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

drc-portals/app/data/c2m2/file/[id_namespace]/[local_id]/genome-browser/hub.txt/route.ts

@@ -0,0 +1,104 @@
+/**
+ * 
+ * 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 help@cfde.cloud
+`
+  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' } })
+}