReportLabel, setSelectedReportLabel] = useState(null);
-
- const handleClickReport = (report, reportLabel) => {
- setSelectedReport(report);
- setSelectedReportLabel(reportLabel);
- };
-
// get states from redux store
const userProfile = useSelector((state) => state.auth.profile);
@@ -83,277 +26,54 @@ function MultiOmicsWorkingGroups() {
-
-
BIC Updates
-
- The Bioinformatics Center is committed to keeping our community
- informed and up-to-date with the latest developments in
- bioinformatics resources, tools, and data. To this end, we provide{' '}
+
+ {/* nav tabs */}
+
-
-
- PRE-CAWG: PRE-COVID Analysis Working Group
-
-
- Processed PreCAWG data are set for internal dissemination of the
- first freeze.
-
-
- -
- Internal freeze notes for full details on the internal freeze and
- steps for onboarding to work with the PreCAWG are available{' '}
-
- this Google Doc
-
-
- -
- Source code is available in{' '}
-
- this GitHub repository
-
-
- -
- Data processing methods are available in{' '}
-
- this Google Drive folder
-
-
- -
- Raw clinical data is available in the motrpac-data-hub bucket:{' '}
-
gs://motrpac-data-hub/human-precovid/phenotype/raw/
-
-
-
-
-
- DAWG-PAC: Data Analysis Working Group - PASS1A/1C
-
-
PASS1A/1C: Acute exercise on young adult rats
-
- The goal of the acute exercise study on young adult rats (designated
- as PASS1A-06) is to conduct a comprehensive analysis of the
- physiological responses following a single exercise session in
- 6-month-old F344 rats. The primary aim was to collect a wide range
- of tissue samples post-exercise for high-quality analysis at
- chemical analysis sites.
-
-
+
+
+ {/* tab panes */}
+
diff --git a/src/MultiOmicsWorkingGroups/preCAWG.jsx b/src/MultiOmicsWorkingGroups/preCAWG.jsx
new file mode 100644
index 00000000..7a050090
--- /dev/null
+++ b/src/MultiOmicsWorkingGroups/preCAWG.jsx
@@ -0,0 +1,786 @@
+import React from 'react';
+import { Link } from 'react-router-dom';
+import IconSet from '../lib/iconSet';
+
+function PreCAWG() {
+ return (
+
+
PRE-CAWG: PRE-COVID Analysis Working Group
+
MoTrPAC Data Package: human-precovid-sed-adu
+
+
+
2024APR01 Freeze 1.1 Release Notes
+
+
+
+
+
+ - Data package nickname:
+ - human-precovid-sed-adu
+ - Type:
+ - Freeze
+ - Distribution date:
+ - 04/01/2024 (Release)
+ - Organism:
+ - Human
+ - Internal Batch:
+ - Precovid
+ - Baseline activity level:
+ - Sedentary
+
+ |
+
+
+ - Age:
+ - Adults
+ - Modality:
+ - resistance and endurance
+ - Exercise duration:
+ - acute and chronic
+ - Freeze version:
+ - 1.1
+ - DMAQC CRF Version:
+ - 1.06
+
+ |
+
+
+
+
Data Access
+
Programmatic Access via Google Cloud
+
+ With this release, internal data access is preferred via the beta
+ version of a custom R package created by Christopher Jin called{' '}
+
+ MotrpacHumanPreSuspension
+
+ . Using this approach ensures seamless updates for any backend changes
+ to the data. Please review the README associated with GitHub repo to get
+ started and ask for help from Christopher Jin or Dan Katz (best contact
+ via the help desk at{' '}
+
+ motrpac-helpdesk@lists.stanford.edu
+
+ ) if needed.
+
+
+ As before, data can also be accessed in the following ways
+ programmatically:
+
+ -
+ From the command line using the{' '}
+
+ Google Cloud Command Line
+ {' '}
+ Interface
+
+ -
+ From a BIC approved download function for R such as{' '}
+
load_adu_norm_data (currently available only in the
+ functions library of the precovid-analyses GitHub repo) or{' '}
+ MotrpacBicQC::dl_read_gcp (package{' '}
+
+ here
+
+ ).
+
+
+
+
All options still require Google Cloud Command Line Interface.
+
Download access
+
+ Data will be available in early April 2024 for direct download from
+ MoTrPAC Data Hub.
+
+
Data Changes
+
Versioning
+
+ Prior file names may have ended in “v1.txt” instead of the BIC standard
+ "v1.0.txt". This has been fixed. All files remain v1.0 as the underlying
+ standard methodology has not changed.
+
+
QC-normalized data
+
+ Metabolomics: during the soft release, data was scaled to{' '}
+ mean = 0, and sd = 1. To allow more
+ flexibility for analysts, this has been undone. The new version of the
+ data follows the following format example:
+
+
+ human-precovid-sed-adu_t11-adipose_metab-t-ka_qc-norm_log2_v1.0.txt
+
+ which replaces:
+
+ human-precovid-sed-adu_t11-adipose_metab-t-ka_qc-norm_log2-scaled_v1.txt
+
+
+
Differential analysis results
+
+ With the release of Freeze 1, there are now differential analysis
+ results available. Data are for differences in changes during the acute
+ bout, comparing the change from pre-exercise baseline at any given
+ timepoint during the acute bout as compared to resting control. Results
+ are adjusted for age, sex, BMI, clinical site, and technical covariates.
