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Add a url for constructing a hub.txt file for the genome-browser #421

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Original file line number Diff line number Diff line change
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/**
*
* Based on:
* https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#UseOneFile
*
* This page essentially defines a hub.txt file for any file in the c2m2
* but it will only work for files that:
*
* 1. have file_format of VCF, bigBED, or bigWig
* 2. have a subject attached with the taxonomy 9606 (human)
* 3. have a publicly accessible ~access_url~ persistent_id with the actual data
*
* We use the genome: hg19 but this may not be accurate,
* it's unclear how we'd determine the correct one at this stage.
*
* A hub can thus be assembled by pointing to the url at:
* https://cfde.cloud/data/c2m2/file/{id_namespace}/{local_id}/genome-browser/hub.txt
*
*/
import c2m2 from "@/lib/prisma/c2m2"

export async function GET(
request: Request,
props: { params: Promise<{ id_namespace: string, local_id: string }> }
) {
const params = await props.params
const file = await c2m2.file.findUnique({
where: {
id_namespace_local_id: { id_namespace: params.id_namespace, local_id: params.local_id }
},
select: {
filename: true,
local_id: true,
file_format: true,
// access_url: true,
persistent_id: true,
project: {
select: {
name: true,
},
},
file_describes_subject: {
select: {
subject: {
select: {
subject_role_taxonomy: {
select: {
taxonomy_id: true,
},
},
},
},
},
take: 1,
}
},
})
if (!file) return new Response(`File not found`, {status: 404})
let response = `
hub CFDEDataPortalHub
shortLabel CFDE Data Portal Hub
longLabel Genome Browser for data in the Common Fund Data Ecosystem
useOneFile on
email [email protected]
`
if (file.file_describes_subject[0].subject.subject_role_taxonomy[0].taxonomy_id === '9606') {
response += `
genome hg19
`
} else {
return new Response(`Unsure which genome to use`, {status: 400})
}
if (file.file_format === 'format:3016') { // VCF
response += `
track vcf
type vcfTabix
shortLabel ${file.local_id}
longLabel ${file.filename} from ${file.project.name}
bigDataUrl ${/*file.access_url*/file.persistent_id}
visibility pack
maxWindowToDraw 200000
`
// } else if (file.file_format === 'format:3003') { // BED
} else if (file.file_format === 'format:3004') { // bigBED
response += `
track bigBed
type bigBed
shortLabel ${file.local_id}
longLabel ${file.filename} from ${file.project.name}
bigDataUrl ${/*file.access_url*/file.persistent_id}
`
} else if (file.file_format === 'format:3006') { // bigWig
response += `
track bigWig
type bigWig
shortLabel ${file.local_id}
longLabel ${file.filename} from ${file.project.name}
bigDataUrl ${/*file.access_url*/file.persistent_id}
`
} else {
return new Response(`Compatible file format found`, {status: 400})
}
return new Response(response, { headers: { 'Content-Type': 'text/plain' } })
}