search

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
27 stars 7 forks source link

error during public submission of MQ data v2.5.1.0 #283

Closed mlocardpaulet closed 2 months ago

mlocardpaulet commented 2 months ago

Describe the bug see screenshot below

To Reproduce Steps to reproduce the behavior:

  1. Upload MQ evidence file from v. 2.5.1.0
  2. Click on 'Parse and bench'
  3. Scroll down to public submission
  4. upload corresponding mqpar.xml
  5. check parsed parameters and confirm that metadata is correct
  6. press 'I really want to upload it'
  7. error (see screenshot below)

Expected behavior there should have been falling balloonsm, and a PR sent to proteobot

Screenshots image

Desktop (please complete the following information):

Additional context I can send the two files (mqpar and evidence) to anyone interested

mlocardpaulet commented 2 months ago

OK, so actually, there was a pull request generated in proteobot (actually two because I tried twice): image

They seem totally fine.

enryH commented 2 months ago

So the error specifies that it is param_loc is of type list. This is raised on the following line

https://github.com/Proteobench/ProteoBench/blob/f33006c666ed60d81658409c2c2fcf78364032d7/proteobench/modules/dda_quant_base/module.py#L204

param_loc is passed to the function. Going up the stack trace, I think the issue is that now the widget records a list of filenames instead of a single filename (which was needed to support FragPipe).

So the error is raised where the filename should be extracted. I think this will happen with any parameter file atm. I can try to give it a go.