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Fix an issue when initializing SequenceServer with unformatted DBs#708

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yannickwurm merged 1 commit intowurmlab:masterfrom
tadast:tt/fix-private-method-call
Dec 9, 2023
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Fix an issue when initializing SequenceServer with unformatted DBs#708
yannickwurm merged 1 commit intowurmlab:masterfrom
tadast:tt/fix-private-method-call

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@tadast
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@tadast tadast commented Dec 4, 2023

Fixes #707

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ghost commented Dec 4, 2023

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tadast commented Dec 4, 2023

To reproduce #707 we need to run sequenceserver -d <path/to/dir/with/unformatted/dbs>, which also launches a sequenceserver instance in a subprocess. I had an attempt to reproduce the issue in a test, but the fact we need to shell to a CLI that then shells out to launch a sequenceserver instance makes managing the process state in the test rather tricky. Here's my attempt that successfully captures the issue in #707, but when the issue is resolved it does not kill the sequenceserver process...

https://gist.github.com/tadast/972c653070d4418ee0a161bc4de308a1

@tadast tadast force-pushed the tt/fix-private-method-call branch from 0c0f150 to 57d137b Compare December 4, 2023 10:58
@yannickwurm yannickwurm merged commit 57b06fe into wurmlab:master Dec 9, 2023
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Thank you @tadast - can we add your rspec gist to the main rspecs?

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tadast commented Dec 12, 2023

can we add your rspec gist to the main rspecs

Sorry @yannickwurm I wasn't explicitly clear - the test in the gist does not quite work fully - it spins up a sequence server web instance as a side effect, and that web app process keeps lingering. I didn't manage to find a nice way to kill that process in the time I'd allocated to this issue. If you think it's worth it, I can have another look

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NoMethodError for SequenceServer.makeblastdb.any_to_format?

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