Merge remote-tracking branch 'origin/main' into orthogroup-tree-table

VEuPathDB · Nov 14, 2024 · 8abb5d6 · 8abb5d6
2 parents 4a83f7d + 298457c
commit 8abb5d6
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Showing 4 changed files with 22 additions and 20 deletions.
diff --git a/packages/libs/web-common/src/config.ts b/packages/libs/web-common/src/config.ts
@@ -35,6 +35,7 @@ export const {
   datasetImportUrl = '',
   showUnreleasedData = false,
   vdiServiceUrl = '',
+  userDatasetsUploadTypes = '',
 } = window.__SITE_CONFIG__;
 
 export const edaExampleAnalysesAuthors = !window.__SITE_CONFIG__

diff --git a/packages/libs/web-common/src/user-dataset-upload-config.tsx b/packages/libs/web-common/src/user-dataset-upload-config.tsx
@@ -45,23 +45,18 @@ export const uploadTypeConfig: DatasetUploadTypeConfig<ImplementedUploadTypes> =
         },
         renderInfo: () => (
           <p className="formInfo">
-            Please upload a zip file with your RNASeq results: your bigWig and
-            fpkm fastq files containing your processed reads.
-            <br />
-            Each file in the collection of FPKM or TPM files should be a two
-            column tab-delimited file where the first column contains gene ids,
-            and the second column contains normalized counts for each gene,
-            either FPKM or TPM. The first line must have column headings
-            'gene_id' and either 'FPKM' or 'TMP'.
-            <br />
-            <br />
-            The files must be mapped to the reference genome that you select
-            above.
-            <br />
-            Only letters, numbers, spaces and dashes are allowed in the file
-            name.
-            <br />
-            Please restrict the name to 100 characters or less.
+            Complete the Upload My Normalized RNA-Seq form. Name, Summary and
+            Upload File/URL are required. Three types of files – bigWig, counts
+            and index – are supported in the uploaded zip file. BigWig files are
+            not required but will allow visualization in the genome browser if
+            included. The counts (FPKM/TPM) files should be tab-delimited and
+            contain two columns with column headers: 'gene_id', and either
+            'FPKM' or 'TMP'. The index file should be named manifest.txt and
+            consist of a tab delimited txt file with three columns (no column
+            headers): sample name, filename, and strandedness
+            (unstranded/stranded). Upload Data Set initiates the transfer and
+            will create a record page for your data set that contains links to
+            the fold change search, and bigWig files if included.
           </p>
         ),
         uploadMethodConfig: {
@@ -82,7 +77,7 @@ export const uploadTypeConfig: DatasetUploadTypeConfig<ImplementedUploadTypes> =
     bigwigfiles: {
       type: 'bigwigfiles',
       displayName: 'bigWig',
-      description: `Integrate your BigWig data in ${projectId}.`,
+      description: `Integrate your bigWig data in ${projectId}.`,
       uploadTitle: 'Upload My bigWig Data Set',
       formConfig: {
         summary: {

diff --git a/packages/sites/genomics-site/webapp/wdkCustomization/js/client/userDatasetRoutes.tsx b/packages/sites/genomics-site/webapp/wdkCustomization/js/client/userDatasetRoutes.tsx
@@ -5,7 +5,10 @@ import { useLocation } from 'react-router-dom';
 import { Loading } from '@veupathdb/wdk-client/lib/Components';
 import { RouteEntry } from '@veupathdb/wdk-client/lib/Core/RouteEntry';
 
-import { communitySite } from '@veupathdb/web-common/lib/config';
+import {
+  communitySite,
+  userDatasetsUploadTypes,
+} from '@veupathdb/web-common/lib/config';
 import ExternalContentController from '@veupathdb/web-common/lib/controllers/ExternalContentController';
 
 import { uploadTypeConfig } from '@veupathdb/web-common/lib/user-dataset-upload-config';
@@ -14,7 +17,9 @@ const UserDatasetRouter = React.lazy(
   () => import('./controllers/UserDatasetRouter')
 );
 
-const availableUploadTypes = ['genelist', 'bigwigfiles', 'rnaseq'];
+const availableUploadTypes = userDatasetsUploadTypes.trim()
+  ? userDatasetsUploadTypes.split(/,\s*/g)
+  : ['genelist', 'bigwigfiles', 'rnaseq'];
 
 const USER_DATASETS_HELP_PAGE = 'user_datasets_help.html';
 

diff --git a/packages/sites/genomics-site/webpack.config.local.mjs b/packages/sites/genomics-site/webpack.config.local.mjs
@@ -48,6 +48,7 @@ export default configure({
         siteSearchServiceUrl: process.env.SITE_SEARCH_SERVICE_ENDPOINT,
         useUserDatasetsWorkspace: process.env.USER_DATASETS_WORKSPACE_ENABLED === 'true',
         datasetImportUrl: process.env.USER_DATASETS_WORKSPACE_IMPORT_SERVICE_ENDPOINT,
+        userDatasetsUploadTypes: process.env.USER_DATASETS_UPLOAD_TYPES,
         useEda: process.env.EDA_ENABLED === "true",
         edaExampleAnalysesAuthor: process.env.EDA_EXAMPLE_ANALYSES_AUTHOR,
         edaServiceUrl: process.env.EDA_SERVICE_ENDPOINT,