Proteobench / ProteoBench

ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows.
https://proteobench.readthedocs.io
Apache License 2.0
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:bug: GitCommandError when doing nothing on the DDA Quant Module page #259

Open enryH opened 4 months ago

enryH commented 4 months ago

Describe the bug Without any interaction an error occurs.

To Reproduce Steps to reproduce the behavior:

  1. Go to DDA Quant Ion Level model
  2. Wait and have an instable internet connection
  3. Scroll down and
  4. See error

Expected behavior App should sit and wait

Screenshots If applicable, add screenshots to help explain your problem.

GitCommandError: Cmd('git') failed due to: exit code(128) cmdline: git clone -v -- https://github.com/Proteobench/Results_quant_ion_DDA.git 
C:\Users\User\AppData\Local\Temp\tmpe4hc3c55
stderr: 'Cloning into 'C:\Users\User\AppData\Local\Temp\tmpe4hc3c55'... 
POST git-upload-pack (185 bytes) 
POST git-upload-pack (277 bytes) 
error: RPC failed; curl 92 HTTP/2 stream 0 was not closed cleanly: CANCEL (err 8) 
error: 4651 bytes of body are still expected fetch-pack: unexpected disconnect while reading sideband packet fatal: early EOF 
fatal: fetch-pack: invalid index-pack output '

Desktop (please complete the following information):

I guess we need to catch an error somwhere.

enryH commented 4 months ago
File "C:\Users\user\Documents\repos\ProteoBench\webinterface\pages\DDA_Quant_ion.py", line 319, in _run_proteobench
    result_performance, all_datapoints, input_df = IonModule().benchmarking(
File "C:\Users\user\Documents\repos\ProteoBench\proteobench\modules\dda_quant_ion\module.py", line 102, in benchmarking
    all_datapoints = self.add_current_data_point(all_datapoints, current_datapoint)
File "C:\Users\user\Documents\repos\ProteoBench\proteobench\modules\dda_quant_base\module.py", line 285, in add_current_data_point
    all_datapoints["old_new"] = "old"
File "C:\Users\user\Documents\repos\ProteoBench\proteobench\github\gh.py", line 22, in read_results_json_repo
    clone_repo_anon(t_dir, remote_git_repo)
File "C:\Users\user\Documents\repos\ProteoBench\proteobench\github\gh.py", line 13, in clone_repo_anon
    repo = Repo.clone_from(remote_git, clone_dir)
File "C:\Users\user\Anaconda3\envs\proteobench\lib\site-packages\git\repo\base.py", line 1308, in clone_from
    return cls._clone(
File "C:\Users\user\Anaconda3\envs\proteobench\lib\site-packages\git\repo\base.py", line 1219, in _clone
    finalize_process(proc, stderr=stderr)
File "C:\Users\user\Anaconda3\envs\proteobench\lib\site-packages\git\util.py", line 419, in finalize_process
    proc.wait(**kwargs)
File "C:\Users\user\Anaconda3\envs\proteobench\lib\site-packages\git\cmd.py", line 604, in wait
    raise GitCommandError(remove_password_if_present(self.args), status, errstr)

This is to get the results json ? Is there a way to get the file locally from a raw github link?