relax - Bugs: bug #20471, BMRB data to Relax

relax - Bugs: bug #20471, BMRB data to Relax - is_empty()...

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bug #20471: BMRB data to Relax - is_empty() AttributeError.

Submitted by:	None
Submitted on:	Fri 01 Feb 2013 01:11:54 PM UTC

Category:	relax's source code	Severity:	3 - Normal
Priority:	5 - Normal	Status:	Fixed
Privacy:	Public	Assigned to:	Edward d Auvergne <bugman>
Originator Name:	Mengjun Xue	Originator Email:	-unavailable-
Open/Closed:	Closed	Release:	2.1.2
Operating System:	All systems

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( Jump to the original submission)

Fri 01 Feb 2013 04:05:15 PM UTC, comment #7: The error message is: Traceback (most recent call last): File "test_suite/system_tests/bmrb.py", line 252, in test_bug_20471_structure_present self.interpreter.bmrb.read(file='17226.txt', dir=path, version=None, sample_conditions=None) File "prompt/uf_objects.py", line 219, in _call_ self._backend(new_args, *uf_kargs) File "generic_fns/bmrb.py", line 208, in read if not ds[pipe_name].is_empty(): File "data/pipe_container.py", line 263, in is_empty if hasattr(self, 'structure') and not self.structure.is_empty(): AttributeError: Internal instance has no attribute 'is_empty'	Edward d Auvergne <bugman>
Fri 01 Feb 2013 04:05:09 PM UTC, SVN revision 18361: Merged revisions 18358-18360 via svnmerge from svn+ssh://bugman@svn.gna.org/svn/relax/trunk ........ r18358 \| bugman \| 2013-02-01 16:53:34 +0100 (Fri, 01 Feb 2013) \| 3 lines Created the Bmrb.test_bug_20471_structure_present to catch bug #20471 (https://gna.org/bugs/?20471). ........ r18359 \| bugman \| 2013-02-01 17:03:20 +0100 (Fri, 01 Feb 2013) \| 7 lines Fix for bug #20471 (https://gna.org/bugs/?20471). The problem was that the data pipe is_empty() method was not handling structural data correctly. The is_empty() method now belongs to the MolContainer objects rather than cdp.structure, and the object cdp.structure is not always present. ........ r18360 \| bugman \| 2013-02-01 17:04:27 +0100 (Fri, 01 Feb 2013) \| 7 lines Fix for bug #20471 (https://gna.org/bugs/?20471). The problem was that the data pipe is_empty() method was not handling structural data correctly. The is_empty() method now belongs to the MolContainer objects rather than cdp.structure, and the object cdp.structure is not always present. ........ (Browse SVN revision 18361)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 04:04:27 PM UTC, SVN revision 18360: Fix for bug #20471 (https://gna.org/bugs/?20471). The problem was that the data pipe is_empty() method was not handling structural data correctly. The is_empty() method now belongs to the MolContainer objects rather than cdp.structure, and the object cdp.structure is not always present. (Browse SVN revision 18360)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 04:03:37 PM UTC, comment #4: The error message is:	Edward d Auvergne <bugman>
Fri 01 Feb 2013 04:03:20 PM UTC, SVN revision 18359: Fix for bug #20471 (https://gna.org/bugs/?20471). The problem was that the data pipe is_empty() method was not handling structural data correctly. The is_empty() method now belongs to the MolContainer objects rather than cdp.structure, and the object cdp.structure is not always present. (Browse SVN revision 18359)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 03:53:34 PM UTC, SVN revision 18358: Created the Bmrb.test_bug_20471_structure_present to catch bug #20471 (https://gna.org/bugs/?20471). (Browse SVN revision 18358)	Edward d Auvergne <bugman>
Fri 01 Feb 2013 01:28:24 PM UTC, comment #1: This bug was first reported as a comment to a support request (https://gna.org/support/?2998#comment6).	Edward d Auvergne <bugman>
Fri 01 Feb 2013 01:11:54 PM UTC, original submission: Hi Edward, Ok, I submit the script, BMRB file, PDB file, and logfile as a new bug report. Regards, Mengjun	Anonymous

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Attach File(s):


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Attached Files

file #17086: 17226.txt added by None (283kB - text/plain)

file #17087: dauvergne_protocol.py added by None (12kB - text/plain)

file #17088: 1RTE_H_trunc.pdb added by None (175kB - chemical/x-pdb)

file #17089: log0201 added by None (33kB - text/plain)

Depends on the following items: None found

Items that depend on this one: None found

Carbon-Copy List

-unavailable- added by bugman (Updated the item)

-unavailable- added by None (Submitted the item)

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Follow 13 latest changes.

Date	Changed By	Updated Field	Previous Value	Replaced By
Fri 01 Feb 2013 04:09:06 PM UTC	bugman	Summary	BMRB data to Relax - is_empyt() AttributeError.	BMRB data to Relax - is_empty() AttributeError.
Fri 01 Feb 2013 04:03:37 PM UTC	bugman	Category	relax sample scripts	relax's source code
		Status	Confirmed	Fixed
		Open/Closed	Open	Closed
		Summary	BMRB data to Relax	BMRB data to Relax - is_empyt() AttributeError.
Fri 01 Feb 2013 03:38:06 PM UTC	bugman	Originator Name		Mengjun Xue
Fri 01 Feb 2013 03:37:18 PM UTC	bugman	Status	None	Confirmed
		Operating System	Microsoft Windows	All systems
Fri 01 Feb 2013 01:27:07 PM UTC	bugman	Assigned to	None	bugman
Fri 01 Feb 2013 01:11:54 PM UTC	None	Attached File	-	Added 17226.txt, #17086
		Attached File	-	Added dauvergne_protocol.py, #17087
		Attached File	-	Added 1RTE_H_trunc.pdb, #17088
		Attached File	-	Added log0201, #17089

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