Thanks for reporting, committed fix 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 ___________________________________________________________ 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:

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