Subject id search #4881
Subject id search #4881
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Additional details and impacted files@@ Coverage Diff @@
## main #4881 +/- ##
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Coverage 84.77% 84.77%
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Hits 16358 16358
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Unfortunately we can't quite index this fully as it is: the name query is for all collaborators, and for all individuals and we can't index on both arrays simultaneously. Fortunately the collection is pretty small and the individuals array is short so this should work out anyway. |
| @@ -145,11 +145,18 @@ | |||
| "case": [ | |||
| IndexModel([("synopsis", TEXT)], default_language="english", name="synopsis_text"), | |||
| IndexModel([("causatives", ASCENDING)], name="causatives"), | |||
| IndexModel([("suspects", ASCENDING)], name="suspects"), | |||
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Noticed this one missing in passing.
| @@ -167,6 +167,7 @@ def _set_case_name_query(self, query: Dict[str, Any], query_term: str): | |||
| query["$or"] = [ | |||
| {"display_name": case_name_regex}, | |||
| {"individuals.display_name": case_name_regex}, | |||
| {"individuals.subject_id": case_name_regex}, | |||
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This is the only change, really.
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Yep, tested both indexes and
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* Fix Clinical-Genomics#4878 - search subject id, add supporting indicies * changelog * add a couple of commas * actually spell * query is for collaborators and individuals. cant do dual array indicies yet. --------- Co-authored-by: Chiara Rasi <[email protected]>
* Fix Clinical-Genomics#4878 - search subject id, add supporting indicies * changelog * add a couple of commas * actually spell * query is for collaborators and individuals. cant do dual array indicies yet. --------- Co-authored-by: Chiara Rasi <[email protected]>
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.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: