Hi Nate,

That's awesome; thanks a million!

I just took a look at the auto generated emails on galaxy-commits; nicely done. 
 Even if it wasn't much work, I think the general benefit to the quality of 
Galaxy as a platform and to the developer community is palpable.

And definitely thanks for expressly letting me know; that is much appreciated.

Happy hacking,
Eric

________________________________________
From: Nate Coraor [n...@bx.psu.edu]
Sent: Tuesday, December 06, 2011 1:04 PM
To: Greg Von Kuster
Cc: Paniagua, Eric; galaxy-dev@lists.bx.psu.edu Dev
Subject: Re: [galaxy-dev] [Internal - Galaxy-dev #2159] (New) 2 questions about 
Galaxy's functional testing support

On Nov 30, 2011, at 6:35 PM, Greg Von Kuster wrote:

> Eric,
>
> We always welcome help from the Galaxy community, so if you are interested in 
> enhancing the Galaxy code, the best way to go about it is to create your own 
> fork off the Galaxy central repo in bitbucket, and when you have something to 
> contribute initiate a pull request for us to review and merge into the 
> central repo.  This way you don't have to deal with ongoing merges.

A bunch of people have asked recently and it wasn't much work, so I just added 
a new config param 'cleanup_job' that allows control over when job-related 
files are cleaned up (always, never, or only on job success).

--nate

>
> Thanks!
>
> On Nov 30, 2011, at 2:24 PM, Paniagua, Eric wrote:
>
>> Thanks for the quick replies again!  Yeah, from a technical standpoint such 
>> support is certainly doable.  My employer strongly discourages modifying the 
>> Galaxy code base too invasively (if at all), which is pretty fair since I'm 
>> not in a position to take responsibility for performing future Galaxy 
>> upgrades which may have messy merges as a consequence of my tinkering 
>> downstream of you.  That's primarily the reason I was curious about whether 
>> such features were in the works or at least on the horizon at the Galaxy 
>> Development Team proper.
>>
>> Anyway, thanks for communicating.  Have a great day :)
>>
>> Best,
>> Eric
>>
>> ________________________________________
>> From: Greg Von Kuster [g...@bx.psu.edu]
>> Sent: Wednesday, November 30, 2011 1:22 PM
>> To: Paniagua, Eric
>> Cc: galaxy-dev@lists.bx.psu.edu Dev
>> Subject: Re: [galaxy-dev] [Internal - Galaxy-dev #2159] (New) 2 questions 
>> about Galaxy's functional testing support
>>
>> On Nov 30, 2011, at 11:11 AM, Paniagua, Eric wrote:
>>
>>> Hi Greg,
>>>
>>> I appreciate your response!  Thanks for clarifying the capabilities and 
>>> limitations of the current functional testing framework.  (BTW, did you 
>>> mean "current" as in "current on galaxy-dist" or also "current on 
>>> galaxy-central" ?)  If I can find the time, these are areas I would be 
>>> interested in helping enhance.
>>
>> Current on Galaxy central, very likely the same as Galaxy dist.
>>
>>>
>>> Sorry my diction was unclear; by "output files" I meant the transient files 
>>> that a running job is free to create and manipulate in its 
>>> job_working_directory.  (I'm writing "transient" rather than "temporary" to 
>>> avoid confusion with, e.g. files created with tempfile.mkstemp - although 
>>> conceivably one might want to be able to inspect their contents on failure 
>>> as well, actually saving them might be a very different problem.)
>>>
>>> Normally, upon successful or failed job completion the job working 
>>> directory and anything in it are erased.  For certain tools, it could be 
>>> helpful in debugging if the developer (or Galaxy system administrator) were 
>>> able to inspect their contents to see, for instance, if they are properly 
>>> formed.
>>>
>>> I can disable removal of job working directories globally, but then of 
>>> course the job working directories also persist for successful jobs, which 
>>> can add up to a lot of unnecessary storage (the reason they're deleted by 
>>> default in the first place).
>>>
>>> I'm not sure how work is divided on your team, but can you tell me (a) if 
>>> the preceding paragraphs actually clarify anything for you,
>>
>> Yes, the functional test framework does not currently deal with anything in 
>> job_working_directory as far as I know.  I am not a primary tool developer 
>> on the development team, however, so there may be some peripheral test 
>> components working in this realm of which I am not aware.  My understanding 
>> of the use of the job_working_directory is that some files are moved out of 
>> it into permanent locations, while others are deleted upon job completion.  
>> You should be able to enhance the job code to enable you to inspect certain 
>> elements of this directory during job processing, but I'm not sure how 
>> difficult this may be.
>>
>>
>>> and (b) whether that issue is on the radar of your team and specifically on 
>>> the radar of the primary developer(s) / maintainer(s) of the testing 
>>> framework?
>>
>> This issue is not currently anywhere on the development team's radar.  Sorry 
>> if this is an inconvenience.
>>
>>>
>>> Thanks again for responding to my email.
>>>
>>> Best,
>>> Eric
>>>
>>> ________________________________
>>> From: Greg Von Kuster [g...@bx.psu.edu]
>>> Sent: Wednesday, November 30, 2011 9:56 AM
>>> To: Paniagua, Eric
>>> Cc: galaxy-dev@lists.bx.psu.edu Dev
>>> Subject: Re: [Internal - Galaxy-dev #2159] (New) [galaxy-dev] 2 questions 
>>> about Galaxy's functional testing support
>>>
>>> Hello Eric,
>>>
>>>
>>> Submitted by epani...@cshl.edu<mailto:epani...@cshl.edu>
>>>
>>> Hi all,
>>>
>>> I've read the Wiki page on Writing Functional Tests 
>>> (http://wiki.g2.bx.psu.edu/Admin/Tools/Writing%20Tests) and I've been 
>>> looking through test/base and test/functional and I am left with two 
>>> questions:
>>>
>>> *   Is it possible to write a test to validate metadata directly on an 
>>> (optionally composite) output dataset?
>>>
>>> I'm sure this is possible, but it would require enhancements to the current 
>>> functional test framework.
>>>
>>>
>>> Everything described on the above page is file oriented.  I see that there 
>>> is TwillTestCase.check_metadata_for_string, but as far as I can tell this 
>>> is a bit nonspecific since it appears to just do a text search on the Edit 
>>> page.
>>>
>>> This is correct.
>>>
>>>
>>>
>>> I don't yet fully understand the context in which tests run, but is there 
>>> some way to access a "live" dataset's metadata directly, either as a 
>>> dictionary or just as attributes?  Or even to get the actual dataset object?
>>>
>>>
>>> Not with the current functional test framework.  Doing this would require 
>>> enhancements to the framework.
>>>
>>>
>>> *   Does the test harness support retaining output files only for failed 
>>> tests?  Ideally with a cap on how much output data to save.  If not, would 
>>> this be difficult to configure?
>>>
>>>
>>> I'm not sure what you mean by "output files" in your question.  If you mean 
>>> output datasets that result from running a functional test for a tool, then 
>>> I believe there is no difference if the test passed or failed.
>>>
>>>
>>> Thanks,
>>> Eric
>>>
>>>
>>> Greg Von Kuster
>>> Galaxy Development Team
>>> g...@bx.psu.edu<mailto:g...@bx.psu.edu>
>>>
>>>
>>>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
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>>>
>>> http://lists.bx.psu.edu/
>>
>> Greg Von Kuster
>> Galaxy Development Team
>> g...@bx.psu.edu
>>
>>
>>
>>
>
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/


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