I'm not following you - it's been 6 months since I wrote that code ;-} 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.
Do you have a stack trace for the merge problem I can look at? 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; email@example.com 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; firstname.lastname@example.org > 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); email@example.com > > 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> > > > > > ___________________________________________________________ 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/