diff --git a/packages/data-portal-explore/src/components/FileTable.tsx b/packages/data-portal-explore/src/components/FileTable.tsx index 09260f9a..573e36c1 100644 --- a/packages/data-portal-explore/src/components/FileTable.tsx +++ b/packages/data-portal-explore/src/components/FileTable.tsx @@ -93,10 +93,14 @@ function generateCdsManifestFile(files: Entity[]): string | undefined { 'parent_data_file_id', ]; const data = _(files) - .filter((f) => !!f.viewers?.cds) + .filter((f) => !!f.viewers?.cds || f.downloadSource === DownloadSourceCategory.synapse) .map((f) => [ - getDrsUri(f.viewers?.cds?.drs_uri, false, true), - f.viewers?.cds?.name, + f.viewers?.cds?.drs_uri + ? getDrsUri(f.viewers.cds.drs_uri, true) + : f.downloadSource === DownloadSourceCategory.synapse + ? `drs://repo-prod.prod.sagebase.org/${f.synapseId}` + : undefined, + f.viewers?.cds?.name ?? getFileBase(f.Filename), f.atlas_name, _.uniq(f.biospecimen.map((b) => b.BiospecimenID)).join(' '), f.assayName, @@ -313,8 +317,10 @@ const CDSInstructions: React.FunctionComponent<{ files: Entity[] }> = ({ (f) => f.downloadSource !== DownloadSourceCategory.dbgap ); - const manifestFile = generateCdsManifestFile(files); - const gen3manifestFile = generateGen3ManifestFile(files); + // Combine dbgap and open access files for manifest generation + const cdsEligibleFiles = dbgapFiles.concat(openAccessFiles); + const manifestFile = generateCdsManifestFile(cdsEligibleFiles); + const gen3manifestFile = generateGen3ManifestFile(cdsEligibleFiles); return (
Your selection include files that are:
-| Access Type | +Number of files | +Download method | +Cloud compute options | +
|---|---|---|---|
| CDS (Controlled access) | +{cdsFiles.length} | +Gen3 client + dbGaP credentials + manifest | +SevenBridges CGC, Terra | +
| Synapse | +{synapseFiles.length} | +Open in Synapse web UI or use Synapse python client | +✅ SevenBridges CGC, Terra | +
| Coming Soon | +{notDownloadableFiles.length} | +Metadata available now. File access in progress. | ++ |
- Follow the instructions below on how to access data from - each of these sources. Further details are avaliable in the{' '} - HTAN Manual. + Files can be downloaded or launched in cloud platforms depending on their access method. + Instructions below are grouped by source. More detail is available in the{' '} + + HTAN Manual + .
{/* CDS Section */} - {cdsFiles.length > 0 &&