From 35ebfd2f9c32243bcec1898cb35b3302650c8f8b Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 12 Nov 2024 11:12:58 -0500 Subject: [PATCH 1/3] Fix caps --- packages/libs/web-common/src/user-dataset-upload-config.tsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/libs/web-common/src/user-dataset-upload-config.tsx b/packages/libs/web-common/src/user-dataset-upload-config.tsx index 58d56229f1..0ad871914e 100644 --- a/packages/libs/web-common/src/user-dataset-upload-config.tsx +++ b/packages/libs/web-common/src/user-dataset-upload-config.tsx @@ -82,7 +82,7 @@ export const uploadTypeConfig: DatasetUploadTypeConfig = 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: { From 582b031a128084e2f905ade4490efe0813adf63e Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 12 Nov 2024 14:07:45 -0500 Subject: [PATCH 2/3] update verbiage --- .../src/user-dataset-upload-config.tsx | 29 ++++++++----------- 1 file changed, 12 insertions(+), 17 deletions(-) diff --git a/packages/libs/web-common/src/user-dataset-upload-config.tsx b/packages/libs/web-common/src/user-dataset-upload-config.tsx index 0ad871914e..2817c21792 100644 --- 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 = }, renderInfo: () => (

- Please upload a zip file with your RNASeq results: your bigWig and - fpkm fastq files containing your processed reads. -
- 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'. -
-
- The files must be mapped to the reference genome that you select - above. -
- Only letters, numbers, spaces and dashes are allowed in the file - name. -
- 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.

), uploadMethodConfig: { From 2797fc8aa8299eabff5805fe55d952719c9c7b6b Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 12 Nov 2024 14:10:41 -0500 Subject: [PATCH 3/3] Allow upload user-dataset types to be configurable --- packages/libs/web-common/src/config.ts | 1 + .../wdkCustomization/js/client/userDatasetRoutes.tsx | 9 +++++++-- packages/sites/genomics-site/webpack.config.local.mjs | 1 + 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/packages/libs/web-common/src/config.ts b/packages/libs/web-common/src/config.ts index 2b399a26e2..2237999d48 100644 --- 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/sites/genomics-site/webapp/wdkCustomization/js/client/userDatasetRoutes.tsx b/packages/sites/genomics-site/webapp/wdkCustomization/js/client/userDatasetRoutes.tsx index 7bdbef30c1..eb28d3baeb 100644 --- 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 index 31da24b884..35e6dbc824 100644 --- 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,