Failed to read DOCR CCPN XML project for this entry

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What steps will reproduce the problem?
1. Look at 
http://nmr.cmbi.ru.nl/NRG-CING//data/ah/1ah1/1ah1_2009-09-17_16-18-02.log

I'm checking 173 (out of all 6,000) entries that failed to be validated by cing 
for nrg-cing. This is 
just one of the problems I found. So far all the others aren't related to 
CCPN/FC. Thanks!

Original issue reported on code.google.com by jurge...@gmail.com on 17 Sep 2009 at 2:30

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OK I know why this happens, thought I'd fixed it but apparently not. It happens 
when
I renumber a sequence based on the info from the coordinate file - if I don't
renumber the whole sequence it is possible that some residues end up with the 
same
sequence code, and this error occurs. I'll see what I can do!

Original comment by wfvran...@gmail.com on 17 Sep 2009 at 3:38

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Hi Wim, what's the status on this one? Thanks!

Original comment by jurge...@gmail.com on 20 Oct 2009 at 11:55

• Added labels: Priority-Medium
• Removed labels: Priority-Low

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Just to have a perfect record here as it comes up for many entries.

Traceback (most recent call last):
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 266, in <module>
    status = main(*sys.argv[1:])
  File "/Users/jd/workspace34/cingStable/python/cing/Scripts/validateEntry.py", line 154, in main
    if not project.initCcpn(ccpnFolder = fileNameTgz):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/Ccpn.py", line 2213, in initCcpn
    if not ccpn.importFromCcpn(modelCount = modelCount):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/Ccpn.py", line 327, in importFromCcpn
    if not self.importFromCcpnMolecule(modelCount = modelCount):
  File "/Users/jd/workspace34/cingStable/python/cing/PluginCode/Ccpn.py", line 409, in importFromCcpnMolecule
    ccpnConstraintLists.extend(constraintStore.sortedConstraintLists())
  File "/Users/jd/workspace34/ccpn/python/ccp/api/nmr/NmrConstraint.py", line 21944, in sortedConstraintLists
    self.load()
  File "/Users/jd/workspace34/ccpn/python/memops/api/Implementation.py", line 5036, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace34/ccpn/python/memops/api/Implementation.py", line 5070, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace34/ccpn/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace34/ccpn/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace34/ccpn/python/memops/xml/Implementation.py", line 4777, in loadFromStream
    val[ii] = clazz.getByKey(oo,vv[1:-1])
  File "/Users/jd/workspace34/ccpn/python/ccp/api/molecule/MolSystem.py", line 1278, in getByKey
    obj1.load()
  File "/Users/jd/workspace34/ccpn/python/memops/api/Implementation.py", line 5036, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace34/ccpn/python/memops/api/Implementation.py", line 5070, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace34/ccpn/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace34/ccpn/python/memops/format/xml/XmlIO.py", line 273, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace34/ccpn/python/memops/xml/Implementation.py", line 4853, in loadFromStream
    obj.checkValid()
  File "/Users/jd/workspace34/ccpn/python/ccp/api/molecule/MolSystem.py", line 3225, in checkValid
    + ": %s" % (self,)
memops.general.Implementation.ApiError: ccp.molecule.MolSystem.Chain.checkValid:
       constraint seqCode_and_seqInsertCode_form_secondary_key_for_residues violated: <ccp.molecule.MolSystem.Chain ['1ah1', 'A']>

Original comment by jurge...@gmail.com on 22 Oct 2009 at 9:11

• Added labels: Priority-High
• Removed labels: Priority-Medium

[GoogleCodeExporter]

I fixed this as far as I remember - but of course the CCPN projects have to be
regenerated for the fix to propagate. Chris is doing a whole new run.

Original comment by wfvran...@gmail.com on 22 Oct 2009 at 9:17

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Ok, so newly generated DOCR files should be used for this. I see.

Original comment by jurge...@gmail.com on 22 Oct 2009 at 9:41

• Changed state: Started

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Original comment by jurge...@gmail.com on 22 Oct 2009 at 10:18

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Tested fine on my development machine for this entry 1ah1.

Original comment by jurge...@gmail.com on 23 Oct 2009 at 9:14

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Worked fine in production. Thanks Wim!

Original comment by jurge...@gmail.com on 28 Oct 2009 at 9:47

• Changed state: Verified