Fix show matching causatives #4412
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northwestwitch
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## main #4412 +/- ##
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- Coverage 84.70% 84.69% -0.01%
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Files 310 310
Lines 18413 18412 -1
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- Hits 15596 15594 -2
- Misses 2817 2818 +1 ☔ View full report in Codecov by Sentry. |
…-Genomics/scout into fix_matching_causatives
…-Genomics/scout into fix_matching_causatives
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Sorry. x_x |
I also feel immediately guilty when it's code I've touched.. And given that I've touched most of the code in scout I feel always guilty (and in general I am guilty) 🤣 |
| @@ -1397,13 +1397,7 @@ def _matching_causatives( | |||
| The subset of all secondary findings found in default gene panels | |||
| ) | |||
| """ | |||
| matching_causatives_filter = list( | |||
| set(other_causatives_filter + other_causatives_in_default_panels_filter) | |||
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In the specific case of the bug other_causatives_filter = [] because there are no panels in the safe search for the institute:
other_causatives_in_default_panels_filter comes from this function:
https://github.com/Clinical-Genomics/scout/blob/413d8301c84b4d070578ab53b7aed6a3ccb3f093/scout/server/blueprints/cases/controllers.py#L389C34-L389C64
I believe that that function is returning the list of genes in the case default panels, which is too limiting for searching for matching causatives in all cases of the institute
| matching_causatives = store.case_matching_causatives( | ||
| case_obj=case_obj, limit_genes=matching_causatives_filter | ||
| ) | ||
| matching_causatives = store.case_matching_causatives(case_obj=case_obj) |
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🥇 In the end it is safer and probably faster really with current indexes.
We conclude it was deviously hard to see, and a bit of the classic Python “[] is False” issue.
In this case a non-transitive version of it were give_me_them([]) + give_me_them([1, 2]) != give_me_them([] +[1, 2]).
In summary, we were likely without matching causatives outside the default panel from Oct. 😞 At any rate, don't blame yourself @alkc - we looked at the PR as well without realising, and it did not easily reproduce on local when I tested.
| @@ -570,7 +570,7 @@ def case_matching_causatives(self, case_obj, limit_genes=None): | |||
| 0:4 | |||
| ] # example: [ "17", "7577559", "G" "A"] | |||
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| for variant_type in ["clinical", "reseach"]: | |||
| for variant_type in ["clinical", "research"]: | |||
CHANGELOG.md
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| @@ -27,6 +27,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/) | |||
| - Rename `Clinical significanc` to `Germline classification` in ClinVar submissions exported files | |||
| - Rename `Comment on clinical significance` to `Comment on classification` in ClinVar submissions exported files | |||
| - Show matching partial causatives on variant page | |||
| - Matching causatives query | |||
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Probably add a slightly meatier explanation, including more exactly what was wrong and perhaps a date-range as well. The functionality is mostly for extra safety and speed, there is a world where we kind of rely on it to pick up less obvious phenotypes.
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This PR adds a functionality or fixes a bug.
Test with these variants:
Solved case --> https://scout-stage.scilifelab.se/cust002/F0015136
Variant not shown in:
Prepare for testing
scout-stageand the server iscg-vm1.ssh <USER.NAME>@cg-vm1.scilifelab.sesudo -iu hiseq.clinicalssh localhostpodman pssystemctl --user stop scout.targetsystemctl --user start scout@<this_branch>systemctl --user status scout.targetscout-stage) to be used for testing by other users.Testing on hasta server (Clinical Genomics Stockholm)
Prepare for testing
ssh <USER.NAME>@hasta.scilifelab.seus; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.conda activate S_scout; pip freeze | grep scout-browserbash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>us; scout --versionpaxaprocedure, which will release the allocated resource (scout-stage) to be used for testing by other users.How to test:
Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.
Review: