Nate Coraor (n...@bx.psu.edu) wrote:
> Duddy, John wrote:
> > I'm not following you - it's been 6 months since I wrote that code ;-}
> 
> I know the feeling!
> 
> > IT looks to me like a DatasetPath() object is always placed in that array, 
> > and with one exception near then, it looks like the change I made generates 
> > those objects the same way.
> 
> It's creating a dict in self.output_dataset_paths, and that dict looks
> like this when outputs_to_working_directory = False:
> 
>     { output_param_name : [ HDA, DatasetPath ], ... }
> 
> And this when True:
> 
>     { output_param_name : [ Dataset, DatasetPath ], ... }
> 
> > Do you have a stack trace for the merge problem I can look at?
> 
> If you put this in do_merge()'s except block:
> 
>     log.exception( stdout )
> 
> You'll get:
> 
>     Traceback (most recent call last):
>       File 
> "/space/nate/galaxy-central-ichorny/lib/galaxy/jobs/splitters/multi.py", line 
> 128, in do_merge
>         output_type = outputs[output][0].datatype
>     AttributeError: 'Dataset' object has no attribute 'datatype'
> 
> I could just change both methods to put an HDA in the list inside the
> dict there, but I haven't looked much into what output_dataset_paths is
> used for, so I wasn't sure what that might break.

Sorta answered it myself, it looks like you created this precisely for
do_merge(), so changing it to contain the HDA fixes the problem (and
shouldn't break anything else).

--nate

> 
> Thanks,
> --nate
> 
> > 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: Thursday, November 03, 2011 2:22 PM
> > To: Duddy, John
> > Cc: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu
> > Subject: Re: Looks like actual user breaks splitting
> > 
> > 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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