On Fri, Mar 18, 2011 at 7:57 AM, Peter Cock
<p.j.a.cock@googlemail.com> 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 +0000
+++ b/lib/galaxy/datatypes/data.py Fri Mar 18 11:49:05 2011 +0000
@@ -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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