Outliers query inclusive of missing fields #5903
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## main #5903 +/- ##
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- Coverage 83.78% 83.77% -0.01%
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Files 336 336
Lines 20960 20962 +2
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Hits 17561 17561
- Misses 3399 3401 +2 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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northwestwitch
changed the title
scout/adapter/mongo/query.py
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| outlier_padjust_query["$or"].append(pval_struct) | ||
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| outlier_padjust_query["$or"].append({pval_name: {"$exists": False}}) |
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Yes, you are on the track. This solves the issue, but breaks the clinical filter.
We will need to test for a condition and/or cross terms as well to make this work with the clinical filter (or in general filtering for both categories, as they will be mutually exclusive.
Co-authored-by: Daniel Nilsson <[email protected]>
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| outlier_padjust_query["$or"].append(pval_struct) | ||
| outlier_padjust_query["$or"].append( | ||
| {"$and": [pval_struct, {mutual_exclusion[pval_name]: {"$exists": False}}]} |
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Enforce mutual exclusivity of the values: whenever a key/value is provided -> the other should't be existing, but if a key/value is not provided then the field might be missing - see line 878. Something like this @dnil? This is complicated 🤯
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This PR adds a functionality or fixes a bug.
Testing on cg-vm1 server (Clinical Genomics Stockholm)
Prepare for testing
scout-stageand the server iscg-vm1.ssh <USER.NAME>@cg-vm1.scilifelab.sesudo -iu hiseq.clinicalssh localhostpodman pssystemctl --user stop scout@<name_of_currently_deployed_branch>systemctl --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: