Thanks for reporting, committed fix
On Fri, Mar 18, 2011 at 7:57 AM, Peter Cock wrote:
> Hi all,
>
> I just got a nasty recursion error when trying to run the functional
> tests for my TMHMM and
> SignalP wrappers - tools which produce tabular output.
>
> galaxy.jobs.runners.local: ERROR: Job wrapper finish method failed
> Traceback (most recent call last):
> File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/jobs/runners/local.py",
> line 125, in run_job
>job_wrapper.finish( stdout, stderr )
> File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/jobs/__init__.py",
> line 578, in finish
>dataset.set_peek()
> File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py",
> line 690, in set_peek
>return self.datatype.set_peek( self, is_multi_byte=is_multi_byte )
> File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py",
> line 227, in set_peek
>data.Text.set_peek( self, dataset, line_count=line_count,
> is_multi_byte=is_multi_byte )
> File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py",
> line 431, in set_peek
>self.set_peek(dataset)
> ...
> File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py",
> line 227, in set_peek
>data.Text.set_peek( self, dataset, line_count=line_count,
> is_multi_byte=is_multi_byte )
> File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py",
> line 431, in set_peek
>self.set_peek(dataset)
> ...
> File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py",
> line 227, in set_peek
>data.Text.set_peek( self, dataset, line_count=line_count,
> is_multi_byte=is_multi_byte )
> File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py",
> line 419, in set_peek
>dataset.peek = get_file_peek( dataset.file_name,
> is_multi_byte=is_multi_byte )
> File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py",
> line 628, in get_file_name
>return self.dataset.get_file_name()
> File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py",
> line 515, in get_file_name
>return os.path.abspath( os.path.join( dir, "dataset_%d.dat" % self.id )
> )
> File "/usr/local/lib/python2.6/posixpath.py", line 348, in abspath
>return normpath(path)
> File "/usr/local/lib/python2.6/posixpath.py", line 314, in normpath
>slash, dot = (u'/', u'.') if isinstance(path, unicode) else ('/', '.')
> RuntimeError: maximum recursion depth exceeded while calling a Python
> object
>
>
> >From the trace, two set_peek methods are calling each other in a loop. I
> deduced
> the problem was an empty tabular files, where
> dataset.metadata.data_lines is zero,
> but the test should really have been for None. Please review and apply
> this patch
> which appears to correctly resolve the issue:
>
>
> diff -r 9fae539215be lib/galaxy/datatypes/data.py
> --- a/lib/galaxy/datatypes/data.py Fri Mar 18 11:46:48 2011 +
> +++ b/lib/galaxy/datatypes/data.py Fri Mar 18 11:49:05 2011 +
> @@ -422,7 +422,7 @@
> dataset.peek = get_file_peek( dataset.file_name,
> is_multi_byte=is_multi_byte )
> if line_count is None:
> # See if line_count is stored in the metadata
> -if dataset.metadata.data_lines:
> +if dataset.metadata.data_lines is not None:
> dataset.blurb = "%s %s" % ( util.commaify(
> str(dataset.metadata.data_lines) ),
> inflector.cond_plural(dataset.metadata.data_lines, "line") )
> else:
> # Number of lines is not known ( this should not
> happen ), and auto-detect is
>
>
>
> Thanks,
>
> Peter
> ___
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