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fix: let raw_pathway_df handle present headers but no data #236

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Merged
merged 23 commits into from
Jul 11, 2025

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tristan-f-r
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@tristan-f-r tristan-f-r commented May 28, 2025

(@ntalluri what exactly did you do for #233? I think this addresses a separate issue, but I'm not entirely sure.)

Closes #233.

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I was running a full pilot run of all the data of the pilot synthetic networks for my thesis.

@tristan-f-r tristan-f-r changed the title test(MEO): empty files fix: let raw_pathway_df handle present headers but no data. May 28, 2025
@tristan-f-r tristan-f-r changed the title fix: let raw_pathway_df handle present headers but no data. fix: let raw_pathway_df handle present headers but no data May 28, 2025
@tristan-f-r tristan-f-r added the infrastructure misc. changes made to SPRAS itself label May 29, 2025
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(currently trying to generate an empty DOMINO test file)

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@ntalluri good catch! DOMINO also would have had a similar error.

Co-authored-by: Neha Talluri <78840540+ntalluri@users.noreply.github.com>
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If more OI2 test cases appear, I will add them. I can not find any more, and the fact that we don't have any issues reporting other OI2 test cases means that most likely these edge cases are caught.

[I can also add some more if anyone has datasets that would bring about these types of errors, but I do not have these.]

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ntalluri commented Jun 12, 2025

This issue has some of the empty files #133 (comment)

One more test case is

protien1 protien2

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If more OI2 test cases appear, I will add them. I can not find any more, and the fact that we don't have any issues reporting other OI2 test cases means that most likely these edge cases are caught.

[I can also add some more if anyone has datasets that would bring about these types of errors, but I do not have these.]

Have you tried running a large test sweep on egfr?

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[I forgot to put in my commit for the protein1-protein2 dataset]

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I have - the only empty header file I've gotten back was protein1 protein2. Perhaps I'm running it wrong?

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I think that is the only one i have run into as well

@ntalluri ntalluri added the needed for benchmarking Priority PRs needed for the benchmarking paper label Jun 25, 2025
@tristan-f-r tristan-f-r requested a review from ntalluri July 10, 2025 20:09
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I also ran into this error during benchmarking - having this patch would be nice 👍

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I also ran into this error during benchmarking - having this patch would be nice 👍

Could you describe what error you ran into incase?

I'll do a final pass of this PR tomorrow, I'm pretty sure this PR is pretty much ready.

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tristan-f-r commented Jul 10, 2025

Could you describe what error you ran into incase?

It was a one-off issue that was on my part (bad input by me led me to passing an empty df to all algorithms inside HTCondor), but tracking this error was annoying until I remembered #233. (I'm also seeing your problem with the logging)

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@tristan-f-r I quickly looked back at the new algorithms added, but I think the only test case that is missing is for BTB. Would you be able to add that one too?

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tristan-f-r commented Jul 10, 2025

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I am going to test this locally but I have a few changes/questions for the test_parse_outputs.py file.

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I tested it locally and a final overview review, looks good to me

@ntalluri ntalluri merged commit 4f6fc5e into Reed-CompBio:main Jul 11, 2025
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@tristan-f-r tristan-f-r deleted the meo-fix branch July 11, 2025 20:05
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MEO Empty File Parse Output Error
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