+ Models are processed by variancePartition::dream to allow
+ for random effects models accounting for random effects of individuals.
+ Analytical details and methods are forthcoming. Note that files
+ containing these results have names annotated with “dream” to indicate
+ this model selection.
+
+
+ DA data location:{' '}
+
+ gs://motrpac-data-hub/analysis/human-precovid-sed-adu/[ome]/da[ome]
+ {' '}
+ represents one of epigenomics, proteomics, metabolomics-targeted,
+ metabolomics-untargeted, or transcriptomics.
+
+
Guidance
+
+ Note that methyl-capture DA and QC-normalized data continues to be in
+ "beta" status. Consortium members may incorporate the data into analysis
+ pipelines, but please be aware that some results may change.
+
+
2024FEB05 Soft Release
+
+
+
+
+
+ - Type:
+ - Initial freeze
+ - Distribution date:
+ - 02/05/2024 (Soft Release)
+ - Organism:
+ - Human
+ - Internal Batch:
+ - Precovid
+ - Baseline activity level:
+ - Sedentary
+ - Age:
+ - Adults
+
+ |
+
+
+ - Modality:
+ - resistance and endurance
+ - Exercise duration:
+ - acute and chronic
+ - Data package nickname:
+ - human-precovid-sed-adu
+ - Freeze version:
+ - 1.0
+ - DMAQC CRF Version:
+ - 1.06
+
+ |
+
+
+
+
Data Notes
+
+ -
+ The methyl capture pipeline has been developed collaboratively
+ BIC and the GET, and while data and metadata have been shared, the BIC
+ is in the final stages of validating the pipeline. Users can begin
+ working with the qc-normalized data, and we anticipate finalizing the
+ results, which might come with minor updates, in the coming weeks.
+
+ -
+ Individual level genomic data, per the genomic data sharing
+ plan, is considered high-risk data. As such, this data requires
+ additional permission to access. If you would like to work with whole
+ genome sequence data, please contact the BIC.
+
+ -
+ The curated biospecimens file is intended for analysts to be a
+ replacement for the EQC file. It has a many-to-one and one-to-many
+ relationship as needed between labelID, BID, pid, and vialLabel,
+ though any labelID-vialLabel pair should be unique. Users should be
+ aware that biospecimen data in this file is pertinent to the collected
+ sample, which is identified by the labelID. Some vialLabels, which go
+ off to chemical analysis, are sometimes made up of multiple combined
+ labelIDs. Thus, if using the biospecimens file to flag vialLabel
+ samples that might not meet the user's criteria, be aware only one of
+ the multiple labelIDs that are mixed into a vialLabel may violate a
+ specific biospecimen criterion. No samples have been removed from the
+ data package based on data from this table. Rather we have relied on
+ outlier analysis as described in the methods.
+
+ - All data sets are tab-separated .txt files.
+ -
+ It is highly recommended that data is downloaded from Google Cloud in
+ one of two ways:
+
+ -
+ From the command line using the{' '}
+
+ Google Cloud Command Line
+ {' '}
+ Interface
+
+ -
+ From a BIC approved download function for R such as{' '}
+
load_adu_norm_data (currently available only in the
+ functions library of the precovid-analyses GitHub repo) or{' '}
+ MotrpacBicQC::dl_read_gcp (package{' '}
+
+ here
+
+ ). Both options still require Google Cloud Command Line Interface.
+
+
+
+
+
Data
+
Omics
+
+ Omics data are available in both raw and QC-normalized format. The
+ QC-normalized data is preferred for analysis, as these data are the
+ result of consortium consensus imputation, normalization, batch
+ correction, and outlier removal decisions.{' '}
+
+ Please note
+ {' '}
+ that in regard to raw and analyzed data “human precovid” means slightly
+ different things, as the precovid phase of clinical participation and
+ multi-omic measurement did include PED and HA participants, but these
+ are excluded from this analytical freeze.{' '}
+ Any reanalysis of the raw data must exclude these participants.
+
+
+ Raw results data location:{' '}
+ gs://motrpac-data-hub/human-precovid/results/
+
+
+ QC-normalized data location:{' '}
+
+ gs://motrpac-data-hub/analysis/human-precovid-sed-adu/[ome]/qc-norm*[ome]
+ {' '}
+ represents one of epigenomics, proteomics, metabolomics-targeted,
+ metabolomics-untargeted, or transcriptomics
+
+
Clinical
+
+ Clinical data for sedentary adults are available in the complete case
+ report form (CRF) data, as transferred by the DMAQC. It includes the
+ Actigraph minute-level analytical data processed by DMAQC. The only BIC
+ processing to the above files is redaction of PHI and de-identification.{' '}
+ A critical data table is the "Key" data set, which includes
+ critical demographics and the randomized group for each participant. In
+ these files, ds indicates the data set, while dd indicates the data
+ dictionary. Missing data files contain lists of missing forms and
+ visits, with a reason provided where applicable, and identified by
+ participant.
