Limit number of cases fetched to be started.
Vince-janv opened this issue · comments
Description
Starting mip-dna cases takes so long that start-available sometimes does not finish with 1 hour when the command is run again. The bug is described here: https://github.com/Clinical-Genomics/bug-reports/issues/1
The same scaling issues might exist in the other pipelines.
Suggested solution:
- Estimate (by looking at the logs) how many cases can be started within an hour for mip and balsamic
- In
cg.meta.workflow.mip.MipAnalysisAPI.get_cases_to_analyze(and maybe balsamic equivalent) pass the limit parameter tocg.store.crud.read.ReadHandler.cases_to_analyze
Time to start a case:
- mip-dna ~ 90 seconds
- balsamic ~140 seconds
- rnafusion ~2 seconds
What margin would we want? 10 min? @Vince-janv
And do we see issues with RNAFusion? Like should this be applied for all pipelines?
6-10 min sounds good. I added RNAFUSION since it's the only one where I think we might start many cases at once. But since they take 2 sec there's no point in adding a limit IMO
Fixed in #3147