DRS Compatibility with non-ga4gh supported protocols

drc-portals/app/ga4gh/drs/v1/objects/[object_id]/access/[access_id]/ftps/ftps.py

@@ -0,0 +1,7 @@
+import sys
+import shutil
+from ufs.access.url import open_from_url
+
+def stream(*, access_url: str):
+  with open_from_url(access_url) as fr:
+    shutil.copyfileobj(fr, sys.stdout)

drc-portals/app/ga4gh/drs/v1/objects/[object_id]/access/[access_id]/ftps/route.ts

@@ -0,0 +1,35 @@
+import prisma from "@/lib/prisma"
+import { safeAsync } from "@/utils/safe"
+import path from 'path'
+import { pythonStream } from "@/utils/python";
+
+const __rootdir = path.resolve(__dirname, '..', '..')
+
+export async function GET(request: Request, { params }: { params: { object_id: string, access_id: string } }) {
+  if (params.access_id !== 'c2m2_file') return null
+  const object = await safeAsync(() => prisma.c2M2FileNode.findUnique({
+    where: {
+      id: params.object_id,
+    },
+    select: {
+      access_url: true,
+    },
+  }))
+  if (!object?.data?.access_url) return null
+  if (!object.data.access_url.startsWith('ftps://')) return null
+  process.env.PYTHONPATH = path.resolve(__rootdir, 'drc-portals', 'app', 'ga4gh', 'drs', 'v1', 'objects', '[object_id]', 'access', '[access_id]', 'ftps')
+  const stdout = pythonStream('ftps.stream', {
+    kargs: [
+      {
+        access_url: object?.data?.access_url,
+      },
+    ],
+  })
+  const stream = new ReadableStream<any>({
+    async start(controller) {
+      stdout.on('data', chunk => controller.enqueue(chunk))
+      stdout.on('end', () => controller.close())
+    }
+  })
+  return new Response(stream, { status: 200 })
+}

drc-portals/app/ga4gh/drs/v1/objects/[object_id]/access/[access_id]/http/route.ts

@@ -0,0 +1,28 @@
+import prisma from "@/lib/prisma"
+import { safeAsync } from "@/utils/safe"
+import http from 'http'
+
+export async function GET(request: Request, { params }: { params: { object_id: string, access_id: string } }) {
+  if (params.access_id !== 'c2m2_file') return null
+  const object = await safeAsync(() => prisma.c2M2FileNode.findUnique({
+    where: {
+      id: params.object_id,
+    },
+    select: {
+      access_url: true,
+    },
+  }))
+  if (!object?.data?.access_url) return null
+  if (!object.data.access_url.startsWith('http://')) return null
+  const res = await new Promise<http.IncomingMessage>((resolve, reject) => {
+    if (!object?.data?.access_url) reject()
+    else http.get(object.data.access_url, res => resolve(res))
+  })
+  const stream = new ReadableStream<any>({
+    async start(controller) {
+      res.on('data', chunk => controller.enqueue(chunk))
+      res.on('end', () => controller.close())
+    }
+  })
+  return new Response(stream, { status: res.statusCode })
+}

drc-portals/app/ga4gh/drs/v1/objects/[object_id]/access/[access_id]/route.ts

@@ -54,6 +54,7 @@ async function getC2M2FileUrl(object_id: string, access_id: string) {
     },
   }))
   if (!object?.data?.access_url) return null
+  // DRS passthrough
   if (object.data.access_url.startsWith('drs://')) {
     // We'll just proxy to the upstream DRS server, hopefully the client doesn't mind this. Redirects don't seem to work
     const upstreamDRS = object.data.access_url.replace(/^drs:\/\/([^/]+)\/(.+)$/g, `https://$1/ga4gh/drs/v1/objects/$2/access/${access_id}`)
@@ -62,7 +63,17 @@ async function getC2M2FileUrl(object_id: string, access_id: string) {
     else if (req.status === 404) return null
     else return req
   }
-  return { url: object.data.access_url }
+  // supported by DRS
+  if (/^(s3|gs|ftp|gsiftp|globus|htsget|https|file):\/\//.exec(object.data.access_url) !== null) {
+    return { url: object.data.access_url }
+  }
+  // supported by us
+  const compat = /^(http|ftps):\/\//.exec(object.data.access_url)
+  if (compat !== null) {
+    return { url: `${process.env.PUBLIC_URL}/ga4gh/drs/v1/objects/${object_id}/access/${access_id}/${compat[1]}` }
+  }
+  // unsupported
+  return null
 }
 
 export async function GET(request: Request, { params }: { params: { object_id: string, access_id: string } }) {