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fix: let raw_pathway_df handle present headers but no data #236
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I was running a full pilot run of all the data of the pilot synthetic networks for my thesis. |
(currently trying to generate an empty DOMINO test file) |
@ntalluri good catch! DOMINO also would have had a similar error. |
test/parse-outputs/input/empty/omicsintegrator2-empty-raw-pathway.txt
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test/parse-outputs/input/empty/omicsintegrator2-empty-raw-pathway-2.txt
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Co-authored-by: Neha Talluri <78840540+ntalluri@users.noreply.github.com>
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.] |
This issue has some of the empty files #133 (comment) One more test case is
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Have you tried running a large test sweep on egfr? |
[I forgot to put in my commit for the protein1-protein2 dataset] |
I have - the only empty header file I've gotten back was |
I think that is the only one i have run into as well |
test/parse-outputs/input/empty/omicsintegrator2-empty-raw-pathway-1.txt
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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. |
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) |
@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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I am going to test this locally but I have a few changes/questions for the test_parse_outputs.py file.
partial revertion of commit b22f145.
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I tested it locally and a final overview review, looks good to me
(@ntalluri what exactly did you do for #233? I think this addresses a separate issue, but I'm not entirely sure.)Closes #233.