+
+
+ CRF data location:{' '}
+
+ gs://motrpac-data-hub/human-precovid/phenotype/human-precovid-sed-adu/raw
+
+
+
+ Key data set:{' '}
+
+ gs://motrpac-data-hub/human-precovid/phenotype/human-precovid-sed-adu/raw/data_sets/human-precovid-sed-adu_clinical_key_ds_crf-redacted_v1.txt
+
+
+
+ The freeze also includes a set of “curated” tables, created by the BIC
+ and designed to facilitate analysis. These include:
+
+ -
+ A table of vital signs and height/weight/BMI as recorded at each
+ visit
+
+ -
+ Baseline and follow up exercise parameters (CPET, 1RM, grip
+ strength)
+
+ -
+ Acute bout exercise parameters and "dose" metrics (EE and RE
+ separately)
+
+ -
+ A table of biospecimen-level data (primary key: labelID-vialLabel
+ pairs). This table contains data about biospecimens that might
+ affect multi-omic data quality. It is recommended that analysts use
+ this file rather than the EQC file to map samples to participants
+ and other metadata.
+
+ -
+ A table of derived variables at baseline from the Actigraph
+ minute-level analytical data
+
+
+
+
+ Curated clinical data location:{' '}
+
+ gs://motrpac-data-hub/human-precovid/phenotype/human-precovid-sed-adu/curated
+
+
+
Metadata
+
QC reports
+
+ These html reports show numerous quality checks of the raw data, and any
+ steps or graphic visualizations that were utilized in decision making
+ for processing raw data to the QC normalized data.
+
+
+ QC report location:{' '}
+
+ gs://motrpac-data-hub/analysis/human-precovid-sed-adu/[ome]/metadata/*qc-report*
+
+
+
Removed samples
+
+ These tables show lists of samples that have been removed from
+ qc-normalized tables for either quality reasons, or because they are
+ outliers.
+
+
+ Removed samples location:{' '}
+
+ gs://motrpac-data-hub/analysis/human-precovid-sed-adu/[ome]/metadata/*removed-samples*
+
+
+
Sample metadata
+
+ These include sample-level metadata that are ome/assay specific. This
+ does not include any biospecimen data or demographic data that is found
+ elsewhere. An example would be percent missing features for a given
+ sample.{' '}
+
+ NOTE:
+ {' '}
+ it is not recommended to use these files as a source of biospecimen or
+ participant metadata, though the files may include such data. Rely on
+ centralized biospecimen and Key files.
+
+
+ Sample metadata location:{' '}
+
+ gs://motrpac-data-hub/analysis/human-precovid-sed-adu/[ome]/metadata/*metadata_samples*
+
+
+
Feature metadata
+
+ These tables include feature-level metadata that are ome/assay specific.
+ This does not include gene mapping, which is provided from a single
+ source.
+
+
+ Feature metadata location:{' '}
+
+ gs://motrpac-data-hub/analysis/human-precovid-sed-adu/[ome]/metadata/*metadata_features*
+
+
+
Code
+
+ All code for generating the data and metadata above is available at:{' '}
+
+ https://github.com/MoTrPAC/precovid-analyses
+
+ . The README.md describes how to interact with the data
+ functionally. Access can be granted by{' '}
+
+ jzhen@stanford.edu
+ {' '}
+ or{' '}
+
+ dankatz@stanford.edu
+
+ . If you'd like to run or manipulate the code, please do not work from
+ the main repo, instead create a branch from the main using your name.
+ Use of other branches on the repo is not recommended.
+
+
Methods
+
+ The methodological description of data processing for each ome is
+ available on Google Drive:{' '}
+
+ MoTrPAC MAWG Teamdrive > Pre-COVID > Writing Methods
+
+
+
+ Analysis Collaboration: Getting started step-by-step
+
+
+
+ );
+}
+
+export default PreCAWG;
diff --git a/src/Navbar/navbar.jsx b/src/Navbar/navbar.jsx
index e27179b6..d24aeba7 100644
--- a/src/Navbar/navbar.jsx
+++ b/src/Navbar/navbar.jsx
@@ -256,7 +256,9 @@ export function Navbar({
className="dropdown-item"
onClick={handleDataObjectFetch}
>
- Endurance Training Data
+ {isAuthenticated && hasAccess && userType === 'internal'
+ ? 'Rat and Human Data'
+ : 'Endurance Training Data'}
+
+
+
Publications - MoTrPAC Data Hub
+
{renderPublications()}
diff --git a/src/Search/deaSearchResultFilters.jsx b/src/Search/deaSearchResultFilters.jsx
index c539a092..4a6c423a 100644
--- a/src/Search/deaSearchResultFilters.jsx
+++ b/src/Search/deaSearchResultFilters.jsx
@@ -7,6 +7,7 @@ import {
assayList,
} from '../lib/searchFilters';
import { searchParamsPropType } from './sharedlib';
+import { trackEvent } from '../GoogleAnalytics/googleAnalytics';
function SearchResultFilters({
searchParams,
@@ -14,6 +15,7 @@ function SearchResultFilters({
handleSearch,
resetSearch,
hasResultFilters,
+ profile,
}) {
const [inputError, setInputError] = useState(false);
// FIXME - this is a hack to get the search filters such as tissue and assay
@@ -164,6 +166,15 @@ function SearchResultFilters({
onClick={(e) => {
e.preventDefault();
handleSearch(searchParams, searchParams.keys, 'filters');
+ // track event in Google Analytics 4
+ trackEvent(
+ 'Differential Abundance Search',
+ 'search_filters',
+ profile && profile.userid
+ ? profile.userid.substring(profile.userid.indexOf('|') + 1)
+ : 'anonymous',
+ searchParams.keys,
+ );
}}
disabled={inputError}
>
@@ -200,10 +211,15 @@ SearchResultFilters.propTypes = {
sex: PropTypes.object,
tissue: PropTypes.object,
}),
+ profile: PropTypes.shape({
+ userid: PropTypes.string,
+ user_metadata: PropTypes.object,
+ }),
};
SearchResultFilters.defaultProps = {
hasResultFilters: {},
+ profile: {},
};
export default SearchResultFilters;
diff --git a/src/Search/searchPage.jsx b/src/Search/searchPage.jsx
index 8317bf84..959612e4 100644
--- a/src/Search/searchPage.jsx
+++ b/src/Search/searchPage.jsx
@@ -248,7 +248,21 @@ export function SearchPage({
(inputEl && inputEl.value && inputEl.value.length)
? formatSearchInput()
: searchParams.keys,
- 'all'
+ 'all',
+ );
+ // track event in Google Analytics 4
+ trackEvent(
+ 'Differential Abundance Search',
+ 'keyword_search',
+ profile && profile.userid
+ ? profile.userid.substring(
+ profile.userid.indexOf('|') + 1,
+ )
+ : 'anonymous',
+ (multiSelections && multiSelections.length) ||
+ (inputEl && inputEl.value && inputEl.value.length)
+ ? formatSearchInput()
+ : searchParams.keys,
);
}}
>
@@ -296,6 +310,7 @@ export function SearchPage({
handleSearch={handleSearch}
resetSearch={resetSearch}
hasResultFilters={hasResultFilters}
+ profile={profile}
/>
diff --git a/src/assets/icons/github.svg b/src/assets/icons/github.svg
new file mode 100644
index 00000000..ccdc8f44
--- /dev/null
+++ b/src/assets/icons/github.svg
@@ -0,0 +1,12 @@
+
+
\ No newline at end of file
diff --git a/src/assets/icons/google-cloud.svg b/src/assets/icons/google-cloud.svg
new file mode 100644
index 00000000..3921c81e
--- /dev/null
+++ b/src/assets/icons/google-cloud.svg
@@ -0,0 +1,30 @@
+
+
\ No newline at end of file
diff --git a/src/assets/icons/google-drive.svg b/src/assets/icons/google-drive.svg
new file mode 100644
index 00000000..c361c154
--- /dev/null
+++ b/src/assets/icons/google-drive.svg
@@ -0,0 +1,40 @@
+
+
\ No newline at end of file
diff --git a/src/lib/assayList.js b/src/lib/assayList.js
index 1dea4711..d6a77c1e 100644
--- a/src/lib/assayList.js
+++ b/src/lib/assayList.js
@@ -1,37 +1,86 @@
-const assays = [
- 'RNA-seq',
- 'RRBS',
- 'ATAC-seq',
- 'Immunoassay',
- 'Targeted 3-Hydroxyisobutyric Acid (3-HIB)',
- 'Targeted Acyl-CoA',
- 'Targeted Acylcarnitines',
- 'Targeted Amines',
- 'Targeted Amino Acids',
- 'Targeted Beta-Aminoisobutyric Acid',
- 'Targeted Ceramide',
- 'Targeted Conventional',
- 'Targeted Ethanolamides',
- 'Targeted Keto Acids',
- 'Targeted Nucleotides',
- 'Targeted Organic Acids',
- 'Targeted Oxylipins',
- 'Targeted Sphingomyelin',
- 'Targeted Tricarboxylic Acid Cycle',
- 'Untargeted HILIC-Positive',
- 'Untargeted Ion-Pair Negative',
- 'Untargeted Lipidomics Reversed-Phase Negative',
- 'Untargeted Lipidomics Reversed-Phase Positive',
- 'Untargeted Reversed-Phase Negative',
- 'Untargeted Reversed-Phase Positive',
- 'Global Proteomics',
- 'Phosphoproteomics',
- 'Acetyl Proteomics',
- 'Protein Ubiquitination',
-];
-
-const assayList = assays.sort((a, b) =>
- a.toLowerCase().localeCompare(b.toLowerCase())
-);
+const assayList = {
+ pass1b_06: [
+ 'Acetyl Proteomics',
+ 'ATAC-seq',
+ 'Global Proteomics',
+ 'Immunoassay',
+ 'Phosphoproteomics',
+ 'Protein Ubiquitination',
+ 'RNA-seq',
+ 'RRBS',
+ 'Targeted 3-Hydroxyisobutyric Acid (3-HIB)',
+ 'Targeted Acyl-CoA',
+ 'Targeted Acylcarnitines',
+ 'Targeted Amines',
+ 'Targeted Amino Acids',
+ 'Targeted Beta-Aminoisobutyric Acid',
+ 'Targeted Ceramide',
+ 'Targeted Conventional',
+ 'Targeted Ethanolamides',
+ 'Targeted Keto Acids',
+ 'Targeted Nucleotides',
+ 'Targeted Organic Acids',
+ 'Targeted Oxylipins',
+ 'Targeted Sphingomyelin',
+ 'Targeted Tricarboxylic Acid Cycle',
+ 'Untargeted HILIC-Positive',
+ 'Untargeted Ion-Pair Negative',
+ 'Untargeted Lipidomics Reversed-Phase Negative',
+ 'Untargeted Lipidomics Reversed-Phase Positive',
+ 'Untargeted Reversed-Phase Negative',
+ 'Untargeted Reversed-Phase Positive',
+ ],
+ pass1a_06: [
+ 'Acetyl Proteomics',
+ 'ATAC-seq',
+ 'Global Proteomics',
+ 'Phosphoproteomics',
+ 'Protein Ubiquitination',
+ 'RNA-seq',
+ 'RRBS',
+ 'Targeted 3-Hydroxyisobutyric Acid (3-HIB)',
+ 'Targeted Acyl-CoA',
+ 'Targeted Acylcarnitines',
+ 'Targeted Amino Acids',
+ 'Targeted Beta-Aminoisobutyric Acid',
+ 'Targeted Ceramide',
+ 'Targeted Conventional',
+ 'Targeted Keto Acids',
+ 'Targeted Nucleotides',
+ 'Targeted Organic Acids',
+ 'Targeted Oxylipins',
+ 'Targeted Sphingomyelin',
+ 'Untargeted HILIC-Positive',
+ 'Untargeted Ion-Pair Negative',
+ 'Untargeted Lipidomics Reversed-Phase Negative',
+ 'Untargeted Lipidomics Reversed-Phase Positive',
+ 'Untargeted Reversed-Phase Negative',
+ 'Untargeted Reversed-Phase Positive',
+ ],
+ human_sed_adu: [
+ 'ATAC-seq',
+ 'Global Proteomics',
+ 'Immunoassay for corticosteroids',
+ 'Immunoassay for glucagon and related metabolic hormones',
+ 'Immunoassay for insulin and related metabolic hormones',
+ 'MethylCap-seq',
+ 'Phosphoproteomics',
+ 'Proteomics Olink',
+ 'RNA-seq',
+ 'Targeted Acyl-CoA',
+ 'Targeted Amines',
+ 'Targeted Conventional',
+ 'Targeted Keto Acids',
+ 'Targeted Nucleotides',
+ 'Targeted Oxylipins',
+ 'Targeted Tricarboxylic Acid Cycle',
+ 'Untargeted HILIC-Positive',
+ 'Untargeted Ion-Pair Negative',
+ 'Untargeted Lipidomics Reversed-Phase Negative',
+ 'Untargeted Lipidomics Reversed-Phase Positive',
+ 'Untargeted Reversed-Phase Negative',
+ 'Untargeted Reversed-Phase Positive',
+ ],
+};
export default assayList;
diff --git a/src/lib/browseDataFilters.jsx b/src/lib/browseDataFilters.jsx
index b49947be..20d4dfd2 100644
--- a/src/lib/browseDataFilters.jsx
+++ b/src/lib/browseDataFilters.jsx
@@ -1,43 +1,84 @@
import assayList from './assayList';
-const tissues = [
- 'Adrenal',
- 'Aorta',
- 'Blood RNA',
- 'Brown Adipose',
- 'Colon',
- 'Cortex',
- 'Gastrocnemius',
- 'Heart',
- 'Hippocampus',
- 'Hypothalamus',
- 'Kidney',
- 'Liver',
- 'Lung',
- 'Ovaries',
- 'Plasma',
- 'Small Intestine',
- 'Spleen',
