sokrypton / sokrypton/ColabFold

Unable to automatically download ColabFold output zip file

Open
#447 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Jupyter Notebook
Stars
2.9k
Forks
747
PR merge metrics
No merged PRs in 30d

Description

Expected Behavior

Download the zip file automatically after the job is run. This will be very useful for users to get the result output even the Google Colab runtime got finished. A user need to keep checking the Colab and make sure to download the zip file oneself before the Colab got disconnected.

Current Behavior

The zip file cannot be downloaded automatically with the following problem:


RedirectMissingLocation Traceback (most recent call last)
in <cell line: 9>()
10 uploaded = drive.CreateFile({'title': f"{jobname}.result.zip"})
11 uploaded.SetContentFile(f"{jobname}.result.zip")
---> 12 uploaded.Upload()
13 print(f"Uploaded {jobname}.result.zip to Google Drive with ID {uploaded.get('id')}")

10 frames
/usr/local/lib/python3.10/dist-packages/httplib2/init.py in _request(self, conn, host, absolute_uri, request_uri, method, body, headers, redirections, cachekey)
1461 if redirections:
1462 if "location" not in response and response.status != 300:
-> 1463 raise RedirectMissingLocation(
1464 _("Redirected but the response is missing a Location: header."), response, content,
1465 )

RedirectMissingLocation: Redirected but the response is missing a Location: header.

Steps to Reproduce (for bugs)

I just ran the code using a Linux's Chrome. Same issue for Mac's Chrome as well. I've turn on "save all" and "save_to_google_drive". It's not saved inside my google drive as well

ColabFold Output (for bugs)

Screenshot_20230514_083621

Your Environment

(https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb?)

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start in AlphaFold2.ipynb by tracing the save_all and save_to_google_drive paths around uploaded.Upload(), which raises RedirectMissingLocation. Reproduce the failure in Colab and inspect how the result zip is transferred after the runtime finishes. Done means the result zip is automatically downloaded or saved to Google Drive without this error.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
bioinformatics, cloud
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.