FC created a CCPN project that fails to read but different from issue 266.

[GoogleCodeExporter]

What steps will reproduce the problem?
1. In NRG-CING setup trying to read the FRED CCPN file but it fails in a 
different way than issue 266.

What is the expected output? What do you see instead?
jd:nmr/log/ cat 
/Library/WebServer/Documents/NRG-CING/prep/F/a1/4a1m/4a1m_FC_assign.log
Model read finished. Duration 1.11764502525 
Model validity check skipped
================================================================================
======================
| CING: Common Interface for NMR structure Generation version 0.95 (r1083)      
AW,JFD,GWV 2004-2011 |
================================================================================
======================
User: jd         on: nmr.cmbi.umcn.nl (darwin/32bit/8cores/2.6.7) at: (37471) 
Fri Oct  7 18:51:39 2011

Going to destination: fcProcessEntry with(out) on entry_code 4a1m with extra 
arguments ['/Library/WebServer/Documents/NRG-CING/recoordSync/4a1m/4a1m.tgz', 
'4a1m_assign.tgz', 'swapCheck']
entry_code                                                                      
               4a1m
allowPopups                                                                     
               False
isInteractive                                                                   
               False
minimalPrompts                                                                  
               True
verbose                                                                         
               True
doSwapCheck                                                                     
               True
doSaveProject                                                                   
               True
doExport                                                                        
               True
DEBUG: Looking at 4a1m
Doing command: tar -xzf 
/Library/WebServer/Documents/NRG-CING/recoordSync/4a1m/4a1m.tgz
Renaming standard directory linkNmrStarData to entry: 4a1m
Warning: Project file has moved from
"/raid/docr/ccpn_tmp/data/recoord/4a1m/linkNmrStarData"
to
"/Volumes/tria3/NRG-CING/prep/F/a1/4a1m/4a1m"

Backup is being changed from
"/raid/docr/NRG/link/4a1m/4a1m_backup"
to
"/Volumes/tria3/NRG-CING/prep/F/a1/4a1m/4a1m_backup"

refData has been changed from
"/raid/docr/workspace/ccpn/trunk/ccpn/data"
to
"/Users/jd/workspace35/ccpn/data"

generalData has been changed from
"/home/docr/.ccpn/data"
to
"/Users/jd/.ccpn/data"

### Checking stereo swaps and deassignment ###
Error loading file for:  <ccp.nmr.NmrConstraint.NmrConstraintStore [1]>
Reading:  <open file 
'/Volumes/tria3/NRG-CING/prep/F/a1/4a1m/4a1m/ccp/nmr/NmrConstraint/1+4a1m_user_2
011-10-03-09-52-54-522_00002.xml', mode 'r' at 0x48c61d8>
Last xml tag read:  None
Parser state was:  reading
Current object was:  <ccp.nmr.NmrConstraint.FixedResonance [1, 1]>
ERROR: Traceback (most recent call last):
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/FC/utils.py", line 284, in <module>
    if fcProcessEntry( entry_code, ccpnTgzFile, outputCcpnTgzFile, functionToRun ):
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/FC/utils.py", line 196, in fcProcessEntry
    swapCheck(nmrConstraintStore, structureEnsemble)
  File "/Users/jd/workspace35/cingStable/python/cing/Scripts/FC/utils.py", line 116, in swapCheck
    swapCheck = StereoAssignmentCleanup(nmrConstraintStore,structureEnsemble,verbose = True)
  File "/Users/jd/workspace35/ccpn/python/ccpnmr/format/process/stereoAssignmentSwap.py", line 353, in __init__
    for constraintList in self.nmrConstraintStore.sortedConstraintLists():
  File "/Users/jd/workspace35/ccpn/python/ccp/api/nmr/NmrConstraint.py", line 22236, in sortedConstraintLists
    self.load()
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5030, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace35/ccpn/python/memops/api/Implementation.py", line 5064, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace35/ccpn/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace35/ccpn/python/memops/xml/Implementation.py", line 4751, in loadFromStream
    stackObj.append(value)
AttributeError: 'FixedResonance' object has no attribute 'append'

CING started at : Fri Oct  7 18:51:37 2011
CING stopped at : Fri Oct  7 18:51:43 2011
CING took       : 6.444 s

Original issue reported on code.google.com by jurge...@gmail.com on 10 Oct 2011 at 8:40

[GoogleCodeExporter]

Occurs also for entries: 4a1m 2l4e 2l4f 2l60 2lgk 2lja 2ljd 2lje 2ljf

Original comment by jurge...@gmail.com on 10 Oct 2011 at 8:58

• Added labels: Entry-4a1m

[GoogleCodeExporter]

Wim, can I move this issue over to the CCPN tracker?
I think it's important to note that this is not a problem in the CING code. I 
like to report this issue for the specific entries also that way thru the 
why_not interface at:

http://www.cmbi.ru.nl/WHY_NOT2/databanks/name/NRG-CING

Original comment by jurge...@gmail.com on 1 Dec 2011 at 10:30

[GoogleCodeExporter]

Move this issue to artifact at:

https://sourceforge.net/tracker/?func=detail&group_id=120914&atid=688631&aid=344
6961

Original comment by jurge...@gmail.com on 1 Dec 2011 at 10:53

• Changed state: Invalid