Add configurable timeout and handle the dataoverflow error during stats estimation #730

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merged 2 commits into from Apr 19, 2016

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cmdcolin commented Apr 12, 2016

The stats estimation was given a timeout in #663 which is super, but it is also strict 500ms which leads to odd behavior such as that described in #727

This PR adds two things

  1. Configurable timeouts via a "storeTimeout" config variable. This timeout can be provided for a given track in their config, similar to how chunkSizeLimit can be modified in the config. The default for BAM, VCF, and BigWig is 3seconds. BigWig I think is important since autoscale global requires the global stats estimator to finish. The BAM is important since it causes behavior like #727 when it times out. Default for others is 500ms.

  2. Handling the chunkSizeLimit error explicitly during stats estimation by replying with the same response as a timeout (i.e. just provide no statistics) which should fix #540 corner cases by allowing the track to be viewed instead of rejecting the track "completely" if it failed during stats estimation

cmdcolin added some commits Apr 12, 2016

@enuggetry enuggetry merged commit 9ab6554 into master Apr 19, 2016

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@enuggetry enuggetry removed the in progress label Apr 19, 2016

@cmdcolin cmdcolin deleted the handle_timeout_chunksize_error branch May 29, 2016

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