FINNGEN / CohortOperations2

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REVIEW v1.0.0 #120

Open javier-gracia-tabuenca-tuni opened 2 days ago

javier-gracia-tabuenca-tuni commented 2 days ago

Major issues in bold

workflow

[ ] automatic testing doing all the checks by hands took me more than 1h (Javier)

DatabaseConnection

Connected to default 100s

[ ] Very slow: Creating tables slowest 50s
[x] Waits for Atlas, move atlas config to config file, and checks to here, 30s #114
[x] Waits for Atlas, not showing wait window
[x] tables not being named as time in each load: move timestap naming inside the run_app function !!!

Import cohorts

Import from endpoints Q17_ANKYLOGLOSSIA_case, Q17_ANKYLOGLOSSIA_cont

[x] Atlas not working

Match cohots

match from Q17_ANKYLOGLOSSIA_cont 40s

[x] picker to show the short name (javier)

Cohort overlaps

1s

[x] picker to show the short name (javier)
[ ] Viewer, plot, "Use same yscale across cohorts" does nothing (Harri)
[ ] Viewer, plot, move inside plot (Harri)

Cohort Demographics

2s

GENERAL

[x] Emojis not working since i changed them to unicode (javier)

javier-gracia-tabuenca-tuni commented 1 day ago

DatabaseConnection

Connected to default 50s

[ ] Very slow: Creating tables slowest 40s
[x] tables still created with same name

Import cohorts

Import from endpoints Q17_ANKYLOGLOSSIA_case, Q17_ANKYLOGLOSSIA_cont 30s

[ ] 'Counting cohorts' appears 2 times? investigate, may save some seconds

import from atlas no generated n 3237 COPY OF ALL 70s

import from atlas/library generated ALL 30s

Delete COPY OF ALL rename

Operate cohorts

all if they are not in case renamed to myControls 40s

Match cohorts

myControls and cases default settings 40s

Cohort Overlaps

in all renamed c5 to matched

GENERAL

[x] logs from analysis modules format as co2