Merge pull request #385 from MoTrPAC/384_JZ_File_Download_Filter_Bug

Connects to #384. Customized file download filtering bug.
MoTrPAC · Jan 14, 2025 · f78ca55 · f78ca55
2 parents 28440e7 + a7faeee
commit f78ca55
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Showing 3 changed files with 84 additions and 38 deletions.
diff --git a/src/BrowseDataPage/helper.jsx b/src/BrowseDataPage/helper.jsx
@@ -244,59 +244,51 @@ export const transformData = (arr) => {
     if (item.assay !== null && item.assay !== undefined) {
       let newMetabAssayVal = item.assay;
       if (
-        newMetabAssayVal.indexOf('Targeted') !== -1 &&
-        newMetabAssayVal.indexOf('Untargeted') !== -1
+        newMetabAssayVal.includes('Targeted')
+        && newMetabAssayVal.includes('Untargeted')
       ) {
         newMetabAssayVal = 'Merged';
         item.assay = newMetabAssayVal;
       }
     }
     if (
-      item.assay !== null &&
-      item.assay !== undefined &&
-      item.omics === 'Metabolomics Targeted'
+      item.assay !== null
+      && item.assay !== undefined
+      && item.omics === 'Metabolomics Targeted'
     ) {
       let newMetabAssayVal = item.assay;
       if (
-        newMetabAssayVal.indexOf('Acylcarnitines') !== -1 &&
-        newMetabAssayVal.indexOf('Oxylipins') !== -1
+        newMetabAssayVal.includes('Acylcarnitines')
+        && newMetabAssayVal.includes('Oxylipins')
       ) {
         newMetabAssayVal = 'Merged';
         item.assay = newMetabAssayVal;
       }
     }
     if (item.tissue_name !== null && item.tissue_name !== undefined) {
       let newTissueVal = item.tissue_name;
+      const tissueMappings = {
+        'Human PBMC': 'Blood',
+        'Human EDTA Packed Cells': 'Blood',
+        'Human PAXgene RNA': 'Blood',
+        'Human Adipose': 'Adipose',
+        'Human Adipose Powder': 'Adipose',
+        'Humnan Adipose Powder': 'Adipose',
+        'Human Muscle': 'Muscle',
+        'Human Muscle Powder': 'Muscle',
+        'Human EDTA Plasma': 'Plasma',
+      };
+
+      Object.keys(tissueMappings).forEach((key) => {
+        if (newTissueVal.indexOf(key) !== -1) {
+          newTissueVal = tissueMappings[key];
+          item.tissue_name = newTissueVal;
+        }
+      });
       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.includes('EDTA Plasma')
+        && item.omics.includes('Metabolomics')
+        && item.study.includes('Acute Exercise')
       ) {
         newTissueVal = 'Plasma';
         item.tissue_name = newTissueVal;

diff --git a/src/DataStatusPage/dataStatusPage.jsx b/src/DataStatusPage/dataStatusPage.jsx
@@ -1,8 +1,9 @@
-import React from 'react';
+import React, { useState } from 'react';
 import PropTypes from 'prop-types';
 import { connect } from 'react-redux';
 import { Redirect } from 'react-router-dom';
 import { Helmet } from 'react-helmet';
+import { Tooltip } from 'react-tooltip';
 import StatusReportGetData from './statusReportGetData';
 import StatusReportImmunoAssay from './statusReportImmunoAssay';
 import QcReportByPhase from './qcReportByPhase.jsx';
@@ -29,6 +30,8 @@ export function DataStatusPage({
   qcReportViewChange,
   profile,
 }) {
+  const [isOpen, setIsOpen] = useState(true);
+
   // Send users to default page if they are not consortium members
   const userType = profile.user_metadata && profile.user_metadata.userType;
   if (userType === 'external') {
@@ -130,15 +133,58 @@ export function DataStatusPage({
     }
   }
 
+  // Render data transfer guidelines link
+  function renderDataTransferGuidelinesLink() {
+    let link = '';
+
+    switch (qcReportView) {
+      case 'metabolomics':
+        link = 'https://docs.google.com/document/d/13i-EQcZ0LYylhoyaTdI4vf-BgZYAbzcGU4m9GKSJCnA/edit?usp=sharing';
+        break;
+      case 'proteomics':
+        link = 'https://docs.google.com/document/d/1U60mx7Wl0sNKsy_S72lJsRdEdB3HbuXQ86Hw7lLWV-w/edit?usp=sharing';
+        break;
+      default:
+        link = 'https://docs.google.com/document/d/1W1b5PVp2yjam4FU2IidGagqdA7lYpkTaD_LMeaN_n_k/edit?usp=sharing';
+    }
+    return link;
+  }
+
   return (
     <div className="dataStatusPage px-3 px-md-4 mb-3 w-100">
       <Helmet>
         <html lang="en" />
         <title>QC Data Monitor - MoTrPAC Data Hub</title>
       </Helmet>
       <div className="d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center mb-4 page-header">
-        <div className="page-title">
+        <div className="page-title d-flex align-items-end">
           <h1 className="mb-0">QC Data Monitor</h1>
+          {qcReportView.match(/metabolomics|proteomics|rnaseq|rrbs|methylcapseq|atacseq|immunoassay/) && (
+            <>
+              <a
+                href={renderDataTransferGuidelinesLink()}
+                target="_blank"
+                rel="noopener noreferrer"
+                className="data-transfer-guidelines-link mb-0 ml-2 text-info"
+                data-tooltip-id="data-transfer-guidelines-link-tooltip"
+                data-tooltip-content="Data Transfer Guidelines"
+                data-tooltip-place="right"
+                onMouseEnter={() => setIsOpen(true)}
+                onClick={() => setIsOpen(false)}
+              >
+                <span className="material-icons">
+                  description
+                </span>
+              </a>
+              <Tooltip
+                id="data-transfer-guidelines-link-tooltip"
+                defaultIsOpen={isOpen}
+                globalCloseEvents={{ clickOutsideAnchor: true }}
+              >
+                Data Transfer Guidelines
+              </Tooltip>
+            </>
+          )}
         </div>
         {renderButtonGroup()}
       </div>

diff --git a/src/sass/dataStatus/_dataStatusTable.scss b/src/sass/dataStatus/_dataStatusTable.scss
@@ -36,6 +36,14 @@
       }
     }
   }
+
+  .page-title {
+    .data-transfer-guidelines-link {
+      span {
+        font-size: 1.85rem;
+      }
+    }
+  }
 }
 
 .data-qc-status-panel {