- 'Testes',
- 'Vastus Lateralis',
- 'Vena Cava',
- 'White Adipose',
-];
+export const tissues = {
+ pass1b_06: [
+ 'Adrenal',
+ 'Blood RNA',
+ 'Brown Adipose',
+ 'Colon',
+ 'Cortex',
+ 'Gastrocnemius',
+ 'Heart',
+ 'Hippocampus',
+ 'Hypothalamus',
+ 'Kidney',
+ 'Liver',
+ 'Lung',
+ 'Ovaries',
+ 'Plasma',
+ 'Small Intestine',
+ 'Spleen',
+ 'Testes',
+ 'Vastus Lateralis',
+ 'Vena Cava',
+ 'White Adipose',
+ ],
+ pass1a_06: [
+ 'Adrenal',
+ 'Aorta',
+ 'Blood RNA',
+ 'Brown Adipose',
+ 'Colon',
+ 'Cortex',
+ 'Gastrocnemius',
+ 'Heart',
+ 'Hippocampus',
+ 'Hypothalamus',
+ 'Kidney',
+ 'Liver',
+ 'Lung',
+ 'Ovaries',
+ 'Plasma',
+ 'Small Intestine',
+ 'Spleen',
+ 'Testes',
+ 'Tibia',
+ 'Vastus Lateralis',
+ 'White Adipose',
+ ],
+ human_sed_adu: ['Adipose', 'Blood', 'Muscle', 'Plasma'],
+};
-export const tissueList = tissues.sort((a, b) =>
- a.toLowerCase().localeCompare(b.toLowerCase())
-);
+export const omes = {
+ pass1b_06: [
+ 'Epigenomics',
+ 'Metabolomics Targeted',
+ 'Metabolomics Untargeted',
+ 'Proteomics Targeted',
+ 'Proteomics Untargeted',
+ 'Transcriptomics',
+ ],
+ pass1a_06: [
+ 'Epigenomics',
+ 'Metabolomics Targeted',
+ 'Metabolomics Untargeted',
+ 'Proteomics Untargeted',
+ 'Transcriptomics',
+ ],
+ human_sed_adu: [
+ 'Epigenomics',
+ 'Metabolomics Targeted',
+ 'Metabolomics Untargeted',
+ 'Proteomics',
+ 'Transcriptomics',
+ ],
+};
const browseDataFilters = [
- {
- keyName: 'study',
- name: 'Intervention',
- filters: ['Acute Exercise', 'Endurance Training'],
- },
{
keyName: 'tissue_name',
name: 'Tissue',
- filters: tissueList,
+ filters: tissues,
},
{
keyName: 'omics',
diff --git a/src/lib/iconSet.js b/src/lib/iconSet.js
index 3a3e64c0..70321835 100644
--- a/src/lib/iconSet.js
+++ b/src/lib/iconSet.js
@@ -15,6 +15,9 @@ import Archive from '../assets/icons/archive.png';
import InternalDataRelease from '../assets/icons/data-release-internal.png';
import ArrowRightAnimated from '../assets/icons/arrow-right-animated.svg';
import ArrowDownAnimated from '../assets/icons/arrow-down-animated.svg';
+import GitHub from '../assets/icons/github.svg';
+import GoogleCloud from '../assets/icons/google-cloud.svg';
+import GoogleDrive from '../assets/icons/google-drive.svg';
const IconSet = {
Clinic,
@@ -34,6 +37,9 @@ const IconSet = {
InternalDataRelease,
ArrowRightAnimated,
ArrowDownAnimated,
+ GitHub,
+ GoogleCloud,
+ GoogleDrive,
};
export default IconSet;
diff --git a/src/sass/_landingPage.scss b/src/sass/_landingPage.scss
index ba6444c7..7d439a35 100644
--- a/src/sass/_landingPage.scss
+++ b/src/sass/_landingPage.scss
@@ -85,6 +85,7 @@
}
p.hero {
+ font-weight: 400;
margin-top: 1.75rem;
a {
@@ -93,10 +94,6 @@
line-height: 1.5;
text-decoration: none;
text-shadow: 0 0 0.1em rgba(0, 0, 0, 0.75);
-
- .about-motrpac-emphasis {
- color: $accent-yellow;
- }
}
}
diff --git a/src/sass/_multiOmicsWorkingGroups.scss b/src/sass/_multiOmicsWorkingGroups.scss
new file mode 100644
index 00000000..89c4f0ac
--- /dev/null
+++ b/src/sass/_multiOmicsWorkingGroups.scss
@@ -0,0 +1,37 @@
+.multiOmicsWorkingGroupsPage {
+ .multi-omics-wg-tab-content {
+ .pre-cawg {
+ .resources-table {
+ th {
+ text-align: center;
+ width: 33.33%;
+ }
+
+ td {
+ text-align: center;
+ vertical-align: top;
+
+ img {
+ width: 6.0em;
+ }
+ }
+ }
+
+ .release-notes-table {
+ td {
+ dl {
+ dt {
+ float: left;
+ clear: left;
+ margin-right: 0.5rem;
+ }
+ }
+ }
+ }
+
+ .nested-order-list {
+ list-style-type: lower-alpha;
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/sass/browseData/_browseData.scss b/src/sass/browseData/_browseData.scss
index 539561ee..40b11aae 100644
--- a/src/sass/browseData/_browseData.scss
