Fix bugs in OncoPrint's tabular download due to OQL #5188
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alisman
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May 12, 2025
alisman
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May 12, 2025
alisman
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May 13, 2025
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alisman
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Jun 5, 2025
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@oplantalech i think we should write some unit tests for this. i've used ai code assist for writing unit tests with good results. you could try it. |
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@alisman Sorry about not getting to this earlier. I've added a test for the case that was failing; if you run the same test without the fix, you can see that the TP53 truncating mutation is not present in the output. |
dippindots
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Aug 5, 2025
dippindots
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Aug 5, 2025
dippindots
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Aug 5, 2025
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@oplantalech I’ve left a few comments on this pull request, could you take a look when you get a chance? I also noticed that some tests show the data order being updated, which might be related. Could you check if that change was intended? Let me know if you’d like to discuss further. |
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@dippindots Looks like all the tests pass now. I think I need to rebase, though |
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The logic of building the tabular download for OncoPrint assumes each track is a different gene. This causes issues when creating the tabular file for a query with multiple tracks of the same gene, only keeping the alterations of the last track of the gene.
For example, for the query with CDKN2B:MUT and CDKN2B:HOMDEL, when we have HOMDELs as the second track, only HOMDELs are shown in the downloaded tabular file (and no MUTs): https://www.cbioportal.org/results/oncoprint?cancer_study_list=ccle_broad_2019&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna&case_set_id=ccle_broad_2019_cnaseq&gene_list=CDKN2B%253AMUT%250ACDKN2B%253AHOMDEL&geneset_list=%20&tab_index=tab_visualize&Action=Submit&show_samples=true
When the same query is with MUT displayed in the second track, and HOMDELs in the first track, then we only see the MUT (and no HOMDELs) in the tabular file: https://www.cbioportal.org/results/oncoprint?cancer_study_list=ccle_broad_2019&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna&case_set_id=ccle_broad_2019_cnaseq&gene_list=CDKN2B%253AHOMDEL%250ACDKN2B%253AMUT&geneset_list=%20&tab_index=tab_visualize&Action=Submit&show_samples=true
This PR fixes this issue, combining the alterations that occur in multiple tracks when they belong to the same gene.