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recursive shed_diff with directories not yet in Tool Shed #208

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merged 1 commit into from May 15, 2015

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peterjc commented May 14, 2015

Previously this error condition would mean a recursive planemo shed_diff would fail on repository not yet uploaded to the Tool Shed. It now prints an error message but continues.

Resolves GitHub issue #201

TODO: Ensure that shed_diff on a single repository gives an error return code, e.g.

$ planemo shed_diff ~/repositories/pico_galaxy/tools/seq_concatenate/ && echo "$? returned"
Repository [seq_concatenate] does not exist in the targeted Tool Shed, can't do shed_diff
0 returned

@peterjc peterjc force-pushed the peterjc:recursive_diff branch from 5d9acea to 553dfa1 May 14, 2015

recursive shed_diff with directories not yet in Tool Shed
Previously this error condition would mean a recursive shed_diff
would fail on repository not yet uploaded to the Tool Shed. It
now prints an error message but continues.

Resolves GitHub issue #201

TODO: Ensure that shed_diff on a single repository gives an error
return code, e.g.

$ planemo shed_diff ~/repositories/pico_galaxy/tools/seq_concatenate/ && echo "$? returned"
Repository [seq_concatenate] does not exist in the targeted Tool Shed, can't do shed_diff
0 returned

@peterjc peterjc force-pushed the peterjc:recursive_diff branch from 553dfa1 to 359c9ed May 14, 2015

error("Repository [%s] does not exist in the targeted Tool Shed, can't do shed_diff"
% realized_repository.name)
# TODO - Should this return an error code which can be checked for in recursive mode?
return 0

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@jmchilton

jmchilton May 14, 2015

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I feel like if you just return a non-zero value here the exit code would be handled correctly by the layers above this.

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@peterjc

peterjc May 14, 2015

Author Contributor

This is the TODO, we need a clean way to signal to the recursive shed_diff that this error should be ignored (i.e. a warning to the terminal only), whereas in non-recursive mode it really is an error which should quit with a non-zero return code.

@jmchilton jmchilton merged commit 359c9ed into galaxyproject:master May 15, 2015

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martenson commented May 15, 2015

thank you @peterjc

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