:bug: Refactor saving of parameters file in DDA quant base module (#283)

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

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:bug: Refactor saving of parameters file in DDA quant base module (#283) #284

Closed enryH closed 2 months ago

enryH commented 2 months ago

iRegaring Issue #283

regression: button now return a list due to FragPipe taking two parameter files (commit https://github.com/Proteobench/ProteoBench/commit/88ff9c845d768bca071f811ffee1608a58f191ef)
regression: not re-submitting previously recorded runs, lead to an error for recording new runs (commit https://github.com/Proteobench/ProteoBench/commit/f81d3960ce85363ca1f9c3f71172f4976301c391)

enryH commented 2 months ago

@mlocardpaulet Can you test it using your examples if possible? I think I could not re-submit an already existing run.

mlocardpaulet commented 2 months ago

@mlocardpaulet Can you test it using your examples if possible? I think I could not re-submit an already existing run.

Thanks a lot for spending time on it! I get an error, and there is no pull request sent to Proteobot... Do you want me to send you fake trimmed files? And/or I am happy to test it again whenever needed.

enryH commented 2 months ago

I also got this error and had to fix it locally (I did not change anything in that file). I thought it was due to not having the secrets define.

@RobbinBouwmeester @wolski Do we have a description of the logic of this module? I guess this file is the one you want to refactor for the UI?

Is it actually necessary to save the file at all?

enryH commented 2 months ago

Okay. The check was added some three months ago in this commit https://github.com/Proteobench/ProteoBench/commit/f81d3960ce85363ca1f9c3f71172f4976301c391.

I guess I will just deal with the error and find a fix. However, this file and the logic it has needs to be documented. Maybe then it will be easier to structure or understand...

enryH commented 2 months ago

Hmm. I think the current checks do not really work for local development and the culprit is this one global variable.

https://github.com/Proteobench/ProteoBench/blob/f33006c666ed60d81658409c2c2fcf78364032d7/webinterface/pages/DDA_Quant_ion.py#L25

Is this changed on the server? @julianu

It effectively does not allow to go into the submit procedure.... I guess it is another regression due to this commit https://github.com/Proteobench/ProteoBench/commit/c597bd5eeb062f092830e49c5ba7ac239fe51641

julianu commented 2 months ago

On the server, the code still looks quite different (from release https://github.com/Proteobench/ProteoBench/commit/08456dae399560a0e8a4905098752fe9af641960).

Here, the code to set the variable still looks like this:

from proteobench.modules.dda_quant_base.parse_settings import (
    INPUT_FORMATS,
    LOCAL_DEVELOPMENT,
    ParseSettings,
)

wolski commented 2 months ago

@enryH

LOCAL_DEVELOPMENT = False in the release 2.4

Can you set it to False or should I make the change and commit it into the branch? Is this the only problem which prevents merging ths pull request?