bugrelax - 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 codeSpecific analysis category: None
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Mengjun XueOriginator Email: -unavailable-
Open/Closed: ClosedRelease: 2.1.2
Operating System: All systems

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(Jump to the original submission 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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
Fri 01 Feb 2013 04:03:37 PM UTC, comment #4:

The error message is:

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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>
Project AdministratorIn charge of this item.
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

 

(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

Attach File(s):
   
   
Comment:
   

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 UTCbugmanSummaryBMRB data to Relax - is_empyt() AttributeError.=>BMRB data to Relax - is_empty() AttributeError.
    Fri 01 Feb 2013 04:03:37 PM UTCbugmanCategoryrelax sample scripts=>relax's source code
      StatusConfirmed=>Fixed
      Open/ClosedOpen=>Closed
      SummaryBMRB data to Relax=>BMRB data to Relax - is_empyt() AttributeError.
    Fri 01 Feb 2013 03:38:06 PM UTCbugmanOriginator Name=>Mengjun Xue
    Fri 01 Feb 2013 03:37:18 PM UTCbugmanStatusNone=>Confirmed
      Operating SystemMicrosoft Windows=>All systems
    Fri 01 Feb 2013 01:27:07 PM UTCbugmanAssigned toNone=>bugman
    Fri 01 Feb 2013 01:11:54 PM UTCNoneAttached 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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