Loading bedgraph files from DataHub

[ajayd-san]

Hey,

Great work on the project!

I want to host a public datahub with bedgraph files. I have both the bedgraph (compressed in gzip) and the index files. What would be the appropriate way to host these files?

Currently my hub.json looks like this:

[
  {
    "type": "bedGraph",
    "name": "heart",
    "url": "https://wang-genomics-data.s3.us-east-2.amazonaws.com/GE513-heart.bedgraph.gz",
    "showOnHubLoad": true
  },
  {
    "type": "bedGraph",
    "name": "brain",
    "url": "https://wang-genomics-data.s3.us-east-2.amazonaws.com/GE513-brain.bedgraph.gz",
    "showOnHubLoad": true
  }
]

Do I also need to specify index files or will the browser load them automatically as long as they are on the in same directory?

Thanks!

[lidaof]

Hi @ajayd-san , you don't need to specify the .gz.tbi path if the .tbi file is located at the same folder with the .bedgraph.gz.
Assume you have this file named as hub.json located as the same folder of the bedgraph.gz files, you can use the url https://wang-genomics-data.s3.us-east-2.amazonaws.com/hub.json to load your hub. Please enable CORS access to your bucket, also the hub should be enabled public access.

[ajayd-san]

Thank you so much!

[ajayd-san]

Hey, so I have the following hub file on a s3 bucket:

  {
    "type": "bedGraph",
    "name": "dm6_sample.bedgraph.gz",
    "url": "https://wang-genomics-data.s3.amazonaws.com/dm6/dm6_sample.bedgraph.gz",
    "showOnHubLoad": false
  }
]

When I try to load this through public hub I get the following errors:

A non-serializable value was detected in an action, in the path: `payload.0`. Value: 
Object { name: "dm6_sample.bedgraph.gz", type: "bedgraph", label: "dm6_sample.bedgraph.gz", filetype: undefined, options: {…}, url: "https://wang-genomics-data.s3.amazonaws.com/dm6/dm6_sample.bedgraph.gz", indexUrl: undefined, metadata: {…}, id: undefined, isSelected: false, … }

A non-serializable value was detected in the state, in the path: `hub.publicTracksPool.0`. Value: 
Object { name: "dm6_sample.bedgraph.gz", type: "bedgraph", label: "dm6_sample.bedgraph.gz", filetype: undefined, options: {…}, url: "https://wang-genomics-data.s3.amazonaws.com/dm6/dm6_sample.bedgraph.gz", indexUrl: undefined, metadata: {…}, id: undefined, isSelected: false, … }
 
Take a look at the reducer(s) handling this action type: hub/addPublicTracksPool.
(See https://redux.js.org/faq/organizing-state#can-i-put-functions-promises-or-other-non-serializable-items-in-my-store-state)

A non-serializable value was detected in the state, in the path: `hub.publicTracksPool.0`. Value: 
Object { name: "dm6_sample.bedgraph.gz", type: "bedgraph", label: "dm6_sample.bedgraph.gz", filetype: undefined, options: {…}, url: "https://wang-genomics-data.s3.amazonaws.com/dm6/dm6_sample.bedgraph.gz", indexUrl: undefined, metadata: {…}, id: undefined, isSelected: false, … }
 
Take a look at the reducer(s) handling this action type: hub/updateLoadedPublicHub.
(See https://redux.js.org/faq/organizing-state#can-i-put-functions-promises-or-other-non-serializable-items-in-my-store-state) [browser:13851:25](http://localhost:5173/browser/)
    overrideMethod (index):13851
    Redux 6
    loadHub PublicDataHubs.tsx:92

From what I can see the hub files only have strings and bools, I don't understand how they are not serializable.

Any info would be appreciated, thanks

[lidaof]

Hi @ajayd-san , just want to confirm that your json file has the starting [ at the begining?
if that's the case, can you post the URL of this file? thanks!

[ajayd-san]

Hey, Yes I can confirm the individual objects are enclosed in an array.

Here is the link: https://wang-genomics-hub-files-only.s3.us-east-2.amazonaws.com/dm6.json

Thanks for your help!

[ajayd-san]

Hey, I just forcefully restarted the server and everything seems to work fine. Weird.

But thanks for your prompt response regardless!

[lidaof]

Hi @ajayd-san good to know it worked finally....sorry for late reply during traveling.