Hi John,

It looks like the first issue is related to the change from
get_output_fnames() -> compute_outputs().  When
outputs_to_working_directory = False (default) this method
stores/returns a HistoryDatasetAssociation, but when True,
stores/returns a Dataset (the original method's behavior).  Thus,
accessing the object's .datatype attribute in the splitter's do_merge()
fails.

Thanks,
--nate

Duddy, John wrote:
> I'll submit a pull request shortly...
> 
> John Duddy
> Sr. Staff Software Engineer
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Tel: 858-736-3584
> E-mail: jdu...@illumina.com
> 
> 
> -----Original Message-----
> From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu] 
> Sent: Wednesday, November 02, 2011 12:24 PM
> To: Duddy, John
> Cc: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu
> Subject: Re: Looks like actual user breaks splitting
> 
> John, Ilya,
> 
> I get further with sequence type inputs but it looks like
> JobWrapper.get_output_datasets_and_fnames() is not returning the right
> thing when outputs_to_working_directory = True
> 
> BTW, the base Data.split() method is broken after the updates to
> Sequence.split() since it wasn't updated to expect
> HistoryDatasetAssociations rather than filenames.  Could you take a look
> at that when you get a chance?
> 
> --nate
> 
> Duddy, John wrote:
> > The datatype you are using does not define a split method. Are you working 
> > with our in-progress gz type or fastqillumina?
> > 
> > John Duddy
> > Sr. Staff Software Engineer
> > Illumina, Inc.
> > 9885 Towne Centre Drive
> > San Diego, CA 92121
> > Tel: 858-736-3584
> > E-mail: jdu...@illumina.com<mailto:jdu...@illumina.com>
> > 
> > From: Chorny, Ilya
> > Sent: Wednesday, November 02, 2011 11:50 AM
> > To: Duddy, John
> > Cc: Nate Coraor (n...@bx.psu.edu); galaxy-dev@lists.bx.psu.edu
> > Subject: Looks like actual user breaks splitting
> > 
> > Hey John,
> > 
> > Any thoughts?
> > 
> > Ilya
> > 
> > Traceback (most recent call last):
> >   File 
> > "/home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/runners/tasks.py", 
> > line 73, in run_job
> >     tasks = splitter.do_split(job_wrapper)
> >   File 
> > "/home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/splitters/multi.py", 
> > line 73, in do_split
> >     input_type.split(input_datasets, get_new_working_directory_name, 
> > parallel_settings)
> >   File "/home/galaxy/ichorny/galaxy-central/lib/galaxy/datatypes/data.py", 
> > line 473, in split
> >     raise Exception("Text file splitting does not support multiple files")
> > Exception: Text file splitting does not support multiple files
> > 
> > Ilya Chorny Ph.D.
> > Bioinformatics Scientist I
> > Illumina, Inc.
> > 9885 Towne Centre Drive
> > San Diego, CA 92121
> > Work: 858.202.4582
> > Email: icho...@illumina.com<mailto:icho...@illumina.com>
> > Website: www.illumina.com<http://www.illumina.com>
> > 
> > 
> 
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