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StaleStateException when high contention on OutlierDetectionService.identifyOutlierByMedianCorrelation #400

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arteymix opened this issue Aug 4, 2022 · 2 comments
Closed
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StaleStateException when high contention on OutlierDetectionService.identifyOutlierByMedianCorrelation #400

arteymix opened this issue Aug 4, 2022 · 2 comments
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bug database Issues that involve the database

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@arteymix
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arteymix commented Aug 4, 2022 •
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  • add a test case to reproduce the issue
@arteymix arteymix added bug database Issues that involve the database labels Aug 4, 2022
@arteymix arteymix added this to the 1.28.0 milestone Aug 4, 2022
arteymix added a commit that referenced this issue Aug 4, 2022
@arteymix
Fix SampleCoexpressionAnalysisService.compute() by using a more strin…
6467faf 
…gent transaction isolation level

This essentially locks the database to prevent dirty read. It's not
ideal, but it fixes the problem in a definite manner.

Revert some changes in 4cfb329 since we
don't need to deal with StaleStateException anymore.

Relates to #400.
arteymix added a commit that referenced this issue Aug 4, 2022
@arteymix
Fix SampleCoexpressionAnalysisService.compute() by using a more strin…
028762a 
…gent transaction isolation level

This essentially locks the database to prevent dirty read. It's not
ideal, but it fixes the problem in a definite manner.

Revert some changes in 4cfb329 since we
don't need to deal with StaleStateException anymore.

Relates to #400.
arteymix added a commit that referenced this issue Aug 4, 2022
@arteymix
Fix SampleCoexpressionAnalysisService.compute() by using a more strin…
20a72ea 
…gent transaction isolation level

This essentially locks the database to prevent dirty read. It's not
ideal, but it fixes the problem in a definite manner.

Revert some changes in 4cfb329 since we
don't need to deal with StaleStateException anymore.

Relates to #400.
@arteymix
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arteymix commented Aug 4, 2022

This problem has been mitigated by using the serializable isolation level which essentialy locks the database while outliers are being computed. Not ideal, but it works. I'll keep this issue open to find a better solution.

@arteymix arteymix mentioned this issue Aug 4, 2022
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@arteymix arteymix removed this from the 1.28.0 milestone Sep 22, 2022
@arteymix arteymix closed this as completed Aug 8, 2023
@arteymix
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arteymix commented Aug 8, 2023

Fixed in 14588b6. We don't compute outliers on-the-fly anymore.

ppavlidis added a commit that referenced this issue Feb 23, 2024
@ppavlidis
refactoring to try to make the SampleCoexpressionAnalysis a shorter t…
0604dd1 
…ransaction

As discussed in #400
For large data sets, it could still run into trouble. Moving the main data reading part to a read-only transaction should help.
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