+++ b/src/sass/browseData/_browseData.scss
@@ -17,6 +17,13 @@
text-decoration: none;
}
}
+
+ .bd-callout-info {
+ ul {
+ padding-left: 1.0rem;
+
+ }
+ }
}
.inline-link-with-icon .material-icons {
@@ -30,6 +37,68 @@
font-size: 5.0rem;
}
}
+
+ .bundle-datasets-item {
+ .card {
+ .bundle-dataset-tags {
+ .badge.badge-pill.badge-purple {
+ background-color: #6f42c1;
+ color: #fff;
+ }
+ }
+
+ .card-footer {
+ background-color: #fff;
+ border-top: none;
+
+ .ready-to-download-link {
+ background-color: #343a40;
+ border-color: #343a40;
+ border-radius: 0.25rem;
+ color: #fff;
+ font-size: 1rem;
+ font-weight: 600;
+ line-height: 1.5;
+ padding: 0.465rem 0.75rem;
+ text-align: center;
+ transition: color 0.15s ease-in-out, background-color 0.15s ease-in-out, border-color 0.15s ease-in-out, box-shadow 0.15s ease-in-out;
+
+ &:hover, &:focus, &:active {
+ background-color: #23272b;
+ border-color: #23272b;
+ text-decoration: none;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ .selective-data-downloads-card {
+ .card-header {
+ .material-icons {
+ font-size: 1.85rem;
+ }
+ }
+
+ &.external-access {
+ max-width: 22rem;
+ }
+ }
+
+ .data-download-selective-files {
+ /* tab UI temporary removed
+ .nav.nav-tabs {
+ margin-left: 15px;
+ margin-right: 15px;
+ }
+ */
+ .link-back {
+ a {
+ text-decoration: none;
+ width: fit-content;
+ }
+ }
}
label {
diff --git a/src/sass/main.scss b/src/sass/main.scss
index 4c1cac94..56a3c12d 100644
--- a/src/sass/main.scss
+++ b/src/sass/main.scss
@@ -37,3 +37,4 @@
@import 'codeRepo/all';
@import 'mainStudy/all';
@import 'publications';
+@import 'multiOmicsWorkingGroups';
diff --git a/yarn.lock b/yarn.lock
index 517c4f29..f986753f 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -2032,9 +2032,9 @@
ts-dedent "^2.0.0"
"@storybook/csf@^0.1.2", "@storybook/csf@^0.1.4":
- version "0.1.6"
- resolved "https://registry.yarnpkg.com/@storybook/csf/-/csf-0.1.6.tgz#247bdf6c371b83af5c4f0bc6654954eaabdb7595"
- integrity sha512-JjWnBptVhBYJ14yq+cHs66BXjykRUWQ5TlD1RhPxMOtavynYyV/Q+QR98/N+XB+mcPtFMm5I2DvNkpj0/Dk8Mw==
+ version "0.1.7"
+ resolved "https://registry.yarnpkg.com/@storybook/csf/-/csf-0.1.7.tgz#dcc6c16a353bc09c8c619ba1a23ba93b2aab0b9d"
+ integrity sha512-53JeLZBibjQxi0Ep+/AJTfxlofJlxy1jXcSKENlnKxHjWEYyHQCumMP5yTFjf7vhNnMjEpV3zx6t23ssFiGRyw==
dependencies:
type-fest "^2.19.0"
@@ -2580,16 +2580,16 @@
"@types/node" "*"
"@types/node@*":
- version "20.12.8"
- resolved "https://registry.yarnpkg.com/@types/node/-/node-20.12.8.tgz#35897bf2bfe3469847ab04634636de09552e8256"
- integrity sha512-NU0rJLJnshZWdE/097cdCBbyW1h4hEg0xpovcoAQYHl8dnEyp/NAOiE45pvc+Bd1Dt+2r94v2eGFpQJ4R7g+2w==
+ version "20.12.10"
+ resolved "https://registry.yarnpkg.com/@types/node/-/node-20.12.10.tgz#8f0c3f12b0f075eee1fe20c1afb417e9765bef76"
+ integrity sha512-Eem5pH9pmWBHoGAT8Dr5fdc5rYA+4NAovdM4EktRPVAAiJhmWWfQrA0cFhAbOsQdSfIHjAud6YdkbL69+zSKjw==
dependencies:
undici-types "~5.26.4"
"@types/node@^18.0.0":
- version "18.19.31"
- resolved "https://registry.yarnpkg.com/@types/node/-/node-18.19.31.tgz#b7d4a00f7cb826b60a543cebdbda5d189aaecdcd"
- integrity sha512-ArgCD39YpyyrtFKIqMDvjz79jto5fcI/SVUs2HwB+f0dAzq68yqOdyaSivLiLugSziTpNXLQrVb7RZFmdZzbhA==
+ version "18.19.32"
+ resolved "https://registry.yarnpkg.com/@types/node/-/node-18.19.32.tgz#96e4c80dca0ccf48505add2a399f36465955e0be"
+ integrity sha512-2bkg93YBSDKk8DLmmHnmj/Rwr18TLx7/n+I23BigFwgexUJoMHZOd8X1OFxuF/W3NN0S2W2E5sVabI5CPinNvA==
dependencies:
undici-types "~5.26.4"
@@ -5042,9 +5042,9 @@ ejs@^3.1.6:
jake "^10.8.5"
electron-to-chromium@^1.4.668:
- version "1.4.756"
- resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.4.756.tgz#7b872ed8c8c5bee571be771730225d6d2a37fe45"
- integrity sha512-RJKZ9+vEBMeiPAvKNWyZjuYyUqMndcP1f335oHqn3BEQbs2NFtVrnK5+6Xg5wSM9TknNNpWghGDUCKGYF+xWXw==
+ version "1.4.758"
+ resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.4.758.tgz#f39e530cae2ca4329a0f0e1840629d8d1da73156"
+ integrity sha512-/o9x6TCdrYZBMdGeTifAP3wlF/gVT+TtWJe3BSmtNh92Mw81U9hrYwW9OAGUh+sEOX/yz5e34sksqRruZbjYrw==
emittery@^0.10.2:
version "0.10.2"
@@ -5077,9 +5077,9 @@ encodeurl@~1.0.2:
integrity sha512-TPJXq8JqFaVYm2CWmPvnP2Iyo4ZSM7/QKcSmuMLDObfpH5fi7RUGmd/rTDf+rut/saiDiQEeVTNgAmJEdAOx0w==
enhanced-resolve@^5.16.0:
- version "5.16.0"
- resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.16.0.tgz#65ec88778083056cb32487faa9aef82ed0864787"
- integrity sha512-O+QWCviPNSSLAD9Ucn8Awv+poAkqn3T1XY5/N7kR7rQO9yfSGWkYZDwpJ+iKF7B8rxaQKWngSqACpgzeapSyoA==
+ version "5.16.1"
+ resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.16.1.tgz#e8bc63d51b826d6f1cbc0a150ecb5a8b0c62e567"
+ integrity sha512-4U5pNsuDl0EhuZpq46M5xPslstkviJuhrdobaRDBk2Jy2KO37FDAJl4lb2KlNabxT0m4MTK2UHNrsAcphE8nyw==
dependencies:
graceful-fs "^4.2.4"
tapable "^2.2.0"
@@ -7873,13 +7873,6 @@ lru-cache@^5.1.1:
dependencies:
yallist "^3.0.2"
-lru-cache@^6.0.0:
- version "6.0.0"
- resolved "https://registry.yarnpkg.com/lru-cache/-/lru-cache-6.0.0.tgz#6d6fe6570ebd96aaf90fcad1dafa3b2566db3a94"
- integrity sha512-Jo6dJ04CmSjuznwJSS3pUeWmd/H0ffTlkXXgwZi+eq1UCmqQwCh+eLsYOYCwY991i2Fah4h1BEMCx4qThGbsiA==
- dependencies:
- yallist "^4.0.0"
-
magic-string@^0.25.0, magic-string@^0.25.7:
version "0.25.9"
resolved "https://registry.yarnpkg.com/magic-string/-/magic-string-0.25.9.tgz#de7f9faf91ef8a1c91d02c2e5314c8277dbcdd1c"
@@ -10126,11 +10119,9 @@ semver@^6.0.0, semver@^6.3.0, semver@^6.3.1:
integrity sha512-BR7VvDCVHO+q2xBEWskxS6DJE1qRnb7DxzUrogb71CWoSficBxYsiAGd+Kl0mmq/MprG9yArRkyrQxTO6XjMzA==
semver@^7.3.2, semver@^7.3.5, semver@^7.3.7, semver@^7.5.3, semver@^7.5.4:
- version "7.6.0"
- resolved "https://registry.yarnpkg.com/semver/-/semver-7.6.0.tgz#1a46a4db4bffcccd97b743b5005c8325f23d4e2d"
- integrity sha512-EnwXhrlwXMk9gKu5/flx5sv/an57AkRplG3hTK68W7FRDN+k+OWBj65M7719OkA82XLBxrcX0KSHj+X5COhOVg==
- dependencies:
- lru-cache "^6.0.0"
+ version "7.6.1"
+ resolved "https://registry.yarnpkg.com/semver/-/semver-7.6.1.tgz#60bfe090bf907a25aa8119a72b9f90ef7ca281b2"
+ integrity sha512-f/vbBsu+fOiYt+lmwZV0rVwJScl46HppnOA1ZvIuBWKOTlllpyJ3bfVax76/OrhCH38dyxoDIA8K7uB963IYgA==
send@0.18.0:
version "0.18.0"
@@ -10929,9 +10920,9 @@ to-regex-range@^5.0.1:
is-number "^7.0.0"
tocbot@^4.25.0:
- version "4.27.19"
- resolved "https://registry.yarnpkg.com/tocbot/-/tocbot-4.27.19.tgz#e288dc2a81332e05cdeb68438d5aa859733f3dbd"
- integrity sha512-0yu8k0L3gCQ1OVNZnKqpbZp+kLd6qtlNEBxsb+e0G/bS0EXMl2tWqWi1Oy9knRX8rTPYfOxd/sI/OzAj3JowGg==
+ version "4.27.20"
+ resolved "https://registry.yarnpkg.com/tocbot/-/tocbot-4.27.20.tgz#c7ba627585894fa306d65b08f53f624949becf19"
+ integrity sha512-6M78FT20+FA5edtx7KowLvhG3gbZ6GRcEkL/0b2TcPbn6Ba+1ayI3SEVxe25zjkWGs0jd04InImaO81Hd8Hukw==
toidentifier@1.0.1:
version "1.0.1"
@@ -12192,11 +12183,6 @@ yallist@^3.0.2:
resolved "https://registry.yarnpkg.com/yallist/-/yallist-3.1.1.tgz#dbb7daf9bfd8bac9ab45ebf602b8cbad0d5d08fd"
integrity sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==
-yallist@^4.0.0:
- version "4.0.0"
- resolved "https://registry.yarnpkg.com/yallist/-/yallist-4.0.0.tgz#9bb92790d9c0effec63be73519e11a35019a3a72"
- integrity sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==
-
yaml@^1.10.0, yaml@^1.10.2, yaml@^1.7.2:
version "1.10.2"
resolved "https://registry.yarnpkg.com/yaml/-/yaml-1.10.2.tgz#2301c5ffbf12b467de8da2333a459e29e7920e4b"