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genome / ptero-workflow

Client-facing API for the PTero system
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Run shell-command purge-backends before submodule update test #220

Closed mkiwala closed 8 years ago

mkiwala commented 8 years ago

This was not necessary before we had a rdbms for shell-command. Looks like we forgot to add this purge-backends when we introduced the shell-command database.

I've already updated the shell script on Jenkins to include the proper database credentials. Once this PR is merged, the next time the submodule update tests run, then the shell-command db should be purged.

davidlmorton commented 8 years ago

I wouldn't think that this would be needed since the [testenv:dev] section of the shell-command's tox.ini file has this:

https://github.com/genome/ptero-shell-command/blob/master/tox.ini#L55

So does the lsf's tox.ini:

https://github.com/genome/ptero-lsf/blob/master/tox.ini#L89

And the procfile used specifies these test-envs be used here:

https://github.com/genome/ptero-workflow/blob/master/tests/scripts/Procfile-for-lsf-with-backing-services#L1-L2

mkiwala commented 8 years ago

@davidlmorton I agree. We should remove the line that I added and the line which purges the lsf database since these should both be handled in their respective tox.ini files.

mkiwala commented 8 years ago

I choose to merge before Travis CI would run tests since the change that I made was to the dev-all-in-one testenv definition and Travis CI would only test the default testenv, which did not change.

Later, the Travis CI tests failed when trying to fetch: 

git fetch origin +refs/pull/220/merge:
fatal: Couldn't find remote ref refs/pull/220/merge
Unexpected end of command stream

This does not seem like an important error.