Hi Peter,

On Oct 8, 2013, at 11:01 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> On Tue, Oct 8, 2013 at 3:47 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Hi Peter and others,
>> Peter wrote:
>>> As an aside, I've asked before about why the function tests look
>>> at *.loc rather than *.loc.sample and not had a clear answer.
>> The functional tests look at .loc files because they will have uncommented,
>> functionally correct entries.  The .loc.sample files usually have commented
>> "sample" entries that provide an idea to the Galaxy admin as to what should
>> actually go into the associated .loc file.  For example, twobit.loc.sample
>> has:
>> #droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit
>> #apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit
>> #droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit
>> #droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit
>> while twobit.loc has:
>> droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit
>> apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit
>> droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit
>> droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit
> It depends on the tool, some example.loc.sample files already
> contain real working entries. In this case if it would be useful
> for the twobit unit tests, why not provide twobit.loc with the
> uncommented lines?

The .loc files are looked at because the .loc.sample files are not required to 
have uncommented unctional entries (although some obviously may have them).

> (Either way the Galaxy Admin will have to edit twobit.loc
> to suit the local setup anyway.)


>>> As soon as the local administrator edits the provided default *.loc
>>> files, this could break functional tests using the *.loc.sample
>>> values.
>> The intent is that the local administrator manually edits the .loc file to
>> include the functionally correct entries based on entries in the .loc.sample
>> file.
>>> The simple fix is for the test framework to preferentially
>>> load the *.loc.sample file if present:
>>> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014370.html
>>> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016159.html
>> I don't agree with this - the sample files should be used as guidance for
>> the admin to create functionally correct .loc files.  This is the same
>> aopproach used for all Galaxy .sample files ( e.g., universe_wsgi.ini.sample
>> <-> universe_wsgi.ini, etc )
> Why then does the tool_conf.xml.sample file get used by the
> test framework then? This is a clear example of *.xml.sample
> being used in the test framework over the 'real' file *.xml.
> I really don't understand this design choice - I would use
> tool_conf.xml (it lists the tools actually installed on our Galaxy,
> and therefore the things worth testing) while by default
> tool_conf.xml.sample includes a whole load of things where
> the binaries etc are missing and so the tests will fail (hiding
> potential real failures in the noise).

I'm not quite sure of the reason for htis as I didn't make this design choice - 
I'm sure "ancient Galaxy history" plays a role in this decision.

> The quick fix is to edit tool_conf.xml.sample but that can
> cause trouble with hg and system updates.
> (I appreciate as more and more tools leave the core framework
> and migrate to the tool shed this is less important,

Yes, this is true.

> --
> Perhaps rather than overloading *.loc.sample with two roles
> (sample configuration/documentation and unit tests), we
> need to introduce *.loc.test for functional testing purposes?

I'm hoping we don''t have to go this route as we have so many priorities.  If 
you would like this implemented though, please add a new Trello card and we'll 
consider it.

> That still leaves open the question of how best to install
> the test databases or files that the *.loc.test file would
> point at for running functional tests.


> Thanks,
> Peter

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